IBD & Intestinal Disorders

SAN DIEGO — Crohn’s disease (CD) has become more common in the United States, and an estimated 1 million Americans have the condition. Still, much is unknown about how to evaluate the individual risk for the disease.

“It’s pretty much accepted that Crohn’s disease does not begin at diagnosis,” said Ryan Ungaro, MD, associate professor of medicine at the Icahn School of Medicine at Mount Sinai, New York City, speaking at Digestive Disease Week (DDW)^® 2025.

Although individual blood markers have been associated with the future risk for CD, what’s needed, he said, is to understand which combination of biomarkers are most predictive.

Now, Ungaro and his team have developed a risk score they found accurate in predicting CD onset within 2 years before its onset.

It’s an early version that will likely be further improved and needs additional validation, Ungaro told GI & Hepatology News.

“Once we can accurately identify individuals at risk for developing Crohn’s disease, we can then imagine a number of potential interventions,” Ungaro said.

Approaches would vary depending on how far away the onset is estimated to be. For people who likely wouldn’t develop disease for many years, one intervention might be close monitoring to enable diagnosis in the earliest stages, when treatment works best, he said. Someone at a high risk of developing CD in the next 2 or 3 years, on the other hand, might be offered a pharmaceutical intervention.

 

Developing and Testing the Risk Score

To develop the risk score, Ungaro and colleagues analyzed data of 200 patients with CD and 100 healthy control participants from PREDICTS, a nested case-controlled study of active US military service members. The study is within the larger Department of Defense Serum Repository, which began in 1985 and has more than 62.5 million samples, all stored at −30 °C.

The researchers collected serum samples at four timepoints up to 6 or more years before the diagnosis. They assayed antimicrobial antibodies using the Prometheus Laboratories platform, proteomic markers using the Olink inflammation panel, and anti–granulocyte macrophage colony-stimulating factor autoantibodies using enzyme-linked immunosorbent assay.

Participants (median age, 33 years for both groups) were randomly divided into equally sized training and testing sets. In both the group, 83% of patients were White and about 90% were men.

Time-varying trajectories of marker abundance were estimated for each biomarker. Then, logistic regression modeled disease status as a function of each marker for different timepoints and multivariate modeling was performed via logistic LASSO regression.

A risk score to predict CD onset within 2 years was developed. Prediction models were fit on the testing set and predictive performance evaluated using receiver operating characteristic curves and area under the curve (AUC).

Blood proteins and antibodies have differing associations with CD depending on the time before diagnosis, the researchers found.

The integrative model to predict CD onset within 2 years incorporated 10 biomarkers associated significantly with CD onset.

The AUC for the model was 0.87 (considered good, with 1 indicating perfect discrimination). It produced a specificity of 99% and a positive predictive value of 84%.

The researchers stratified the model scores into quartiles and found the CD incidence within 2 years increased from 2% in the first quartile to 57.7% in the fourth. The relative risk of developing CD in the top quartile individuals vs lower quartile individuals was 10.4.

The serologic and proteomic markers show dynamic changes years before the diagnosis, Ungaro said.

 

A Strong Start

The research represents “an ambitious and exciting frontier for the future of IBD [inflammatory bowel disease] care,” said Victor G. Chedid, MD, MS, consultant and assistant professor of medicine at Mayo Clinic, Rochester, Minnesota, who reviewed the findings but was not involved in the study.

Currently, physicians treat IBD once it manifests, and it’s difficult to predict who will get CD, he said.

The integrative model’s AUC of 0.87 is impressive, and its specificity and positive predictive value levels show it is highly accurate in predicting the onset of CD within 2 years, Chedid added.

Further validation in larger and more diverse population is needed, Chedid said, but he sees the potential for the model to be practical in clinical practice.

“Additionally, the use of blood-based biomarkers makes the model relatively noninvasive and easy to implement in a clinical setting,” he said.

Now, the research goal is to understand the best biomarkers for characterizing the different preclinical phases of CD and to test different interventions in prevention trials, Ungaro told GI & Hepatology News.

A few trials are planned or ongoing, he noted. The trial PIONIR trial will look at the impact of a specific diet on the risk of developing CD, and the INTERCEPT trial aims to develop a blood-based risk score that can identify individuals with a high risk of developing CD within 5 years after initial evaluation.

Ungaro reported being on the advisory board of and/or receiving speaker or consulting fees from AbbVie, Bristol Myer Squibb, Celltrion, ECM Therapeutics, Genentech, Jansen, Eli Lilly, Pfizer, Roivant, Sanofi, and Takeda. Chedid reported having no relevant disclosures.

The PROMISE Consortium is funded by the Helmsley Charitable Trust.

A version of this article appeared on Medscape.com.

SAN DIEGO — Crohn’s disease (CD) has become more common in the United States, and an estimated 1 million Americans have the condition. Still, much is unknown about how to evaluate the individual risk for the disease.

“It’s pretty much accepted that Crohn’s disease does not begin at diagnosis,” said Ryan Ungaro, MD, associate professor of medicine at the Icahn School of Medicine at Mount Sinai, New York City, speaking at Digestive Disease Week (DDW)^® 2025.

Although individual blood markers have been associated with the future risk for CD, what’s needed, he said, is to understand which combination of biomarkers are most predictive.

Now, Ungaro and his team have developed a risk score they found accurate in predicting CD onset within 2 years before its onset.

It’s an early version that will likely be further improved and needs additional validation, Ungaro told GI & Hepatology News.

“Once we can accurately identify individuals at risk for developing Crohn’s disease, we can then imagine a number of potential interventions,” Ungaro said.

Approaches would vary depending on how far away the onset is estimated to be. For people who likely wouldn’t develop disease for many years, one intervention might be close monitoring to enable diagnosis in the earliest stages, when treatment works best, he said. Someone at a high risk of developing CD in the next 2 or 3 years, on the other hand, might be offered a pharmaceutical intervention.

 

Developing and Testing the Risk Score

To develop the risk score, Ungaro and colleagues analyzed data of 200 patients with CD and 100 healthy control participants from PREDICTS, a nested case-controlled study of active US military service members. The study is within the larger Department of Defense Serum Repository, which began in 1985 and has more than 62.5 million samples, all stored at −30 °C.

The researchers collected serum samples at four timepoints up to 6 or more years before the diagnosis. They assayed antimicrobial antibodies using the Prometheus Laboratories platform, proteomic markers using the Olink inflammation panel, and anti–granulocyte macrophage colony-stimulating factor autoantibodies using enzyme-linked immunosorbent assay.

Participants (median age, 33 years for both groups) were randomly divided into equally sized training and testing sets. In both the group, 83% of patients were White and about 90% were men.

Time-varying trajectories of marker abundance were estimated for each biomarker. Then, logistic regression modeled disease status as a function of each marker for different timepoints and multivariate modeling was performed via logistic LASSO regression.

A risk score to predict CD onset within 2 years was developed. Prediction models were fit on the testing set and predictive performance evaluated using receiver operating characteristic curves and area under the curve (AUC).

Blood proteins and antibodies have differing associations with CD depending on the time before diagnosis, the researchers found.

The integrative model to predict CD onset within 2 years incorporated 10 biomarkers associated significantly with CD onset.

The AUC for the model was 0.87 (considered good, with 1 indicating perfect discrimination). It produced a specificity of 99% and a positive predictive value of 84%.

The researchers stratified the model scores into quartiles and found the CD incidence within 2 years increased from 2% in the first quartile to 57.7% in the fourth. The relative risk of developing CD in the top quartile individuals vs lower quartile individuals was 10.4.

The serologic and proteomic markers show dynamic changes years before the diagnosis, Ungaro said.

 

A Strong Start

The research represents “an ambitious and exciting frontier for the future of IBD [inflammatory bowel disease] care,” said Victor G. Chedid, MD, MS, consultant and assistant professor of medicine at Mayo Clinic, Rochester, Minnesota, who reviewed the findings but was not involved in the study.

Currently, physicians treat IBD once it manifests, and it’s difficult to predict who will get CD, he said.

The integrative model’s AUC of 0.87 is impressive, and its specificity and positive predictive value levels show it is highly accurate in predicting the onset of CD within 2 years, Chedid added.

Further validation in larger and more diverse population is needed, Chedid said, but he sees the potential for the model to be practical in clinical practice.

“Additionally, the use of blood-based biomarkers makes the model relatively noninvasive and easy to implement in a clinical setting,” he said.

Now, the research goal is to understand the best biomarkers for characterizing the different preclinical phases of CD and to test different interventions in prevention trials, Ungaro told GI & Hepatology News.

A few trials are planned or ongoing, he noted. The trial PIONIR trial will look at the impact of a specific diet on the risk of developing CD, and the INTERCEPT trial aims to develop a blood-based risk score that can identify individuals with a high risk of developing CD within 5 years after initial evaluation.

Ungaro reported being on the advisory board of and/or receiving speaker or consulting fees from AbbVie, Bristol Myer Squibb, Celltrion, ECM Therapeutics, Genentech, Jansen, Eli Lilly, Pfizer, Roivant, Sanofi, and Takeda. Chedid reported having no relevant disclosures.

The PROMISE Consortium is funded by the Helmsley Charitable Trust.

A version of this article appeared on Medscape.com.

SAN DIEGO — Crohn’s disease (CD) has become more common in the United States, and an estimated 1 million Americans have the condition. Still, much is unknown about how to evaluate the individual risk for the disease.

“It’s pretty much accepted that Crohn’s disease does not begin at diagnosis,” said Ryan Ungaro, MD, associate professor of medicine at the Icahn School of Medicine at Mount Sinai, New York City, speaking at Digestive Disease Week (DDW)^® 2025.

Although individual blood markers have been associated with the future risk for CD, what’s needed, he said, is to understand which combination of biomarkers are most predictive.

Now, Ungaro and his team have developed a risk score they found accurate in predicting CD onset within 2 years before its onset.

It’s an early version that will likely be further improved and needs additional validation, Ungaro told GI & Hepatology News.

“Once we can accurately identify individuals at risk for developing Crohn’s disease, we can then imagine a number of potential interventions,” Ungaro said.

Approaches would vary depending on how far away the onset is estimated to be. For people who likely wouldn’t develop disease for many years, one intervention might be close monitoring to enable diagnosis in the earliest stages, when treatment works best, he said. Someone at a high risk of developing CD in the next 2 or 3 years, on the other hand, might be offered a pharmaceutical intervention.

 

Developing and Testing the Risk Score

To develop the risk score, Ungaro and colleagues analyzed data of 200 patients with CD and 100 healthy control participants from PREDICTS, a nested case-controlled study of active US military service members. The study is within the larger Department of Defense Serum Repository, which began in 1985 and has more than 62.5 million samples, all stored at −30 °C.

The researchers collected serum samples at four timepoints up to 6 or more years before the diagnosis. They assayed antimicrobial antibodies using the Prometheus Laboratories platform, proteomic markers using the Olink inflammation panel, and anti–granulocyte macrophage colony-stimulating factor autoantibodies using enzyme-linked immunosorbent assay.

Participants (median age, 33 years for both groups) were randomly divided into equally sized training and testing sets. In both the group, 83% of patients were White and about 90% were men.

Time-varying trajectories of marker abundance were estimated for each biomarker. Then, logistic regression modeled disease status as a function of each marker for different timepoints and multivariate modeling was performed via logistic LASSO regression.

A risk score to predict CD onset within 2 years was developed. Prediction models were fit on the testing set and predictive performance evaluated using receiver operating characteristic curves and area under the curve (AUC).

Blood proteins and antibodies have differing associations with CD depending on the time before diagnosis, the researchers found.

The integrative model to predict CD onset within 2 years incorporated 10 biomarkers associated significantly with CD onset.

The AUC for the model was 0.87 (considered good, with 1 indicating perfect discrimination). It produced a specificity of 99% and a positive predictive value of 84%.

The researchers stratified the model scores into quartiles and found the CD incidence within 2 years increased from 2% in the first quartile to 57.7% in the fourth. The relative risk of developing CD in the top quartile individuals vs lower quartile individuals was 10.4.

The serologic and proteomic markers show dynamic changes years before the diagnosis, Ungaro said.

 

A Strong Start

The research represents “an ambitious and exciting frontier for the future of IBD [inflammatory bowel disease] care,” said Victor G. Chedid, MD, MS, consultant and assistant professor of medicine at Mayo Clinic, Rochester, Minnesota, who reviewed the findings but was not involved in the study.

Currently, physicians treat IBD once it manifests, and it’s difficult to predict who will get CD, he said.

The integrative model’s AUC of 0.87 is impressive, and its specificity and positive predictive value levels show it is highly accurate in predicting the onset of CD within 2 years, Chedid added.

Further validation in larger and more diverse population is needed, Chedid said, but he sees the potential for the model to be practical in clinical practice.

“Additionally, the use of blood-based biomarkers makes the model relatively noninvasive and easy to implement in a clinical setting,” he said.

Now, the research goal is to understand the best biomarkers for characterizing the different preclinical phases of CD and to test different interventions in prevention trials, Ungaro told GI & Hepatology News.

A few trials are planned or ongoing, he noted. The trial PIONIR trial will look at the impact of a specific diet on the risk of developing CD, and the INTERCEPT trial aims to develop a blood-based risk score that can identify individuals with a high risk of developing CD within 5 years after initial evaluation.

Ungaro reported being on the advisory board of and/or receiving speaker or consulting fees from AbbVie, Bristol Myer Squibb, Celltrion, ECM Therapeutics, Genentech, Jansen, Eli Lilly, Pfizer, Roivant, Sanofi, and Takeda. Chedid reported having no relevant disclosures.

The PROMISE Consortium is funded by the Helmsley Charitable Trust.

A version of this article appeared on Medscape.com.

SAN DIEGO — In tough-to-treat chronic inflammatory bowel disease (IBD), a precision-medicine strategy based on patients’ molecular profiles showed efficacy in guiding anti–tumor necrosis factor (TNF) therapy treatment decisions to improve outcomes.

“This is the first study implementing multi-biomarker signatures in informed decisions instead of single biomarker–based trial algorithms [in IBD],” said first author Florian Tran, MD, in presenting the late-breaking study at Digestive Disease Week (DDW) 2025.

“We have now been able to demonstrate for the first time that precision medicine can be successfully applied in the context of chronic inflammatory bowel diseases, leading to improved long-term outcomes,” said Tran, a professor of pathophysiology of chronic inflammation at the Institute of Clinical Molecular Biology and department of internal medicine, Kiel University and University Hospital Schleswig Holstein, Kiel, Germany.

Anti-TNF therapies can be highly effective in a range of immune-mediated inflammatory diseases, including IBD, but not all patients respond. Key singular candidates of biomarkers that could better predict a response show relatively low predictive power or a failure to replicate in independent studies.

In previous research, Tran and colleagues reported identification of early dynamic molecular changes in the blood that are more robustly predictive of responses to anti-TNF therapy.

“We have generated compelling evidence that therapy-induced changes in inflammatory pathways can reliably predict patient outcomes,” he said.

Among them are dynamic transcriptome changes that emerge early during treatment and can predict response to anti-TNF therapy, as well as clinical response trajectories that differ based on subgroups.

To further investigate the benefits of the multi-biomarker signatures collectively, as opposed to single biomarker–based algorithms, Tran and colleagues conducted the phase 3, open-label GUIDE-IBD trial, enrolling 102 adults with a confirmed diagnosis of Crohn’s disease (CD) or ulcerative colitis (UC) at three German university hospitals between February 2021 and January 2024.

All patients had been assigned the anti-TNF drug infliximab for the first time.

Study participants were randomized to receive either the molecular-guided care or standard medical care, with stratifications based on diagnosis, recruiting center, and baseline corticosteroid use.

Those in the molecular group received real-time molecular assessments at baseline and weeks 2, 6, 14, and 26, which included peripheral blood samples and biopsies of known messenger ribonucleic acid–based biomarkers.

The assessments also looked at infliximab and anti-drug antibody levels.

Molecular reports were then provided through molecular medicine boards for patients in the molecular-guidance group at weeks 2, 14, 26, and 52, whereas data from the standard-care group was not communicated.

Based on the biomarker data, therapy decisions were made such as adjustments to dosing, intervals, comedication, and switches in therapy.

The primary endpoint was the combined end point of disease control, defined as clinical remission (CD Activity Index < 150, partial Mayo score < 2), endoscopic remission (simplified endoscopic score for CD ≤ 4 [≤ 2 for isolated ileal disease], endoscopic Mayo score ≤ 1), or biochemical remission (C-reactive protein < 5 mg/L, fecal calprotectin < 250 mg/g).

A total of 87 patients completed the study with available primary endpoint data to week 52; there were 38 in the molecular care group and 49 in the standard care group. In each group, approximately half of the patients had CD and half had UC.

For the primary endpoint, comprehensive disease control was significantly more frequent in the molecular care group at week 52 (55.3%) than in the standard-care group (26.5%), with an absolute difference of 29% (P = .0072).

Furthermore, the secondary endpoint of the combined rate of endoscopic and clinical remission at week 52 was also higher in the molecular group (60.5%) than in the standard-care group (32.7%; P = .0163).

An exploratory analysis further showed therapy switches were more common in the molecular group (47%) than in the standard-care group (29%), with an increased rate of drug switching between 14 weeks and 26 weeks.

More patients in the molecular guidance group achieved comprehensive disease control (deep remission) at week 52 (P = .0135).

“The [molecular guidance] group was more likely to switch therapies after the induction period, reducing the number of patients who are suboptimally treated under infliximab,” Tran noted.

The results underscore that “even in the absence of a single ‘magic’ biomarker, precision medicine can materially improve patient outcomes by integrating complex molecular data into everyday clinical decisions, enabling more effective therapy choices and reducing unnecessary drug side effects,” he said.

 

Approach Pioneered in Oncology

Tran noted that the collaboration necessary for the approach was based on strategies pioneered in cancer centers, which have resulted in significant improvements in cancer therapy outcomes.

“For the first time in IBD, we have now integrated multidimensional molecular data and innovative drug-dosing models into these inflammation boards,” he said.

Key components of the intervention include a highly structured patient care process with fixed assessment timepoints, as well as “a multidisciplinary, quality-controlled decision-making process that is meticulously documented,” he explained.

The results underscore that “we must move away from sole physician–driven treatment decisions in IBD toward a structured expert-board model for therapy decision-making.” 

 

Benefits in Other IBD Therapies Unclear

Commenting on the study, Ashwin N. Ananthakrishnan, MBBS, MPH, AGAF, an associate professor of medicine with Massachusetts General Hospital, Boston, noted that “this approach may help optimize existing treatment early and ensure that ineffective treatments don’t get dragged on.”

Importantly, however, a key limitation is that “this does not tell you upfront whether a treatment is likely to work or what the best treatment is,” Ananthakrishnan said in an interview. “That is a critically important unmet need in IBD.”

While doses are escalated, if needed, with infliximab and other biologic drugs, that may not be the case with other therapies, he explained.

“For other agents, such as JAK [Janus kinase] inhibitors, we actually start at a higher dose and then reduce for maintenance,” said Ananthakrishnan.

How this approach would work for these drugs or “for drugs where blood levels are not reflective of efficacy is also not clear,” he said.

Tran’s disclosures included relationships with AbbVie, Bristol-Myers-Squibb, CED Service, Celltrion Healthcare, Eli Lilly, Ferring Pharmaceutical, Janssen, Johnson & Johnson, Takeda, LEK Consulting, and Sanofi/Regeneron. Ananthakrishnan had no disclosures to report.

A version of this article appeared on Medscape.com.

SAN DIEGO — In tough-to-treat chronic inflammatory bowel disease (IBD), a precision-medicine strategy based on patients’ molecular profiles showed efficacy in guiding anti–tumor necrosis factor (TNF) therapy treatment decisions to improve outcomes.

“This is the first study implementing multi-biomarker signatures in informed decisions instead of single biomarker–based trial algorithms [in IBD],” said first author Florian Tran, MD, in presenting the late-breaking study at Digestive Disease Week (DDW) 2025.

“We have now been able to demonstrate for the first time that precision medicine can be successfully applied in the context of chronic inflammatory bowel diseases, leading to improved long-term outcomes,” said Tran, a professor of pathophysiology of chronic inflammation at the Institute of Clinical Molecular Biology and department of internal medicine, Kiel University and University Hospital Schleswig Holstein, Kiel, Germany.

Anti-TNF therapies can be highly effective in a range of immune-mediated inflammatory diseases, including IBD, but not all patients respond. Key singular candidates of biomarkers that could better predict a response show relatively low predictive power or a failure to replicate in independent studies.

In previous research, Tran and colleagues reported identification of early dynamic molecular changes in the blood that are more robustly predictive of responses to anti-TNF therapy.

“We have generated compelling evidence that therapy-induced changes in inflammatory pathways can reliably predict patient outcomes,” he said.

Among them are dynamic transcriptome changes that emerge early during treatment and can predict response to anti-TNF therapy, as well as clinical response trajectories that differ based on subgroups.

To further investigate the benefits of the multi-biomarker signatures collectively, as opposed to single biomarker–based algorithms, Tran and colleagues conducted the phase 3, open-label GUIDE-IBD trial, enrolling 102 adults with a confirmed diagnosis of Crohn’s disease (CD) or ulcerative colitis (UC) at three German university hospitals between February 2021 and January 2024.

All patients had been assigned the anti-TNF drug infliximab for the first time.

Study participants were randomized to receive either the molecular-guided care or standard medical care, with stratifications based on diagnosis, recruiting center, and baseline corticosteroid use.

Those in the molecular group received real-time molecular assessments at baseline and weeks 2, 6, 14, and 26, which included peripheral blood samples and biopsies of known messenger ribonucleic acid–based biomarkers.

The assessments also looked at infliximab and anti-drug antibody levels.

Molecular reports were then provided through molecular medicine boards for patients in the molecular-guidance group at weeks 2, 14, 26, and 52, whereas data from the standard-care group was not communicated.

Based on the biomarker data, therapy decisions were made such as adjustments to dosing, intervals, comedication, and switches in therapy.

The primary endpoint was the combined end point of disease control, defined as clinical remission (CD Activity Index < 150, partial Mayo score < 2), endoscopic remission (simplified endoscopic score for CD ≤ 4 [≤ 2 for isolated ileal disease], endoscopic Mayo score ≤ 1), or biochemical remission (C-reactive protein < 5 mg/L, fecal calprotectin < 250 mg/g).

A total of 87 patients completed the study with available primary endpoint data to week 52; there were 38 in the molecular care group and 49 in the standard care group. In each group, approximately half of the patients had CD and half had UC.

For the primary endpoint, comprehensive disease control was significantly more frequent in the molecular care group at week 52 (55.3%) than in the standard-care group (26.5%), with an absolute difference of 29% (P = .0072).

Furthermore, the secondary endpoint of the combined rate of endoscopic and clinical remission at week 52 was also higher in the molecular group (60.5%) than in the standard-care group (32.7%; P = .0163).

An exploratory analysis further showed therapy switches were more common in the molecular group (47%) than in the standard-care group (29%), with an increased rate of drug switching between 14 weeks and 26 weeks.

More patients in the molecular guidance group achieved comprehensive disease control (deep remission) at week 52 (P = .0135).

“The [molecular guidance] group was more likely to switch therapies after the induction period, reducing the number of patients who are suboptimally treated under infliximab,” Tran noted.

The results underscore that “even in the absence of a single ‘magic’ biomarker, precision medicine can materially improve patient outcomes by integrating complex molecular data into everyday clinical decisions, enabling more effective therapy choices and reducing unnecessary drug side effects,” he said.

 

Approach Pioneered in Oncology

Tran noted that the collaboration necessary for the approach was based on strategies pioneered in cancer centers, which have resulted in significant improvements in cancer therapy outcomes.

“For the first time in IBD, we have now integrated multidimensional molecular data and innovative drug-dosing models into these inflammation boards,” he said.

Key components of the intervention include a highly structured patient care process with fixed assessment timepoints, as well as “a multidisciplinary, quality-controlled decision-making process that is meticulously documented,” he explained.

The results underscore that “we must move away from sole physician–driven treatment decisions in IBD toward a structured expert-board model for therapy decision-making.” 

 

Benefits in Other IBD Therapies Unclear

Commenting on the study, Ashwin N. Ananthakrishnan, MBBS, MPH, AGAF, an associate professor of medicine with Massachusetts General Hospital, Boston, noted that “this approach may help optimize existing treatment early and ensure that ineffective treatments don’t get dragged on.”

Importantly, however, a key limitation is that “this does not tell you upfront whether a treatment is likely to work or what the best treatment is,” Ananthakrishnan said in an interview. “That is a critically important unmet need in IBD.”

While doses are escalated, if needed, with infliximab and other biologic drugs, that may not be the case with other therapies, he explained.

“For other agents, such as JAK [Janus kinase] inhibitors, we actually start at a higher dose and then reduce for maintenance,” said Ananthakrishnan.

How this approach would work for these drugs or “for drugs where blood levels are not reflective of efficacy is also not clear,” he said.

Tran’s disclosures included relationships with AbbVie, Bristol-Myers-Squibb, CED Service, Celltrion Healthcare, Eli Lilly, Ferring Pharmaceutical, Janssen, Johnson & Johnson, Takeda, LEK Consulting, and Sanofi/Regeneron. Ananthakrishnan had no disclosures to report.

A version of this article appeared on Medscape.com.

SAN DIEGO — In tough-to-treat chronic inflammatory bowel disease (IBD), a precision-medicine strategy based on patients’ molecular profiles showed efficacy in guiding anti–tumor necrosis factor (TNF) therapy treatment decisions to improve outcomes.

“This is the first study implementing multi-biomarker signatures in informed decisions instead of single biomarker–based trial algorithms [in IBD],” said first author Florian Tran, MD, in presenting the late-breaking study at Digestive Disease Week (DDW) 2025.

“We have now been able to demonstrate for the first time that precision medicine can be successfully applied in the context of chronic inflammatory bowel diseases, leading to improved long-term outcomes,” said Tran, a professor of pathophysiology of chronic inflammation at the Institute of Clinical Molecular Biology and department of internal medicine, Kiel University and University Hospital Schleswig Holstein, Kiel, Germany.

Anti-TNF therapies can be highly effective in a range of immune-mediated inflammatory diseases, including IBD, but not all patients respond. Key singular candidates of biomarkers that could better predict a response show relatively low predictive power or a failure to replicate in independent studies.

In previous research, Tran and colleagues reported identification of early dynamic molecular changes in the blood that are more robustly predictive of responses to anti-TNF therapy.

“We have generated compelling evidence that therapy-induced changes in inflammatory pathways can reliably predict patient outcomes,” he said.

Among them are dynamic transcriptome changes that emerge early during treatment and can predict response to anti-TNF therapy, as well as clinical response trajectories that differ based on subgroups.

To further investigate the benefits of the multi-biomarker signatures collectively, as opposed to single biomarker–based algorithms, Tran and colleagues conducted the phase 3, open-label GUIDE-IBD trial, enrolling 102 adults with a confirmed diagnosis of Crohn’s disease (CD) or ulcerative colitis (UC) at three German university hospitals between February 2021 and January 2024.

All patients had been assigned the anti-TNF drug infliximab for the first time.

Study participants were randomized to receive either the molecular-guided care or standard medical care, with stratifications based on diagnosis, recruiting center, and baseline corticosteroid use.

Those in the molecular group received real-time molecular assessments at baseline and weeks 2, 6, 14, and 26, which included peripheral blood samples and biopsies of known messenger ribonucleic acid–based biomarkers.

The assessments also looked at infliximab and anti-drug antibody levels.

Molecular reports were then provided through molecular medicine boards for patients in the molecular-guidance group at weeks 2, 14, 26, and 52, whereas data from the standard-care group was not communicated.

Based on the biomarker data, therapy decisions were made such as adjustments to dosing, intervals, comedication, and switches in therapy.

The primary endpoint was the combined end point of disease control, defined as clinical remission (CD Activity Index < 150, partial Mayo score < 2), endoscopic remission (simplified endoscopic score for CD ≤ 4 [≤ 2 for isolated ileal disease], endoscopic Mayo score ≤ 1), or biochemical remission (C-reactive protein < 5 mg/L, fecal calprotectin < 250 mg/g).

A total of 87 patients completed the study with available primary endpoint data to week 52; there were 38 in the molecular care group and 49 in the standard care group. In each group, approximately half of the patients had CD and half had UC.

For the primary endpoint, comprehensive disease control was significantly more frequent in the molecular care group at week 52 (55.3%) than in the standard-care group (26.5%), with an absolute difference of 29% (P = .0072).

Furthermore, the secondary endpoint of the combined rate of endoscopic and clinical remission at week 52 was also higher in the molecular group (60.5%) than in the standard-care group (32.7%; P = .0163).

An exploratory analysis further showed therapy switches were more common in the molecular group (47%) than in the standard-care group (29%), with an increased rate of drug switching between 14 weeks and 26 weeks.

More patients in the molecular guidance group achieved comprehensive disease control (deep remission) at week 52 (P = .0135).

“The [molecular guidance] group was more likely to switch therapies after the induction period, reducing the number of patients who are suboptimally treated under infliximab,” Tran noted.

The results underscore that “even in the absence of a single ‘magic’ biomarker, precision medicine can materially improve patient outcomes by integrating complex molecular data into everyday clinical decisions, enabling more effective therapy choices and reducing unnecessary drug side effects,” he said.

 

Approach Pioneered in Oncology

Tran noted that the collaboration necessary for the approach was based on strategies pioneered in cancer centers, which have resulted in significant improvements in cancer therapy outcomes.

“For the first time in IBD, we have now integrated multidimensional molecular data and innovative drug-dosing models into these inflammation boards,” he said.

Key components of the intervention include a highly structured patient care process with fixed assessment timepoints, as well as “a multidisciplinary, quality-controlled decision-making process that is meticulously documented,” he explained.

The results underscore that “we must move away from sole physician–driven treatment decisions in IBD toward a structured expert-board model for therapy decision-making.” 

 

Benefits in Other IBD Therapies Unclear

Commenting on the study, Ashwin N. Ananthakrishnan, MBBS, MPH, AGAF, an associate professor of medicine with Massachusetts General Hospital, Boston, noted that “this approach may help optimize existing treatment early and ensure that ineffective treatments don’t get dragged on.”

Importantly, however, a key limitation is that “this does not tell you upfront whether a treatment is likely to work or what the best treatment is,” Ananthakrishnan said in an interview. “That is a critically important unmet need in IBD.”

While doses are escalated, if needed, with infliximab and other biologic drugs, that may not be the case with other therapies, he explained.

“For other agents, such as JAK [Janus kinase] inhibitors, we actually start at a higher dose and then reduce for maintenance,” said Ananthakrishnan.

How this approach would work for these drugs or “for drugs where blood levels are not reflective of efficacy is also not clear,” he said.

Tran’s disclosures included relationships with AbbVie, Bristol-Myers-Squibb, CED Service, Celltrion Healthcare, Eli Lilly, Ferring Pharmaceutical, Janssen, Johnson & Johnson, Takeda, LEK Consulting, and Sanofi/Regeneron. Ananthakrishnan had no disclosures to report.

A version of this article appeared on Medscape.com.

An irritable bowel syndrome (IBS) elimination diet based on a novel IBS–specific, immunoglobulin G (IgG) was superior to a sham diet for abdominal pain, an 8-center, randomized double-blind controlled trial found.

While elimination diets can provide a personalized approach to dietary therapy, existing studies have had serious methodological issues, noted lead author Prashant Singh, MBBS, of the Division of Gastroenterology and Hepatology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Mich., and colleagues in Gastroenterology.

For example, previous studies on IgG-based diets used assays developed without determining IBS trigger foods or establishing a 95% confidence interval–based cutoff using a healthy control comparison group.

 

Study Details

From June 2018 to December 2021, 238 IBS patients testing positive for at least one food on 18-food IgG ELISA (enzyme-linked immunosorbent assay) testing and an average daily abdominal pain intensity score of 3.0 to 7.5 on an 11.0-point scale during a 2-week run-in period were randomized for 8 weeks to an experimental antibody-guided diet or to a sham diet. The primary outcome was a 30% decrease in abdominal pain intensity (API) for 2 of the last 4 weeks of treatment.

The overall study population had a mean age of about 40 years, and more than three-quarters were female. The 3 IBS types – constipation-predominant (IBS-C), diarrhea-predominant (IBS-D), and mixed bowel habits-predominant (IBS-M) – accounted for about a third each in both arms.

The experimental diet eliminated foods based on a positive ELISA result. Its sham counterpart had the same number of foods removed as the number of positive-testing food sensitivities, but the foods eliminated in the sham diet had tested negative on the IgG assay.

Participants reported daily abdominal pain intensity, bloating, and stool consistency, and frequency. They also reported dietary compliance and daily medication use.

Of the 238 randomized adults, 223 were included in the modified intention-to-treat analysis. A significantly greater proportion of subjects in the experimental group met the primary outcome than those in the sham group: 59.6% vs 42.1%, P = .02). “This highlights the potential effectiveness of a personalized elimination diet based on a novel IBS-specific IgG assay,” the authors wrote.

Symptom improvement between arms began to separate out at around 2 weeks, suggesting the effect of the experimental diet was relatively rapid in onset, and continued for at least 8 weeks. The durability of response, however, needs to be assessed in future studies “and it is unclear if there is a role for repeat IgG testing to monitor treatment response,” the authors wrote.

Subgroup analysis revealed that a higher proportion of those with IBS-C and IBS-M in the experimental diet group met the primary endpoint vs the sham group: 67.1% vs 35.8% and 66% vs 29.5%, respectively.

Interestingly, more patients in the experimental arm were noncompliant with their diet. “It is possible that subjects found the experimental diet more difficult to comply with compared with the sham diet or that because the experimental diet was more likely to improve symptoms, dietary indiscretion may have been more common in this group (a phenomenon seen with other elimination diets such as gluten-free diet in celiac disease),” the authors wrote.

Adverse events, deemed unrelated to either regimen, were 3 in the experimental arm vs 8 in the sham arm, which had 2 urinary tract infections.

The authors called for a larger, adequately powered study to assess the efficacy of an elimination diet based on this novel immunoglobulin G assay in patients with IBS-C and IBS-M. Future studies should perform detailed adherence assessments using food diaries.

“Mechanisms of how immunoglobulin G-antibody response to food antigen generates symptoms in irritable bowel syndrome are not well understood. Delineating this might provide new insights into food-related irritable bowel syndrome pathophysiology,” they concluded.

This study was funded by Biomerica Inc.

An irritable bowel syndrome (IBS) elimination diet based on a novel IBS–specific, immunoglobulin G (IgG) was superior to a sham diet for abdominal pain, an 8-center, randomized double-blind controlled trial found.

While elimination diets can provide a personalized approach to dietary therapy, existing studies have had serious methodological issues, noted lead author Prashant Singh, MBBS, of the Division of Gastroenterology and Hepatology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Mich., and colleagues in Gastroenterology.

For example, previous studies on IgG-based diets used assays developed without determining IBS trigger foods or establishing a 95% confidence interval–based cutoff using a healthy control comparison group.

 

Study Details

From June 2018 to December 2021, 238 IBS patients testing positive for at least one food on 18-food IgG ELISA (enzyme-linked immunosorbent assay) testing and an average daily abdominal pain intensity score of 3.0 to 7.5 on an 11.0-point scale during a 2-week run-in period were randomized for 8 weeks to an experimental antibody-guided diet or to a sham diet. The primary outcome was a 30% decrease in abdominal pain intensity (API) for 2 of the last 4 weeks of treatment.

The overall study population had a mean age of about 40 years, and more than three-quarters were female. The 3 IBS types – constipation-predominant (IBS-C), diarrhea-predominant (IBS-D), and mixed bowel habits-predominant (IBS-M) – accounted for about a third each in both arms.

The experimental diet eliminated foods based on a positive ELISA result. Its sham counterpart had the same number of foods removed as the number of positive-testing food sensitivities, but the foods eliminated in the sham diet had tested negative on the IgG assay.

Participants reported daily abdominal pain intensity, bloating, and stool consistency, and frequency. They also reported dietary compliance and daily medication use.

Of the 238 randomized adults, 223 were included in the modified intention-to-treat analysis. A significantly greater proportion of subjects in the experimental group met the primary outcome than those in the sham group: 59.6% vs 42.1%, P = .02). “This highlights the potential effectiveness of a personalized elimination diet based on a novel IBS-specific IgG assay,” the authors wrote.

Symptom improvement between arms began to separate out at around 2 weeks, suggesting the effect of the experimental diet was relatively rapid in onset, and continued for at least 8 weeks. The durability of response, however, needs to be assessed in future studies “and it is unclear if there is a role for repeat IgG testing to monitor treatment response,” the authors wrote.

Subgroup analysis revealed that a higher proportion of those with IBS-C and IBS-M in the experimental diet group met the primary endpoint vs the sham group: 67.1% vs 35.8% and 66% vs 29.5%, respectively.

Interestingly, more patients in the experimental arm were noncompliant with their diet. “It is possible that subjects found the experimental diet more difficult to comply with compared with the sham diet or that because the experimental diet was more likely to improve symptoms, dietary indiscretion may have been more common in this group (a phenomenon seen with other elimination diets such as gluten-free diet in celiac disease),” the authors wrote.

Adverse events, deemed unrelated to either regimen, were 3 in the experimental arm vs 8 in the sham arm, which had 2 urinary tract infections.

The authors called for a larger, adequately powered study to assess the efficacy of an elimination diet based on this novel immunoglobulin G assay in patients with IBS-C and IBS-M. Future studies should perform detailed adherence assessments using food diaries.

“Mechanisms of how immunoglobulin G-antibody response to food antigen generates symptoms in irritable bowel syndrome are not well understood. Delineating this might provide new insights into food-related irritable bowel syndrome pathophysiology,” they concluded.

This study was funded by Biomerica Inc.

An irritable bowel syndrome (IBS) elimination diet based on a novel IBS–specific, immunoglobulin G (IgG) was superior to a sham diet for abdominal pain, an 8-center, randomized double-blind controlled trial found.

While elimination diets can provide a personalized approach to dietary therapy, existing studies have had serious methodological issues, noted lead author Prashant Singh, MBBS, of the Division of Gastroenterology and Hepatology, Department of Internal Medicine, Michigan Medicine, Ann Arbor, Mich., and colleagues in Gastroenterology.

For example, previous studies on IgG-based diets used assays developed without determining IBS trigger foods or establishing a 95% confidence interval–based cutoff using a healthy control comparison group.

 

Study Details

From June 2018 to December 2021, 238 IBS patients testing positive for at least one food on 18-food IgG ELISA (enzyme-linked immunosorbent assay) testing and an average daily abdominal pain intensity score of 3.0 to 7.5 on an 11.0-point scale during a 2-week run-in period were randomized for 8 weeks to an experimental antibody-guided diet or to a sham diet. The primary outcome was a 30% decrease in abdominal pain intensity (API) for 2 of the last 4 weeks of treatment.

The overall study population had a mean age of about 40 years, and more than three-quarters were female. The 3 IBS types – constipation-predominant (IBS-C), diarrhea-predominant (IBS-D), and mixed bowel habits-predominant (IBS-M) – accounted for about a third each in both arms.

The experimental diet eliminated foods based on a positive ELISA result. Its sham counterpart had the same number of foods removed as the number of positive-testing food sensitivities, but the foods eliminated in the sham diet had tested negative on the IgG assay.

Participants reported daily abdominal pain intensity, bloating, and stool consistency, and frequency. They also reported dietary compliance and daily medication use.

Of the 238 randomized adults, 223 were included in the modified intention-to-treat analysis. A significantly greater proportion of subjects in the experimental group met the primary outcome than those in the sham group: 59.6% vs 42.1%, P = .02). “This highlights the potential effectiveness of a personalized elimination diet based on a novel IBS-specific IgG assay,” the authors wrote.

Symptom improvement between arms began to separate out at around 2 weeks, suggesting the effect of the experimental diet was relatively rapid in onset, and continued for at least 8 weeks. The durability of response, however, needs to be assessed in future studies “and it is unclear if there is a role for repeat IgG testing to monitor treatment response,” the authors wrote.

Subgroup analysis revealed that a higher proportion of those with IBS-C and IBS-M in the experimental diet group met the primary endpoint vs the sham group: 67.1% vs 35.8% and 66% vs 29.5%, respectively.

Interestingly, more patients in the experimental arm were noncompliant with their diet. “It is possible that subjects found the experimental diet more difficult to comply with compared with the sham diet or that because the experimental diet was more likely to improve symptoms, dietary indiscretion may have been more common in this group (a phenomenon seen with other elimination diets such as gluten-free diet in celiac disease),” the authors wrote.

Adverse events, deemed unrelated to either regimen, were 3 in the experimental arm vs 8 in the sham arm, which had 2 urinary tract infections.

The authors called for a larger, adequately powered study to assess the efficacy of an elimination diet based on this novel immunoglobulin G assay in patients with IBS-C and IBS-M. Future studies should perform detailed adherence assessments using food diaries.

“Mechanisms of how immunoglobulin G-antibody response to food antigen generates symptoms in irritable bowel syndrome are not well understood. Delineating this might provide new insights into food-related irritable bowel syndrome pathophysiology,” they concluded.

This study was funded by Biomerica Inc.

SAN DIEGO — The session started with a question that many in the audience at Digestive Disease Week (DDW) 2025 seemed to relate to: “How many of you find yourself squeezing workouts into a weekend after a hectic work week?”

Although regular exercise three or more times a week is often viewed as preferable, Shiyi Yu, MD, a resident physician in the Department of Gastroenterology at Guangdong Provincial People’s Hospital in Guangzhou, China, had good news for weekend warriors.

Both patterns reduce digestive disease almost equally.

Her study compared weekend warriors with those she called “active regulars” and sedentary folks to see how activity patterns affect digestive disease risks.

Her bottom line: “Your gut does not care about your schedule.”

The researchers analyzed wrist-based accelerometer data from 89,595 participants in the UK Biobank. To categorize participants as active or inactive, they used the World Health Organization 2020 guidelines for physical activity, which recommend at least 150-300 minutes of moderate-intensity aerobic physical activity or at least 75-150 minutes of vigorous-intensity aerobic physical activity, or an equivalent combination throughout the week. Median age of participants was 63.3 years and 48.8% were men.

They divided participants into three groups:

• About 43% were weekend warriors who met or exceeded 150 minutes of moderate to vigorous physical activity (MVPA), with 50% or more of total MVPA achieved in 1-2 days.
• About 23% were active regulars who met or exceeded 150 minutes a week but spread over more days.
• About 34% were inactive participants who were active less than 150 minutes a week.

The researchers followed the participants for a median of 7.9 years, looking for the incidence of multiple digestive diseases, identified using the International Classification of Diseases, 10th Revision, codes. These included diverticulosis, constipation, metabolic dysfunction–associated steatotic liver disease, cholelithiasis, and gastroesophageal reflux disease. 

Both activity patterns “showed similar risk reduction with no significant difference,” Yu said. At the threshold ≥ 150 minutes, for instance, hazard ratios for any digestive disease were 0.83 for weekend warriors and 0.79 for active regulars, compared with sedentary participants.

The analysis was repeated using a median threshold ≥ 230.4 minutes of MVPA a week, and the researchers found the same results.

As a validation cohort, the researchers used more than 6,000 participants from the National Institutes of Health’s All of Us Research Program with over 6 months of wrist-based accelerometer data.

A recent meta-epidemiology study found that the weekend warrior pattern offers other health benefits, including reducing the risk for cardiovascular disease mortality, mental disorders, and metabolic syndrome.

 

A Pleasant Surprise

The digestive disease study’s findings were “a surprise and a pleasant one,” said Aasma Shaukat, MD, MPH, AGAF, professor of medicine and a gastroenterologist at NYU Grossman School of Medicine, New York City.

“We often think if we’re not able to exercise regularly, then there’s no hope for us,” said Shaukat, who moderated the session. “But this implies that even if we have time only during the weekend to engage in physical activity, it still confers benefits in reducing our risk of any GI health disorder, as well as cardiovascular or other health disorders, compared to people inactive at baseline.”

“It gives us flexibility in terms of how we structure our exercise. Obviously, people should try to get into the habit of doing regular activity; it’s more sustainable. But a good alternative, according to this research, is that packing all of that in over the weekend seems to confer benefit. So all is not lost.”

Will this change her conversation with patients moving forward? Absolutely, Shaukat said. She generally recommends physical activity for at least 30 minutes three times a week. Now Shaukat said she can tell patients: “If that’s not possible, take that time out during the weekend for your health”.

This study was funded by grants from the National Natural Science Foundation of China and its Regional Innovation and Development Joint Foundation. Yu and Shaukat reported no disclosures.

A version of this article appeared on Medscape.com.

SAN DIEGO — The session started with a question that many in the audience at Digestive Disease Week (DDW) 2025 seemed to relate to: “How many of you find yourself squeezing workouts into a weekend after a hectic work week?”

Although regular exercise three or more times a week is often viewed as preferable, Shiyi Yu, MD, a resident physician in the Department of Gastroenterology at Guangdong Provincial People’s Hospital in Guangzhou, China, had good news for weekend warriors.

Both patterns reduce digestive disease almost equally.

Her study compared weekend warriors with those she called “active regulars” and sedentary folks to see how activity patterns affect digestive disease risks.

Her bottom line: “Your gut does not care about your schedule.”

The researchers analyzed wrist-based accelerometer data from 89,595 participants in the UK Biobank. To categorize participants as active or inactive, they used the World Health Organization 2020 guidelines for physical activity, which recommend at least 150-300 minutes of moderate-intensity aerobic physical activity or at least 75-150 minutes of vigorous-intensity aerobic physical activity, or an equivalent combination throughout the week. Median age of participants was 63.3 years and 48.8% were men.

They divided participants into three groups:

• About 43% were weekend warriors who met or exceeded 150 minutes of moderate to vigorous physical activity (MVPA), with 50% or more of total MVPA achieved in 1-2 days.
• About 23% were active regulars who met or exceeded 150 minutes a week but spread over more days.
• About 34% were inactive participants who were active less than 150 minutes a week.

The researchers followed the participants for a median of 7.9 years, looking for the incidence of multiple digestive diseases, identified using the International Classification of Diseases, 10th Revision, codes. These included diverticulosis, constipation, metabolic dysfunction–associated steatotic liver disease, cholelithiasis, and gastroesophageal reflux disease. 

Both activity patterns “showed similar risk reduction with no significant difference,” Yu said. At the threshold ≥ 150 minutes, for instance, hazard ratios for any digestive disease were 0.83 for weekend warriors and 0.79 for active regulars, compared with sedentary participants.

The analysis was repeated using a median threshold ≥ 230.4 minutes of MVPA a week, and the researchers found the same results.

As a validation cohort, the researchers used more than 6,000 participants from the National Institutes of Health’s All of Us Research Program with over 6 months of wrist-based accelerometer data.

A recent meta-epidemiology study found that the weekend warrior pattern offers other health benefits, including reducing the risk for cardiovascular disease mortality, mental disorders, and metabolic syndrome.

 

A Pleasant Surprise

The digestive disease study’s findings were “a surprise and a pleasant one,” said Aasma Shaukat, MD, MPH, AGAF, professor of medicine and a gastroenterologist at NYU Grossman School of Medicine, New York City.

“We often think if we’re not able to exercise regularly, then there’s no hope for us,” said Shaukat, who moderated the session. “But this implies that even if we have time only during the weekend to engage in physical activity, it still confers benefits in reducing our risk of any GI health disorder, as well as cardiovascular or other health disorders, compared to people inactive at baseline.”

“It gives us flexibility in terms of how we structure our exercise. Obviously, people should try to get into the habit of doing regular activity; it’s more sustainable. But a good alternative, according to this research, is that packing all of that in over the weekend seems to confer benefit. So all is not lost.”

Will this change her conversation with patients moving forward? Absolutely, Shaukat said. She generally recommends physical activity for at least 30 minutes three times a week. Now Shaukat said she can tell patients: “If that’s not possible, take that time out during the weekend for your health”.

This study was funded by grants from the National Natural Science Foundation of China and its Regional Innovation and Development Joint Foundation. Yu and Shaukat reported no disclosures.

A version of this article appeared on Medscape.com.

SAN DIEGO — The session started with a question that many in the audience at Digestive Disease Week (DDW) 2025 seemed to relate to: “How many of you find yourself squeezing workouts into a weekend after a hectic work week?”

Although regular exercise three or more times a week is often viewed as preferable, Shiyi Yu, MD, a resident physician in the Department of Gastroenterology at Guangdong Provincial People’s Hospital in Guangzhou, China, had good news for weekend warriors.

Both patterns reduce digestive disease almost equally.

Her study compared weekend warriors with those she called “active regulars” and sedentary folks to see how activity patterns affect digestive disease risks.

Her bottom line: “Your gut does not care about your schedule.”

The researchers analyzed wrist-based accelerometer data from 89,595 participants in the UK Biobank. To categorize participants as active or inactive, they used the World Health Organization 2020 guidelines for physical activity, which recommend at least 150-300 minutes of moderate-intensity aerobic physical activity or at least 75-150 minutes of vigorous-intensity aerobic physical activity, or an equivalent combination throughout the week. Median age of participants was 63.3 years and 48.8% were men.

They divided participants into three groups:

• About 43% were weekend warriors who met or exceeded 150 minutes of moderate to vigorous physical activity (MVPA), with 50% or more of total MVPA achieved in 1-2 days.
• About 23% were active regulars who met or exceeded 150 minutes a week but spread over more days.
• About 34% were inactive participants who were active less than 150 minutes a week.

The researchers followed the participants for a median of 7.9 years, looking for the incidence of multiple digestive diseases, identified using the International Classification of Diseases, 10th Revision, codes. These included diverticulosis, constipation, metabolic dysfunction–associated steatotic liver disease, cholelithiasis, and gastroesophageal reflux disease. 

Both activity patterns “showed similar risk reduction with no significant difference,” Yu said. At the threshold ≥ 150 minutes, for instance, hazard ratios for any digestive disease were 0.83 for weekend warriors and 0.79 for active regulars, compared with sedentary participants.

The analysis was repeated using a median threshold ≥ 230.4 minutes of MVPA a week, and the researchers found the same results.

As a validation cohort, the researchers used more than 6,000 participants from the National Institutes of Health’s All of Us Research Program with over 6 months of wrist-based accelerometer data.

A recent meta-epidemiology study found that the weekend warrior pattern offers other health benefits, including reducing the risk for cardiovascular disease mortality, mental disorders, and metabolic syndrome.

 

A Pleasant Surprise

The digestive disease study’s findings were “a surprise and a pleasant one,” said Aasma Shaukat, MD, MPH, AGAF, professor of medicine and a gastroenterologist at NYU Grossman School of Medicine, New York City.

“We often think if we’re not able to exercise regularly, then there’s no hope for us,” said Shaukat, who moderated the session. “But this implies that even if we have time only during the weekend to engage in physical activity, it still confers benefits in reducing our risk of any GI health disorder, as well as cardiovascular or other health disorders, compared to people inactive at baseline.”

“It gives us flexibility in terms of how we structure our exercise. Obviously, people should try to get into the habit of doing regular activity; it’s more sustainable. But a good alternative, according to this research, is that packing all of that in over the weekend seems to confer benefit. So all is not lost.”

Will this change her conversation with patients moving forward? Absolutely, Shaukat said. She generally recommends physical activity for at least 30 minutes three times a week. Now Shaukat said she can tell patients: “If that’s not possible, take that time out during the weekend for your health”.

This study was funded by grants from the National Natural Science Foundation of China and its Regional Innovation and Development Joint Foundation. Yu and Shaukat reported no disclosures.

A version of this article appeared on Medscape.com.

SAN DIEGO — An artificial intelligence (AI)–enhanced digital collaborative care model led to rapid, clinically significant, and sustained symptom relief for patients with irritable bowel syndrome (IBS) seen at Cleveland Clinic, Cleveland, Ohio, an observational study found.

Symptom tracking at 4-week intervals showed that “almost everybody got better” regardless of IBS subtype, with relief starting in the first 4 weeks, Stephen Lupe, PsyD, gastrointestinal psychologist and director of Behavioral Medicine, Department of Gastroenterology, Hepatology, and Nutrition at Cleveland Clinic, Cleveland, said in an interview with GI & Hepatology News.

The findings were presented at Digestive Disease Week (DDW) 2025.

 

Digital Boost to Collaborative Care Model

The combination of dietary interventions and brain-gut behavioral therapy has demonstrated excellent outcomes for patients with IBS, but patients struggle to access these needed services, Lupe noted. A medical home collaborative care model in which patients get care from a multidisciplinary team has been shown to be a good way to successfully deliver this combination of care.

“When you do collaborative in-person care, people get better quicker,” Lupe said.

However, scaling access to this model remains a challenge. For their study, Cleveland Clinic researchers added an AI-enhanced digital platform, Ayble Health, to the in-person collaborative care model to expand access to disease-management services and evaluated whether it improved clinical outcomes for study’s 171 participants, who were recruited via social media advertisements.

Here’s how the platform works. Once a patient enrolls in Ayble Health, a personalized care plan is recommended based on a virtual visit, screening questionnaire, and baseline survey.

The platform includes brain-gut programs, including guided audio content on mindfulness, hypnosis, meditation, cognitive behavioral therapy, and breathing techniques; personalized nutrition support to find and remove trigger foods, a food barcode scanner, and a comprehensive groceries database; and AI-powered wellness tools to help manage and track symptoms. Lupe worked with Ayble Health to develop the platform’s behavioral health content and care pathways.

Patients may choose to follow any combination of three care pathways: A care team overseen by gastro-psychologists, dietitians, and gastroenterologists; a holistic nutrition program including a personalized elimination diet; and a brain-gut behavioral therapy program with gut-directed hypnosis, cognitive behavioral therapy, and acceptance and commitment therapy. They go at their own pace, can connect with Ayble Health’s virtual care team to help with education and goal setting, and continue to consult their Cleveland Clinic providers as needed for evaluation and treatment.

“The care team is still there. We’ve just augmented it to make sure that as many people as possible get behavioral skills training and dietary support, with monitoring between visits — instead of the traditional, ‘I’ll see you in 6 months approach,” Lupe explained.

 

IBS Symptom Scores Improve

Of the study’s 171 patients, 20 had IBS-diarrhea, 23 had IBS-constipation, 32 had IBS-mixed, and 8 had IBS-unspecified. The remaining 88 patients reported IBS without indication of subtype.

At intake, all patients had active IBS symptoms, with scores ≥ 75 on the IBS symptom severity scale (IBS-SSS). Most patients enrolled in more than one care pathway, and 95% of participants completed at least 4 weeks on their chosen pathways.

Overall, patients saw an average 140-point decrease in IBS-SSS from intake through follow-up lasting up to 42 weeks. A drop in IBS-SSS score ≥ 50 points was considered a clinically meaningful change.

Symptom improvements occurred as early as week 4, were sustained and were uniform across IBS subtypes, suggesting that the AI-enhanced digital collaborative care model has wide utility in patients with IBS, Lupe said.

Patients with the most severe IBS symptoms showed the greatest improvement, but even 50% of those with mild symptoms had clinically meaningful changes in IBS-SSS.

Improvement in IBS symptoms was seen across all care pathways, but the combination of multiple pathways improved outcomes better than a single care pathway alone. The combination of nutrition and brain-gut behavioral therapy demonstrated the greatest reduction in IBS-SSS scores and proportion of patients achieving clinically meaningful results (95%).

The digital comprehensive car model for IBS is now “up and running” at Cleveland Clinic, and the team plans to proactively reach out to patients with gastrointestinal disorders recently seen at their center to alert them to the availability of this tool, Lupe said.

A randomized controlled trial is planned to further validate these observational findings, he added.

 

‘Wave of the Future’

The digital collaborative care model is “innovative, and I think is the wave of the future,” Kyle Staller, MD, MPH, gastroenterologist and director of the Gastrointestinal Motility Laboratory at Massachusetts General Hospital, Boston, who wasn’t involved in the study, told GI & Hepatology News.

“These digital platforms bundle nondrug options, such as cognitive-behavioral therapy, dietary therapy, hypnotherapy, so patients can choose what suits them, rather than the gastroenterologist hunting down each individual resource, which requires a lot of work,” Staller said.

The study “provides real-world evidence that a deliberative, digital, collaborative care model that houses various types of nondrug IBS treatment under one roof can provide meaningful benefit to patients,” Staller told GI & Hepatology News.

Importantly, he said, “patients chose which option they wanted. At the end of the day, the way that we should be thinking about IBS care is really making sure that we engage the patient with treatment choices,” Staller said.

This study had no specific funding. Three authors had relationships with Ayble Health. Lupe is a scientific advisor for Boomerang Health and paid lecturer for Takeda Pharmaceuticals. Staller disclosed having relationships with Mahana Therapeutics, Ardelyx Inc, Gemelli Biotech, Salix Pharmaceuticals, and Takeda Pharmaceuticals.

A version of this article appeared on Medscape.com.

SAN DIEGO — An artificial intelligence (AI)–enhanced digital collaborative care model led to rapid, clinically significant, and sustained symptom relief for patients with irritable bowel syndrome (IBS) seen at Cleveland Clinic, Cleveland, Ohio, an observational study found.

Symptom tracking at 4-week intervals showed that “almost everybody got better” regardless of IBS subtype, with relief starting in the first 4 weeks, Stephen Lupe, PsyD, gastrointestinal psychologist and director of Behavioral Medicine, Department of Gastroenterology, Hepatology, and Nutrition at Cleveland Clinic, Cleveland, said in an interview with GI & Hepatology News.

The findings were presented at Digestive Disease Week (DDW) 2025.

 

Digital Boost to Collaborative Care Model

The combination of dietary interventions and brain-gut behavioral therapy has demonstrated excellent outcomes for patients with IBS, but patients struggle to access these needed services, Lupe noted. A medical home collaborative care model in which patients get care from a multidisciplinary team has been shown to be a good way to successfully deliver this combination of care.

“When you do collaborative in-person care, people get better quicker,” Lupe said.

However, scaling access to this model remains a challenge. For their study, Cleveland Clinic researchers added an AI-enhanced digital platform, Ayble Health, to the in-person collaborative care model to expand access to disease-management services and evaluated whether it improved clinical outcomes for study’s 171 participants, who were recruited via social media advertisements.

Here’s how the platform works. Once a patient enrolls in Ayble Health, a personalized care plan is recommended based on a virtual visit, screening questionnaire, and baseline survey.

The platform includes brain-gut programs, including guided audio content on mindfulness, hypnosis, meditation, cognitive behavioral therapy, and breathing techniques; personalized nutrition support to find and remove trigger foods, a food barcode scanner, and a comprehensive groceries database; and AI-powered wellness tools to help manage and track symptoms. Lupe worked with Ayble Health to develop the platform’s behavioral health content and care pathways.

Patients may choose to follow any combination of three care pathways: A care team overseen by gastro-psychologists, dietitians, and gastroenterologists; a holistic nutrition program including a personalized elimination diet; and a brain-gut behavioral therapy program with gut-directed hypnosis, cognitive behavioral therapy, and acceptance and commitment therapy. They go at their own pace, can connect with Ayble Health’s virtual care team to help with education and goal setting, and continue to consult their Cleveland Clinic providers as needed for evaluation and treatment.

“The care team is still there. We’ve just augmented it to make sure that as many people as possible get behavioral skills training and dietary support, with monitoring between visits — instead of the traditional, ‘I’ll see you in 6 months approach,” Lupe explained.

 

IBS Symptom Scores Improve

Of the study’s 171 patients, 20 had IBS-diarrhea, 23 had IBS-constipation, 32 had IBS-mixed, and 8 had IBS-unspecified. The remaining 88 patients reported IBS without indication of subtype.

At intake, all patients had active IBS symptoms, with scores ≥ 75 on the IBS symptom severity scale (IBS-SSS). Most patients enrolled in more than one care pathway, and 95% of participants completed at least 4 weeks on their chosen pathways.

Overall, patients saw an average 140-point decrease in IBS-SSS from intake through follow-up lasting up to 42 weeks. A drop in IBS-SSS score ≥ 50 points was considered a clinically meaningful change.

Symptom improvements occurred as early as week 4, were sustained and were uniform across IBS subtypes, suggesting that the AI-enhanced digital collaborative care model has wide utility in patients with IBS, Lupe said.

Patients with the most severe IBS symptoms showed the greatest improvement, but even 50% of those with mild symptoms had clinically meaningful changes in IBS-SSS.

Improvement in IBS symptoms was seen across all care pathways, but the combination of multiple pathways improved outcomes better than a single care pathway alone. The combination of nutrition and brain-gut behavioral therapy demonstrated the greatest reduction in IBS-SSS scores and proportion of patients achieving clinically meaningful results (95%).

The digital comprehensive car model for IBS is now “up and running” at Cleveland Clinic, and the team plans to proactively reach out to patients with gastrointestinal disorders recently seen at their center to alert them to the availability of this tool, Lupe said.

A randomized controlled trial is planned to further validate these observational findings, he added.

 

‘Wave of the Future’

The digital collaborative care model is “innovative, and I think is the wave of the future,” Kyle Staller, MD, MPH, gastroenterologist and director of the Gastrointestinal Motility Laboratory at Massachusetts General Hospital, Boston, who wasn’t involved in the study, told GI & Hepatology News.

“These digital platforms bundle nondrug options, such as cognitive-behavioral therapy, dietary therapy, hypnotherapy, so patients can choose what suits them, rather than the gastroenterologist hunting down each individual resource, which requires a lot of work,” Staller said.

The study “provides real-world evidence that a deliberative, digital, collaborative care model that houses various types of nondrug IBS treatment under one roof can provide meaningful benefit to patients,” Staller told GI & Hepatology News.

Importantly, he said, “patients chose which option they wanted. At the end of the day, the way that we should be thinking about IBS care is really making sure that we engage the patient with treatment choices,” Staller said.

This study had no specific funding. Three authors had relationships with Ayble Health. Lupe is a scientific advisor for Boomerang Health and paid lecturer for Takeda Pharmaceuticals. Staller disclosed having relationships with Mahana Therapeutics, Ardelyx Inc, Gemelli Biotech, Salix Pharmaceuticals, and Takeda Pharmaceuticals.

A version of this article appeared on Medscape.com.

SAN DIEGO — An artificial intelligence (AI)–enhanced digital collaborative care model led to rapid, clinically significant, and sustained symptom relief for patients with irritable bowel syndrome (IBS) seen at Cleveland Clinic, Cleveland, Ohio, an observational study found.

Symptom tracking at 4-week intervals showed that “almost everybody got better” regardless of IBS subtype, with relief starting in the first 4 weeks, Stephen Lupe, PsyD, gastrointestinal psychologist and director of Behavioral Medicine, Department of Gastroenterology, Hepatology, and Nutrition at Cleveland Clinic, Cleveland, said in an interview with GI & Hepatology News.

The findings were presented at Digestive Disease Week (DDW) 2025.

 

Digital Boost to Collaborative Care Model

The combination of dietary interventions and brain-gut behavioral therapy has demonstrated excellent outcomes for patients with IBS, but patients struggle to access these needed services, Lupe noted. A medical home collaborative care model in which patients get care from a multidisciplinary team has been shown to be a good way to successfully deliver this combination of care.

“When you do collaborative in-person care, people get better quicker,” Lupe said.

However, scaling access to this model remains a challenge. For their study, Cleveland Clinic researchers added an AI-enhanced digital platform, Ayble Health, to the in-person collaborative care model to expand access to disease-management services and evaluated whether it improved clinical outcomes for study’s 171 participants, who were recruited via social media advertisements.

Here’s how the platform works. Once a patient enrolls in Ayble Health, a personalized care plan is recommended based on a virtual visit, screening questionnaire, and baseline survey.

The platform includes brain-gut programs, including guided audio content on mindfulness, hypnosis, meditation, cognitive behavioral therapy, and breathing techniques; personalized nutrition support to find and remove trigger foods, a food barcode scanner, and a comprehensive groceries database; and AI-powered wellness tools to help manage and track symptoms. Lupe worked with Ayble Health to develop the platform’s behavioral health content and care pathways.

Patients may choose to follow any combination of three care pathways: A care team overseen by gastro-psychologists, dietitians, and gastroenterologists; a holistic nutrition program including a personalized elimination diet; and a brain-gut behavioral therapy program with gut-directed hypnosis, cognitive behavioral therapy, and acceptance and commitment therapy. They go at their own pace, can connect with Ayble Health’s virtual care team to help with education and goal setting, and continue to consult their Cleveland Clinic providers as needed for evaluation and treatment.

“The care team is still there. We’ve just augmented it to make sure that as many people as possible get behavioral skills training and dietary support, with monitoring between visits — instead of the traditional, ‘I’ll see you in 6 months approach,” Lupe explained.

 

IBS Symptom Scores Improve

Of the study’s 171 patients, 20 had IBS-diarrhea, 23 had IBS-constipation, 32 had IBS-mixed, and 8 had IBS-unspecified. The remaining 88 patients reported IBS without indication of subtype.

At intake, all patients had active IBS symptoms, with scores ≥ 75 on the IBS symptom severity scale (IBS-SSS). Most patients enrolled in more than one care pathway, and 95% of participants completed at least 4 weeks on their chosen pathways.

Overall, patients saw an average 140-point decrease in IBS-SSS from intake through follow-up lasting up to 42 weeks. A drop in IBS-SSS score ≥ 50 points was considered a clinically meaningful change.

Symptom improvements occurred as early as week 4, were sustained and were uniform across IBS subtypes, suggesting that the AI-enhanced digital collaborative care model has wide utility in patients with IBS, Lupe said.

Patients with the most severe IBS symptoms showed the greatest improvement, but even 50% of those with mild symptoms had clinically meaningful changes in IBS-SSS.

Improvement in IBS symptoms was seen across all care pathways, but the combination of multiple pathways improved outcomes better than a single care pathway alone. The combination of nutrition and brain-gut behavioral therapy demonstrated the greatest reduction in IBS-SSS scores and proportion of patients achieving clinically meaningful results (95%).

The digital comprehensive car model for IBS is now “up and running” at Cleveland Clinic, and the team plans to proactively reach out to patients with gastrointestinal disorders recently seen at their center to alert them to the availability of this tool, Lupe said.

A randomized controlled trial is planned to further validate these observational findings, he added.

 

‘Wave of the Future’

The digital collaborative care model is “innovative, and I think is the wave of the future,” Kyle Staller, MD, MPH, gastroenterologist and director of the Gastrointestinal Motility Laboratory at Massachusetts General Hospital, Boston, who wasn’t involved in the study, told GI & Hepatology News.

“These digital platforms bundle nondrug options, such as cognitive-behavioral therapy, dietary therapy, hypnotherapy, so patients can choose what suits them, rather than the gastroenterologist hunting down each individual resource, which requires a lot of work,” Staller said.

The study “provides real-world evidence that a deliberative, digital, collaborative care model that houses various types of nondrug IBS treatment under one roof can provide meaningful benefit to patients,” Staller told GI & Hepatology News.

Importantly, he said, “patients chose which option they wanted. At the end of the day, the way that we should be thinking about IBS care is really making sure that we engage the patient with treatment choices,” Staller said.

This study had no specific funding. Three authors had relationships with Ayble Health. Lupe is a scientific advisor for Boomerang Health and paid lecturer for Takeda Pharmaceuticals. Staller disclosed having relationships with Mahana Therapeutics, Ardelyx Inc, Gemelli Biotech, Salix Pharmaceuticals, and Takeda Pharmaceuticals.

A version of this article appeared on Medscape.com.

The US National Institute of Standards and Technology (NIST) has developed precisely measured human fecal material to foster a new era in gut microbiome research. 

According to AGA’s Center for Gut Microbiome Research & Education, this critical resource will help advance the utility and reproducibility of microbiome-based diagnostics — “which still remain relatively meaningless clinically, although patients continue to buy direct-to-consumer tests, and a standard reference material will mean there’s a better way to ensure quality control and accuracy.” 

Though not a therapeutic, Human Fecal Material RM is expected to speed up gastrointestinal (GI) therapeutics since many microbiome-based drugs are inspired by fecal transplants with human stool as the developmental starting point. A standardized reference material will be an important resource as industry develops and tests new drugs. It can be purchased online at the NIST Store (shop.nist.gov).

The product consists of eight frozen vials of exhaustively studied human feces suspended in aqueous solution. Available are more than 25 pages of data identifying the key microbes and biomolecules in the material. Scientists, including those working at biopharmaceutical and biotech companies, can use this material to further their research and develop new drugs that target the microbiome, including treatments that contain living bacteria. 

 

Development

According to NIST, the stool material is “the most precisely measured, scientifically analyzed, and richly characterized human fecal standard ever produced. 

“The project ran for about 6 years from start to finish, the last 2 for manufacturing, characterization, and writing,” said NIST molecular geneticist Scott A. Jackson, PhD, who helped develop the product. “We hope our reference material will lay the foundation for gut microbiome research to thrive and reach its full potential.” 

As founder of NIST’s Complex Microbial Systems Group, Jackson is leading international efforts to improve microbiome and metagenomic measurements by organizing inter-lab studies and refining reference materials and methods. 

The project collected stool from two cohorts of donors, ie, vegetarians and omnivores, with each cohort comprising four to six donors. Material from each cohort was pooled and homogenized before being aliquoted into 5000 vials per cohort. About 300 tubes from each cohort were picked, and aliquots then underwent multiomic analyses. 

Offering his perspective on the new product, Sudhir K. Dutta, MBBS, associate professor in the Division of Gastroenterology and Hepatology at Johns Hopkins University School of Medicine, Baltimore, said, “This tool will be 100% useful for microbiome research.”

And according to Lori Holtz, MD, MSPH, professor of pediatric gastroenterology, hepatology, and nutrition at Washington University School of Medicine in St. Louis, Missouri, the material will aid microbiome research by allowing interpretability and repeatability across studies. “Microbiome research is a relatively new field, and protocols differ from group to group and lab to lab, so it’s been difficult to compare results across studies,” she told GI & Hepatology News. “A standard stool product will allow for greater comparability in preclinical studies and later clinical trials testing interventions to alter the microbiome.”

The NIST developers are looking forward to reaction from the GI research community. “Over the last several years, we’ve released smaller pilot batches of material to smaller groups of stakeholders,” said Jackson. “We’ve used the feedback on these earlier batches to inform the manufacturing and characterization of the final batch that was released in March, but we don’t yet have any feedback yet on the current material.”

Jackson, Dutta, and Holtz disclosed having no relevant competing interests.

A version of this article appeared on Medscape.com.

The US National Institute of Standards and Technology (NIST) has developed precisely measured human fecal material to foster a new era in gut microbiome research. 

According to AGA’s Center for Gut Microbiome Research & Education, this critical resource will help advance the utility and reproducibility of microbiome-based diagnostics — “which still remain relatively meaningless clinically, although patients continue to buy direct-to-consumer tests, and a standard reference material will mean there’s a better way to ensure quality control and accuracy.” 

Though not a therapeutic, Human Fecal Material RM is expected to speed up gastrointestinal (GI) therapeutics since many microbiome-based drugs are inspired by fecal transplants with human stool as the developmental starting point. A standardized reference material will be an important resource as industry develops and tests new drugs. It can be purchased online at the NIST Store (shop.nist.gov).

The product consists of eight frozen vials of exhaustively studied human feces suspended in aqueous solution. Available are more than 25 pages of data identifying the key microbes and biomolecules in the material. Scientists, including those working at biopharmaceutical and biotech companies, can use this material to further their research and develop new drugs that target the microbiome, including treatments that contain living bacteria. 

 

Development

According to NIST, the stool material is “the most precisely measured, scientifically analyzed, and richly characterized human fecal standard ever produced. 

“The project ran for about 6 years from start to finish, the last 2 for manufacturing, characterization, and writing,” said NIST molecular geneticist Scott A. Jackson, PhD, who helped develop the product. “We hope our reference material will lay the foundation for gut microbiome research to thrive and reach its full potential.” 

As founder of NIST’s Complex Microbial Systems Group, Jackson is leading international efforts to improve microbiome and metagenomic measurements by organizing inter-lab studies and refining reference materials and methods. 

The project collected stool from two cohorts of donors, ie, vegetarians and omnivores, with each cohort comprising four to six donors. Material from each cohort was pooled and homogenized before being aliquoted into 5000 vials per cohort. About 300 tubes from each cohort were picked, and aliquots then underwent multiomic analyses. 

Offering his perspective on the new product, Sudhir K. Dutta, MBBS, associate professor in the Division of Gastroenterology and Hepatology at Johns Hopkins University School of Medicine, Baltimore, said, “This tool will be 100% useful for microbiome research.”

And according to Lori Holtz, MD, MSPH, professor of pediatric gastroenterology, hepatology, and nutrition at Washington University School of Medicine in St. Louis, Missouri, the material will aid microbiome research by allowing interpretability and repeatability across studies. “Microbiome research is a relatively new field, and protocols differ from group to group and lab to lab, so it’s been difficult to compare results across studies,” she told GI & Hepatology News. “A standard stool product will allow for greater comparability in preclinical studies and later clinical trials testing interventions to alter the microbiome.”

The NIST developers are looking forward to reaction from the GI research community. “Over the last several years, we’ve released smaller pilot batches of material to smaller groups of stakeholders,” said Jackson. “We’ve used the feedback on these earlier batches to inform the manufacturing and characterization of the final batch that was released in March, but we don’t yet have any feedback yet on the current material.”

Jackson, Dutta, and Holtz disclosed having no relevant competing interests.

A version of this article appeared on Medscape.com.

The US National Institute of Standards and Technology (NIST) has developed precisely measured human fecal material to foster a new era in gut microbiome research. 

According to AGA’s Center for Gut Microbiome Research & Education, this critical resource will help advance the utility and reproducibility of microbiome-based diagnostics — “which still remain relatively meaningless clinically, although patients continue to buy direct-to-consumer tests, and a standard reference material will mean there’s a better way to ensure quality control and accuracy.” 

Though not a therapeutic, Human Fecal Material RM is expected to speed up gastrointestinal (GI) therapeutics since many microbiome-based drugs are inspired by fecal transplants with human stool as the developmental starting point. A standardized reference material will be an important resource as industry develops and tests new drugs. It can be purchased online at the NIST Store (shop.nist.gov).

The product consists of eight frozen vials of exhaustively studied human feces suspended in aqueous solution. Available are more than 25 pages of data identifying the key microbes and biomolecules in the material. Scientists, including those working at biopharmaceutical and biotech companies, can use this material to further their research and develop new drugs that target the microbiome, including treatments that contain living bacteria. 

 

Development

According to NIST, the stool material is “the most precisely measured, scientifically analyzed, and richly characterized human fecal standard ever produced. 

“The project ran for about 6 years from start to finish, the last 2 for manufacturing, characterization, and writing,” said NIST molecular geneticist Scott A. Jackson, PhD, who helped develop the product. “We hope our reference material will lay the foundation for gut microbiome research to thrive and reach its full potential.” 

As founder of NIST’s Complex Microbial Systems Group, Jackson is leading international efforts to improve microbiome and metagenomic measurements by organizing inter-lab studies and refining reference materials and methods. 

The project collected stool from two cohorts of donors, ie, vegetarians and omnivores, with each cohort comprising four to six donors. Material from each cohort was pooled and homogenized before being aliquoted into 5000 vials per cohort. About 300 tubes from each cohort were picked, and aliquots then underwent multiomic analyses. 

Offering his perspective on the new product, Sudhir K. Dutta, MBBS, associate professor in the Division of Gastroenterology and Hepatology at Johns Hopkins University School of Medicine, Baltimore, said, “This tool will be 100% useful for microbiome research.”

And according to Lori Holtz, MD, MSPH, professor of pediatric gastroenterology, hepatology, and nutrition at Washington University School of Medicine in St. Louis, Missouri, the material will aid microbiome research by allowing interpretability and repeatability across studies. “Microbiome research is a relatively new field, and protocols differ from group to group and lab to lab, so it’s been difficult to compare results across studies,” she told GI & Hepatology News. “A standard stool product will allow for greater comparability in preclinical studies and later clinical trials testing interventions to alter the microbiome.”

The NIST developers are looking forward to reaction from the GI research community. “Over the last several years, we’ve released smaller pilot batches of material to smaller groups of stakeholders,” said Jackson. “We’ve used the feedback on these earlier batches to inform the manufacturing and characterization of the final batch that was released in March, but we don’t yet have any feedback yet on the current material.”

Jackson, Dutta, and Holtz disclosed having no relevant competing interests.

A version of this article appeared on Medscape.com.

WASHINGTON — When a published case of auto-brewery syndrome (ABS) in China — caused by Klebsiella pneumoniae — received widespread publicity in 2019, patients reacted, sending emails to lead author Jing Yuan, in Beijing, China. Many of these inquiries were from patients in the United States who believed they might have ABS.

“Can you check to see if I have ABS?” patients asked Yuan.

For help, Yuan contacted Bernd Schnabl, MD, AGAF, at the University of California, San Diego, whose research was addressing alcohol-associated liver disease and who was also interested in the gut-liver axis and the role of gut microbiome–derived ethanol in metabolic dysfunction–associated steatotic liver disease (MASLD).

“She asked me, ‘Are you interested in looking into ABS?” Schnabl recalled at the Gut Microbiota for Health (GMFH) World Summit 2025. He dug in and formed what may be the largest research cohort thus far of patients with ABS — a group of 22 patients with their diagnosis confirmed through observed glucose challenge.

His soon-to-be-published research on this cohort has confirmed excess ethanol production — and elevations of both proteobacteria and fermentation pathways — in patients whose ABS symptoms had flared.

ABS is considered a rare condition, but “I’d argue that it’s rarely diagnosed because many physicians don’t know of the diagnosis, and many are actually very skeptical about the disease,” Schnabl said at the meeting, convened by AGA and the European Society of Neurogastroenterology and Motility.

Patients experience symptoms of intoxication when ethanol produced by dysregulated gut microbiota exceeds the capacity of the liver to metabolize it and accumulates in the blood, he explained.

“Patients constantly talk about brain fog; they can’t concentrate, and it can be very severe,” he said. “They don’t get a firm diagnosis and go from one medical center to another, and they also suffer from complications of alcohol use disorder including serious family, social, and legal problems.”

 

Advancing Knowledge, Findings From the Cohort

The phenomenon of ethanol production by gut microbiota has been known for over a century, Schnabl wrote with two co-authors in a 2024 review in Nature Reviews Gastroenterology & Hepatology of “endogenous ethanol production in health and disease.”

And in recent decades, he said at the meeting, research has linked endogenous ethanol production to MASLD, positioning it as a potential contributor to disease pathogenesis. In one of the most recently published studies, patients with MASLD had higher concentrations of ethanol in their systemic circulation after a mixed meal test than did healthy controls — and even higher ethanol concentrations in their portal vein blood, “suggesting that this ethanol is coming from the gut microbiome,” Schnabl said.

The paper from China that led Schnabl to establish his cohort was spurred on by a patient with both ABS and MASLD cirrhosis. The patient was found to have strains of high alcohol–producing K pneumoniae in the gut microbiome. When the researchers transplanted these strains into mice via fecal microbiota transplantation (FMT), the mice developed MASLD.

Schnabl’s study focused just on ABS, which is alternatively sometimes called gut fermentation syndrome. The 22 patients in his ABS cohort — each of whom provided stool samples corresponding to remission or flare of ABS symptoms — had a median age of 45 years and were predominantly men, slightly overweight and not obese, and without liver disease. (About 48 patients with suspected ABS were screened, and 20 were excluded after an observed glucose challenge failed to establish a diagnosis; 6 withdrew from the study.)

During remission (no symptoms), patients’ mean blood alcohol content (BAC) level was zero, but during a flare, the mean BAC level was 136 mg/dL. “To put it into perspective, the legal limit for driving in the US is 80 mg/dL,” Schnabl said. Within a mean of 4 hours after the oral glucose load used for diagnosis, patients’ mean BAC level was 73 mg/dL, he noted.

To assess ethanol production by the patients’ microbiota, Schnabl and his team cultured the stool samples — anaerobically adding glucose and measuring ethanol production — and compared the results with findings from stool samples collected from household partners who generally were of the opposite sex. Among their findings: cultures of stool from patients experiencing a flare produced significantly more ethanol than stool from household partners and samples from patients in remission.

To assess whether ethanol was produced by bacteria or fungi, the researchers measured ethanol production in cultures treated with either the antifungal amphotericin B or the antibiotic chloramphenicol. “Chloramphenicol clearly decreased the ethanol production,” Schnabl said. “So at least in this culture test, bacteria produced most of the alcohol in our patients.”

Taxonomic profiling, moreover, revealed “significantly elevated levels” of proteobacteria — with relative abundance of Escherichia coli and K pneumoniae — in patients who were flaring, he said. And functional profiling of the fecal microbiota showed much higher activity of fermentation pathways during patients’ flares than in household partners or healthy controls. (Healthy controls were incorporated into the taxonomic and functional profiling parts of the research.)

 

A Clinical Approach to ABS

Schnabl said at the meeting that stool cultures of both household partners and patients in long-term remission “all produced some low amount of ethanol, which was initially puzzling to us” but became less surprising as he and his colleagues reviewed more of the literature.

Asked during a discussion period whether ABS could explain chronic fatigue, a commonly reported chronic symptom in populations, Schnabl said it’s possible. And in an interview after the meeting, he elaborated. “The literature clearly says ABS is a rare disease, but I argue that more patients may have ABS; they just don’t know it. And I suspect some may have mild symptoms, like brain fog, feeling tired,” he said. “But at this point, this is complete speculation.”

Physicians should “be aware that if a patient has unexplained symptoms that could be aligned with ABS, checking the blood alcohol level” may be warranted, he said in the interview. A PEth (phosphatidylethanol) test — a biomarker test used to check for longer-term alcohol consumption — is an option, but it is important to appreciate it will not discriminate between exogenous alcohol drinking and endogenous ethanol production.

There are no standardized diagnostic tests for ABS, but at the meeting, Schnabl outlined a clinical approach, starting with a standardized oral glucose tolerance challenge test to detect elevated ethanol concentrations.

A fecal yeast test is warranted for diagnosed patients on the basis of some case reports in which ABS symptoms have improved with antifungal treatments. When the fecal yeast test is negative, “ideally you want to identify the ethanol-producing intestinal bacteria in the patient,” he said, using cultures and fecal metagenomics sequencing.

Treatment could then be tailored to the identified microbial strain, with options being selective antibiotics, probiotics and/or prebiotics, and — likely in the future — phages or FMT, he said. (These options, all aimed at restoring gut homeostasis, are also discussed in his 2024 review.)

Schnabl and his team recently performed FMT in a patient with ABS in whom E coli was determined to be producing excessive ethanol. The FMT, performed after antibiotic pretreatment, resulted in decreases in the relative abundance of proteobacteria and E coli levels, lower blood alcohol levels and fermentation enrichment pathways, and normalized liver enzymes.

After 6 months, however, the patient relapsed, and the measurements reversed. “We decided to do FMT every month, and we treated the patient for 6 months,” Schnabl said, noting that ABS had rendered the patient dysfunctional and unable to work. “He has been out of treatment for over a year now and is not flaring any longer.”

Schnabl and Elizabeth Hohmann, MD, at Massachusetts General Hospital, Boston, are currently recruiting patients with confirmed ABS for a National Institutes of Health–funded phase 1 safety and tolerability study of FMT for ABS.

Schnabl disclosed serving as an external scientific advisor/consultant to Ambys Medicines, Boehringer Ingelheim, Gelesis, Mabwell Therapeutics, Surrozen, and Takeda; and as the founder/BOD/BEO of Nterica Bio.

A version of this article appeared on Medscape.com.

WASHINGTON — When a published case of auto-brewery syndrome (ABS) in China — caused by Klebsiella pneumoniae — received widespread publicity in 2019, patients reacted, sending emails to lead author Jing Yuan, in Beijing, China. Many of these inquiries were from patients in the United States who believed they might have ABS.

“Can you check to see if I have ABS?” patients asked Yuan.

For help, Yuan contacted Bernd Schnabl, MD, AGAF, at the University of California, San Diego, whose research was addressing alcohol-associated liver disease and who was also interested in the gut-liver axis and the role of gut microbiome–derived ethanol in metabolic dysfunction–associated steatotic liver disease (MASLD).

“She asked me, ‘Are you interested in looking into ABS?” Schnabl recalled at the Gut Microbiota for Health (GMFH) World Summit 2025. He dug in and formed what may be the largest research cohort thus far of patients with ABS — a group of 22 patients with their diagnosis confirmed through observed glucose challenge.

His soon-to-be-published research on this cohort has confirmed excess ethanol production — and elevations of both proteobacteria and fermentation pathways — in patients whose ABS symptoms had flared.

ABS is considered a rare condition, but “I’d argue that it’s rarely diagnosed because many physicians don’t know of the diagnosis, and many are actually very skeptical about the disease,” Schnabl said at the meeting, convened by AGA and the European Society of Neurogastroenterology and Motility.

Patients experience symptoms of intoxication when ethanol produced by dysregulated gut microbiota exceeds the capacity of the liver to metabolize it and accumulates in the blood, he explained.

“Patients constantly talk about brain fog; they can’t concentrate, and it can be very severe,” he said. “They don’t get a firm diagnosis and go from one medical center to another, and they also suffer from complications of alcohol use disorder including serious family, social, and legal problems.”

 

Advancing Knowledge, Findings From the Cohort

The phenomenon of ethanol production by gut microbiota has been known for over a century, Schnabl wrote with two co-authors in a 2024 review in Nature Reviews Gastroenterology & Hepatology of “endogenous ethanol production in health and disease.”

And in recent decades, he said at the meeting, research has linked endogenous ethanol production to MASLD, positioning it as a potential contributor to disease pathogenesis. In one of the most recently published studies, patients with MASLD had higher concentrations of ethanol in their systemic circulation after a mixed meal test than did healthy controls — and even higher ethanol concentrations in their portal vein blood, “suggesting that this ethanol is coming from the gut microbiome,” Schnabl said.

The paper from China that led Schnabl to establish his cohort was spurred on by a patient with both ABS and MASLD cirrhosis. The patient was found to have strains of high alcohol–producing K pneumoniae in the gut microbiome. When the researchers transplanted these strains into mice via fecal microbiota transplantation (FMT), the mice developed MASLD.

Schnabl’s study focused just on ABS, which is alternatively sometimes called gut fermentation syndrome. The 22 patients in his ABS cohort — each of whom provided stool samples corresponding to remission or flare of ABS symptoms — had a median age of 45 years and were predominantly men, slightly overweight and not obese, and without liver disease. (About 48 patients with suspected ABS were screened, and 20 were excluded after an observed glucose challenge failed to establish a diagnosis; 6 withdrew from the study.)

During remission (no symptoms), patients’ mean blood alcohol content (BAC) level was zero, but during a flare, the mean BAC level was 136 mg/dL. “To put it into perspective, the legal limit for driving in the US is 80 mg/dL,” Schnabl said. Within a mean of 4 hours after the oral glucose load used for diagnosis, patients’ mean BAC level was 73 mg/dL, he noted.

To assess ethanol production by the patients’ microbiota, Schnabl and his team cultured the stool samples — anaerobically adding glucose and measuring ethanol production — and compared the results with findings from stool samples collected from household partners who generally were of the opposite sex. Among their findings: cultures of stool from patients experiencing a flare produced significantly more ethanol than stool from household partners and samples from patients in remission.

To assess whether ethanol was produced by bacteria or fungi, the researchers measured ethanol production in cultures treated with either the antifungal amphotericin B or the antibiotic chloramphenicol. “Chloramphenicol clearly decreased the ethanol production,” Schnabl said. “So at least in this culture test, bacteria produced most of the alcohol in our patients.”

Taxonomic profiling, moreover, revealed “significantly elevated levels” of proteobacteria — with relative abundance of Escherichia coli and K pneumoniae — in patients who were flaring, he said. And functional profiling of the fecal microbiota showed much higher activity of fermentation pathways during patients’ flares than in household partners or healthy controls. (Healthy controls were incorporated into the taxonomic and functional profiling parts of the research.)

 

A Clinical Approach to ABS

Schnabl said at the meeting that stool cultures of both household partners and patients in long-term remission “all produced some low amount of ethanol, which was initially puzzling to us” but became less surprising as he and his colleagues reviewed more of the literature.

Asked during a discussion period whether ABS could explain chronic fatigue, a commonly reported chronic symptom in populations, Schnabl said it’s possible. And in an interview after the meeting, he elaborated. “The literature clearly says ABS is a rare disease, but I argue that more patients may have ABS; they just don’t know it. And I suspect some may have mild symptoms, like brain fog, feeling tired,” he said. “But at this point, this is complete speculation.”

Physicians should “be aware that if a patient has unexplained symptoms that could be aligned with ABS, checking the blood alcohol level” may be warranted, he said in the interview. A PEth (phosphatidylethanol) test — a biomarker test used to check for longer-term alcohol consumption — is an option, but it is important to appreciate it will not discriminate between exogenous alcohol drinking and endogenous ethanol production.

There are no standardized diagnostic tests for ABS, but at the meeting, Schnabl outlined a clinical approach, starting with a standardized oral glucose tolerance challenge test to detect elevated ethanol concentrations.

A fecal yeast test is warranted for diagnosed patients on the basis of some case reports in which ABS symptoms have improved with antifungal treatments. When the fecal yeast test is negative, “ideally you want to identify the ethanol-producing intestinal bacteria in the patient,” he said, using cultures and fecal metagenomics sequencing.

Treatment could then be tailored to the identified microbial strain, with options being selective antibiotics, probiotics and/or prebiotics, and — likely in the future — phages or FMT, he said. (These options, all aimed at restoring gut homeostasis, are also discussed in his 2024 review.)

Schnabl and his team recently performed FMT in a patient with ABS in whom E coli was determined to be producing excessive ethanol. The FMT, performed after antibiotic pretreatment, resulted in decreases in the relative abundance of proteobacteria and E coli levels, lower blood alcohol levels and fermentation enrichment pathways, and normalized liver enzymes.

After 6 months, however, the patient relapsed, and the measurements reversed. “We decided to do FMT every month, and we treated the patient for 6 months,” Schnabl said, noting that ABS had rendered the patient dysfunctional and unable to work. “He has been out of treatment for over a year now and is not flaring any longer.”

Schnabl and Elizabeth Hohmann, MD, at Massachusetts General Hospital, Boston, are currently recruiting patients with confirmed ABS for a National Institutes of Health–funded phase 1 safety and tolerability study of FMT for ABS.

Schnabl disclosed serving as an external scientific advisor/consultant to Ambys Medicines, Boehringer Ingelheim, Gelesis, Mabwell Therapeutics, Surrozen, and Takeda; and as the founder/BOD/BEO of Nterica Bio.

A version of this article appeared on Medscape.com.

WASHINGTON — When a published case of auto-brewery syndrome (ABS) in China — caused by Klebsiella pneumoniae — received widespread publicity in 2019, patients reacted, sending emails to lead author Jing Yuan, in Beijing, China. Many of these inquiries were from patients in the United States who believed they might have ABS.

“Can you check to see if I have ABS?” patients asked Yuan.

For help, Yuan contacted Bernd Schnabl, MD, AGAF, at the University of California, San Diego, whose research was addressing alcohol-associated liver disease and who was also interested in the gut-liver axis and the role of gut microbiome–derived ethanol in metabolic dysfunction–associated steatotic liver disease (MASLD).

“She asked me, ‘Are you interested in looking into ABS?” Schnabl recalled at the Gut Microbiota for Health (GMFH) World Summit 2025. He dug in and formed what may be the largest research cohort thus far of patients with ABS — a group of 22 patients with their diagnosis confirmed through observed glucose challenge.

His soon-to-be-published research on this cohort has confirmed excess ethanol production — and elevations of both proteobacteria and fermentation pathways — in patients whose ABS symptoms had flared.

ABS is considered a rare condition, but “I’d argue that it’s rarely diagnosed because many physicians don’t know of the diagnosis, and many are actually very skeptical about the disease,” Schnabl said at the meeting, convened by AGA and the European Society of Neurogastroenterology and Motility.

Patients experience symptoms of intoxication when ethanol produced by dysregulated gut microbiota exceeds the capacity of the liver to metabolize it and accumulates in the blood, he explained.

“Patients constantly talk about brain fog; they can’t concentrate, and it can be very severe,” he said. “They don’t get a firm diagnosis and go from one medical center to another, and they also suffer from complications of alcohol use disorder including serious family, social, and legal problems.”

 

Advancing Knowledge, Findings From the Cohort

The phenomenon of ethanol production by gut microbiota has been known for over a century, Schnabl wrote with two co-authors in a 2024 review in Nature Reviews Gastroenterology & Hepatology of “endogenous ethanol production in health and disease.”

And in recent decades, he said at the meeting, research has linked endogenous ethanol production to MASLD, positioning it as a potential contributor to disease pathogenesis. In one of the most recently published studies, patients with MASLD had higher concentrations of ethanol in their systemic circulation after a mixed meal test than did healthy controls — and even higher ethanol concentrations in their portal vein blood, “suggesting that this ethanol is coming from the gut microbiome,” Schnabl said.

The paper from China that led Schnabl to establish his cohort was spurred on by a patient with both ABS and MASLD cirrhosis. The patient was found to have strains of high alcohol–producing K pneumoniae in the gut microbiome. When the researchers transplanted these strains into mice via fecal microbiota transplantation (FMT), the mice developed MASLD.

Schnabl’s study focused just on ABS, which is alternatively sometimes called gut fermentation syndrome. The 22 patients in his ABS cohort — each of whom provided stool samples corresponding to remission or flare of ABS symptoms — had a median age of 45 years and were predominantly men, slightly overweight and not obese, and without liver disease. (About 48 patients with suspected ABS were screened, and 20 were excluded after an observed glucose challenge failed to establish a diagnosis; 6 withdrew from the study.)

During remission (no symptoms), patients’ mean blood alcohol content (BAC) level was zero, but during a flare, the mean BAC level was 136 mg/dL. “To put it into perspective, the legal limit for driving in the US is 80 mg/dL,” Schnabl said. Within a mean of 4 hours after the oral glucose load used for diagnosis, patients’ mean BAC level was 73 mg/dL, he noted.

To assess ethanol production by the patients’ microbiota, Schnabl and his team cultured the stool samples — anaerobically adding glucose and measuring ethanol production — and compared the results with findings from stool samples collected from household partners who generally were of the opposite sex. Among their findings: cultures of stool from patients experiencing a flare produced significantly more ethanol than stool from household partners and samples from patients in remission.

To assess whether ethanol was produced by bacteria or fungi, the researchers measured ethanol production in cultures treated with either the antifungal amphotericin B or the antibiotic chloramphenicol. “Chloramphenicol clearly decreased the ethanol production,” Schnabl said. “So at least in this culture test, bacteria produced most of the alcohol in our patients.”

Taxonomic profiling, moreover, revealed “significantly elevated levels” of proteobacteria — with relative abundance of Escherichia coli and K pneumoniae — in patients who were flaring, he said. And functional profiling of the fecal microbiota showed much higher activity of fermentation pathways during patients’ flares than in household partners or healthy controls. (Healthy controls were incorporated into the taxonomic and functional profiling parts of the research.)

 

A Clinical Approach to ABS

Schnabl said at the meeting that stool cultures of both household partners and patients in long-term remission “all produced some low amount of ethanol, which was initially puzzling to us” but became less surprising as he and his colleagues reviewed more of the literature.

Asked during a discussion period whether ABS could explain chronic fatigue, a commonly reported chronic symptom in populations, Schnabl said it’s possible. And in an interview after the meeting, he elaborated. “The literature clearly says ABS is a rare disease, but I argue that more patients may have ABS; they just don’t know it. And I suspect some may have mild symptoms, like brain fog, feeling tired,” he said. “But at this point, this is complete speculation.”

Physicians should “be aware that if a patient has unexplained symptoms that could be aligned with ABS, checking the blood alcohol level” may be warranted, he said in the interview. A PEth (phosphatidylethanol) test — a biomarker test used to check for longer-term alcohol consumption — is an option, but it is important to appreciate it will not discriminate between exogenous alcohol drinking and endogenous ethanol production.

There are no standardized diagnostic tests for ABS, but at the meeting, Schnabl outlined a clinical approach, starting with a standardized oral glucose tolerance challenge test to detect elevated ethanol concentrations.

A fecal yeast test is warranted for diagnosed patients on the basis of some case reports in which ABS symptoms have improved with antifungal treatments. When the fecal yeast test is negative, “ideally you want to identify the ethanol-producing intestinal bacteria in the patient,” he said, using cultures and fecal metagenomics sequencing.

Treatment could then be tailored to the identified microbial strain, with options being selective antibiotics, probiotics and/or prebiotics, and — likely in the future — phages or FMT, he said. (These options, all aimed at restoring gut homeostasis, are also discussed in his 2024 review.)

Schnabl and his team recently performed FMT in a patient with ABS in whom E coli was determined to be producing excessive ethanol. The FMT, performed after antibiotic pretreatment, resulted in decreases in the relative abundance of proteobacteria and E coli levels, lower blood alcohol levels and fermentation enrichment pathways, and normalized liver enzymes.

After 6 months, however, the patient relapsed, and the measurements reversed. “We decided to do FMT every month, and we treated the patient for 6 months,” Schnabl said, noting that ABS had rendered the patient dysfunctional and unable to work. “He has been out of treatment for over a year now and is not flaring any longer.”

Schnabl and Elizabeth Hohmann, MD, at Massachusetts General Hospital, Boston, are currently recruiting patients with confirmed ABS for a National Institutes of Health–funded phase 1 safety and tolerability study of FMT for ABS.

Schnabl disclosed serving as an external scientific advisor/consultant to Ambys Medicines, Boehringer Ingelheim, Gelesis, Mabwell Therapeutics, Surrozen, and Takeda; and as the founder/BOD/BEO of Nterica Bio.

A version of this article appeared on Medscape.com.

Short-term adherence to a palatable elemental diet (PED) significantly improved symptoms and the gut microbiota in adults with microbiome-driven gastrointestinal disorders, according to a new study.

“Elemental diets have long shown promise for treating gastrointestinal disorders like Crohn’s disease, eosinophilic esophagitis, SIBO (small intestinal bacterial overgrowth), and IMO (intestinal methanogen overgrowth), but poor palatability has limited their use,” lead author Ali Rezaie, MD, medical director of the Gastrointestinal (GI) Motility Program and director of Bioinformatics at Cedars-Sinai Medical Center, Los Angeles, told GI & Hepatology News.

Elemental diets are specialized formulas tailored to meet an individual’s specific nutritional needs and daily requirements for vitamins, minerals, fat, free amino acids, and carbohydrates.

In SIBO and IMO specifically, only about half the patients respond to antibiotics, and many require repeat treatments, which underscores the need for effective nonantibiotic alternatives, said Rezaie. “This is the first prospective trial using a PED, aiming to make this approach both viable and accessible for patients,” he noted.

 

Assessing a Novel Diet in IMO and SIBO

In the study, which was recently published in Clinical Gastroenterology and Hepatology, Rezaie and colleagues enrolled 30 adults with IMO (40%), SIBO (20%), or both (40%). The mean participant age was 45 years, and 63% were women.

All participants completed 2 weeks of a PED, transitioned to 2-3 days of a bland diet, and then resumed their regular diets for 2 weeks.

The diet consisted of multiple 300-calorie packets, adjusted for individual caloric needs. Participants could consume additional packets for hunger but were prohibited from eating other foods. There was no restriction on water intake.

The primary endpoint was changes in stool microbiome after the PED and reintroduction of regular food. Secondary endpoints included lactose breath test normalization to determine bacterial overgrowth in the gut, symptom response, and adverse events.

Researchers collected 29 stool samples at baseline, 27 post-PED, and 27 at study conclusion (2 weeks post-diet).

 

Key Outcomes

Although the stool samples’ alpha diversity decreased after the PED, the difference was not statistically significant at the end of the study. However, 30 bacterial families showed significant differences in relative abundance post-PED.

Daily symptom severity improved significantly during the second week of the diet compared with baseline, with reduction in abdominal discomfort, bloating, distention, constipation, and flatulence. Further significant improvements in measures such as abdominal pain, diarrhea, fatigue, urgency, and brain fog were observed after reintroducing regular food.

“We observed 73% breath test normalization and 83% global symptom relief — with 100% adherence and tolerance to 2 weeks of exclusive PED,” Rezaie told GI & Hepatology News. No serious adverse events occurred during the study, he added.

Lactose breath test normalization rates post-PED were 58% in patients with IMO, 100% in patients with SIBO, and 75% in those with both conditions.

The extent of patient response to PED was notable, given that 83% had failed prior treatments, Rezaie said.

“While we expected benefit based on palatability improvements and prior retrospective data, the rapid reduction in methane and hydrogen gas — and the sustained microbiome modulation even after reintroducing a regular diet — exceeded expectations,” he said. A significant reduction in visceral fat was another novel finding.

“This study reinforces the power of diet as a therapeutic tool,” Rezaie said, adding that the results show that elemental diets can be palatable, thereby improving patient adherence, tolerance, and, eventually, effectiveness. This is particularly valuable for patients with SIBO and IMO who do not tolerate or respond to antibiotics, prefer nonpharmacologic options, or experience recurrent symptoms after antibiotic treatment.

 

Limitations and Next Steps

Study limitations included the lack of a placebo group with a sham diet, the short follow-up after reintroducing a regular diet, and the inability to assess microbial gene function.

However, the results support the safety, tolerance, and benefit of a PED in patients with IMO/SIBO. Personalized dietary interventions that support the growth of beneficial bacteria may be an effective approach to treating these disorders, Rezaie and colleagues noted in their publication.

Although the current study is a promising first step, longer-term studies are needed to evaluate the durability of microbiome and symptom improvements, Rezaie said.

 

Making the Most of Microbiome Manipulation

Elemental diets may help modulate the gut microbiome while reducing immune activation, making them attractive for microbiome-targeted gastrointestinal therapies, Jatin Roper, MD, a gastroenterologist at Duke University, Durham, North Carolina, told GI & Hepatology News.

“Antibiotics are only effective in half of SIBO cases and often require retreatment, so better therapies are needed,” said Roper, who was not affiliated with the study. He added that its findings confirmed the researchers’ hypothesis that a PED can be both safe and effective in patients with SIBO.

Roper noted the 83% symptom improvement as the study’s most unexpected and encouraging finding, as it represents a substantial improvement compared with standard antibiotic therapy. “It is also surprising that the tolerance rate of the elemental diet in this study was 100%,” he said.

However, diet palatability remains a major barrier in real-world practice.

“Adherence rates are likely to be far lower than in trials in which patients are closely monitored, and this challenge will not be easily overcome,” he added.

The study’s limitations, including the lack of metagenomic analysis and a placebo group, are important to address in future research, Roper said. In particular, controlled trials of elemental diets are needed to determine whether microbiome changes are directly responsible for symptom improvement.

The study was supported in part by Good LFE and the John and Geraldine Cusenza Foundation. Rezaie disclosed serving as a consultant/speaker for Bausch Health and having equity in Dieta Health, Gemelli Biotech, and Good LFE. Roper had no financial conflicts to disclose.

A version of this article first appeared on Medscape.com.

Short-term adherence to a palatable elemental diet (PED) significantly improved symptoms and the gut microbiota in adults with microbiome-driven gastrointestinal disorders, according to a new study.

“Elemental diets have long shown promise for treating gastrointestinal disorders like Crohn’s disease, eosinophilic esophagitis, SIBO (small intestinal bacterial overgrowth), and IMO (intestinal methanogen overgrowth), but poor palatability has limited their use,” lead author Ali Rezaie, MD, medical director of the Gastrointestinal (GI) Motility Program and director of Bioinformatics at Cedars-Sinai Medical Center, Los Angeles, told GI & Hepatology News.

Elemental diets are specialized formulas tailored to meet an individual’s specific nutritional needs and daily requirements for vitamins, minerals, fat, free amino acids, and carbohydrates.

In SIBO and IMO specifically, only about half the patients respond to antibiotics, and many require repeat treatments, which underscores the need for effective nonantibiotic alternatives, said Rezaie. “This is the first prospective trial using a PED, aiming to make this approach both viable and accessible for patients,” he noted.

 

Assessing a Novel Diet in IMO and SIBO

In the study, which was recently published in Clinical Gastroenterology and Hepatology, Rezaie and colleagues enrolled 30 adults with IMO (40%), SIBO (20%), or both (40%). The mean participant age was 45 years, and 63% were women.

All participants completed 2 weeks of a PED, transitioned to 2-3 days of a bland diet, and then resumed their regular diets for 2 weeks.

The diet consisted of multiple 300-calorie packets, adjusted for individual caloric needs. Participants could consume additional packets for hunger but were prohibited from eating other foods. There was no restriction on water intake.

The primary endpoint was changes in stool microbiome after the PED and reintroduction of regular food. Secondary endpoints included lactose breath test normalization to determine bacterial overgrowth in the gut, symptom response, and adverse events.

Researchers collected 29 stool samples at baseline, 27 post-PED, and 27 at study conclusion (2 weeks post-diet).

 

Key Outcomes

Although the stool samples’ alpha diversity decreased after the PED, the difference was not statistically significant at the end of the study. However, 30 bacterial families showed significant differences in relative abundance post-PED.

Daily symptom severity improved significantly during the second week of the diet compared with baseline, with reduction in abdominal discomfort, bloating, distention, constipation, and flatulence. Further significant improvements in measures such as abdominal pain, diarrhea, fatigue, urgency, and brain fog were observed after reintroducing regular food.

“We observed 73% breath test normalization and 83% global symptom relief — with 100% adherence and tolerance to 2 weeks of exclusive PED,” Rezaie told GI & Hepatology News. No serious adverse events occurred during the study, he added.

Lactose breath test normalization rates post-PED were 58% in patients with IMO, 100% in patients with SIBO, and 75% in those with both conditions.

The extent of patient response to PED was notable, given that 83% had failed prior treatments, Rezaie said.

“While we expected benefit based on palatability improvements and prior retrospective data, the rapid reduction in methane and hydrogen gas — and the sustained microbiome modulation even after reintroducing a regular diet — exceeded expectations,” he said. A significant reduction in visceral fat was another novel finding.

“This study reinforces the power of diet as a therapeutic tool,” Rezaie said, adding that the results show that elemental diets can be palatable, thereby improving patient adherence, tolerance, and, eventually, effectiveness. This is particularly valuable for patients with SIBO and IMO who do not tolerate or respond to antibiotics, prefer nonpharmacologic options, or experience recurrent symptoms after antibiotic treatment.

 

Limitations and Next Steps

Study limitations included the lack of a placebo group with a sham diet, the short follow-up after reintroducing a regular diet, and the inability to assess microbial gene function.

However, the results support the safety, tolerance, and benefit of a PED in patients with IMO/SIBO. Personalized dietary interventions that support the growth of beneficial bacteria may be an effective approach to treating these disorders, Rezaie and colleagues noted in their publication.

Although the current study is a promising first step, longer-term studies are needed to evaluate the durability of microbiome and symptom improvements, Rezaie said.

 

Making the Most of Microbiome Manipulation

Elemental diets may help modulate the gut microbiome while reducing immune activation, making them attractive for microbiome-targeted gastrointestinal therapies, Jatin Roper, MD, a gastroenterologist at Duke University, Durham, North Carolina, told GI & Hepatology News.

“Antibiotics are only effective in half of SIBO cases and often require retreatment, so better therapies are needed,” said Roper, who was not affiliated with the study. He added that its findings confirmed the researchers’ hypothesis that a PED can be both safe and effective in patients with SIBO.

Roper noted the 83% symptom improvement as the study’s most unexpected and encouraging finding, as it represents a substantial improvement compared with standard antibiotic therapy. “It is also surprising that the tolerance rate of the elemental diet in this study was 100%,” he said.

However, diet palatability remains a major barrier in real-world practice.

“Adherence rates are likely to be far lower than in trials in which patients are closely monitored, and this challenge will not be easily overcome,” he added.

The study’s limitations, including the lack of metagenomic analysis and a placebo group, are important to address in future research, Roper said. In particular, controlled trials of elemental diets are needed to determine whether microbiome changes are directly responsible for symptom improvement.

The study was supported in part by Good LFE and the John and Geraldine Cusenza Foundation. Rezaie disclosed serving as a consultant/speaker for Bausch Health and having equity in Dieta Health, Gemelli Biotech, and Good LFE. Roper had no financial conflicts to disclose.

A version of this article first appeared on Medscape.com.

Short-term adherence to a palatable elemental diet (PED) significantly improved symptoms and the gut microbiota in adults with microbiome-driven gastrointestinal disorders, according to a new study.

“Elemental diets have long shown promise for treating gastrointestinal disorders like Crohn’s disease, eosinophilic esophagitis, SIBO (small intestinal bacterial overgrowth), and IMO (intestinal methanogen overgrowth), but poor palatability has limited their use,” lead author Ali Rezaie, MD, medical director of the Gastrointestinal (GI) Motility Program and director of Bioinformatics at Cedars-Sinai Medical Center, Los Angeles, told GI & Hepatology News.

Elemental diets are specialized formulas tailored to meet an individual’s specific nutritional needs and daily requirements for vitamins, minerals, fat, free amino acids, and carbohydrates.

In SIBO and IMO specifically, only about half the patients respond to antibiotics, and many require repeat treatments, which underscores the need for effective nonantibiotic alternatives, said Rezaie. “This is the first prospective trial using a PED, aiming to make this approach both viable and accessible for patients,” he noted.

 

Assessing a Novel Diet in IMO and SIBO

In the study, which was recently published in Clinical Gastroenterology and Hepatology, Rezaie and colleagues enrolled 30 adults with IMO (40%), SIBO (20%), or both (40%). The mean participant age was 45 years, and 63% were women.

All participants completed 2 weeks of a PED, transitioned to 2-3 days of a bland diet, and then resumed their regular diets for 2 weeks.

The diet consisted of multiple 300-calorie packets, adjusted for individual caloric needs. Participants could consume additional packets for hunger but were prohibited from eating other foods. There was no restriction on water intake.

The primary endpoint was changes in stool microbiome after the PED and reintroduction of regular food. Secondary endpoints included lactose breath test normalization to determine bacterial overgrowth in the gut, symptom response, and adverse events.

Researchers collected 29 stool samples at baseline, 27 post-PED, and 27 at study conclusion (2 weeks post-diet).

 

Key Outcomes

Although the stool samples’ alpha diversity decreased after the PED, the difference was not statistically significant at the end of the study. However, 30 bacterial families showed significant differences in relative abundance post-PED.

Daily symptom severity improved significantly during the second week of the diet compared with baseline, with reduction in abdominal discomfort, bloating, distention, constipation, and flatulence. Further significant improvements in measures such as abdominal pain, diarrhea, fatigue, urgency, and brain fog were observed after reintroducing regular food.

“We observed 73% breath test normalization and 83% global symptom relief — with 100% adherence and tolerance to 2 weeks of exclusive PED,” Rezaie told GI & Hepatology News. No serious adverse events occurred during the study, he added.

Lactose breath test normalization rates post-PED were 58% in patients with IMO, 100% in patients with SIBO, and 75% in those with both conditions.

The extent of patient response to PED was notable, given that 83% had failed prior treatments, Rezaie said.

“While we expected benefit based on palatability improvements and prior retrospective data, the rapid reduction in methane and hydrogen gas — and the sustained microbiome modulation even after reintroducing a regular diet — exceeded expectations,” he said. A significant reduction in visceral fat was another novel finding.

“This study reinforces the power of diet as a therapeutic tool,” Rezaie said, adding that the results show that elemental diets can be palatable, thereby improving patient adherence, tolerance, and, eventually, effectiveness. This is particularly valuable for patients with SIBO and IMO who do not tolerate or respond to antibiotics, prefer nonpharmacologic options, or experience recurrent symptoms after antibiotic treatment.

 

Limitations and Next Steps

Study limitations included the lack of a placebo group with a sham diet, the short follow-up after reintroducing a regular diet, and the inability to assess microbial gene function.

However, the results support the safety, tolerance, and benefit of a PED in patients with IMO/SIBO. Personalized dietary interventions that support the growth of beneficial bacteria may be an effective approach to treating these disorders, Rezaie and colleagues noted in their publication.

Although the current study is a promising first step, longer-term studies are needed to evaluate the durability of microbiome and symptom improvements, Rezaie said.

 

Making the Most of Microbiome Manipulation

Elemental diets may help modulate the gut microbiome while reducing immune activation, making them attractive for microbiome-targeted gastrointestinal therapies, Jatin Roper, MD, a gastroenterologist at Duke University, Durham, North Carolina, told GI & Hepatology News.

“Antibiotics are only effective in half of SIBO cases and often require retreatment, so better therapies are needed,” said Roper, who was not affiliated with the study. He added that its findings confirmed the researchers’ hypothesis that a PED can be both safe and effective in patients with SIBO.

Roper noted the 83% symptom improvement as the study’s most unexpected and encouraging finding, as it represents a substantial improvement compared with standard antibiotic therapy. “It is also surprising that the tolerance rate of the elemental diet in this study was 100%,” he said.

However, diet palatability remains a major barrier in real-world practice.

“Adherence rates are likely to be far lower than in trials in which patients are closely monitored, and this challenge will not be easily overcome,” he added.

The study’s limitations, including the lack of metagenomic analysis and a placebo group, are important to address in future research, Roper said. In particular, controlled trials of elemental diets are needed to determine whether microbiome changes are directly responsible for symptom improvement.

The study was supported in part by Good LFE and the John and Geraldine Cusenza Foundation. Rezaie disclosed serving as a consultant/speaker for Bausch Health and having equity in Dieta Health, Gemelli Biotech, and Good LFE. Roper had no financial conflicts to disclose.

A version of this article first appeared on Medscape.com.

WASHINGTON, DC — Research on the gut microbiome — and clinical attention to it — has focused mainly on bacteria, but bacteriophages and fungi play critical roles as well, with significant influences on health and disease, experts said at the Gut Microbiota for Health (GMFH) World Summit 2025.

Fungi account for < 1% of the total genetic material in the microbiome but 1%-2% of its total biomass. “Despite their relative rarity, they have an important and outsized influence on gut health” — an impact that results from their unique interface with the immune system, said Kyla Ost, PhD, of the Anschutz Medical Campus, University of Colorado, in Denver, whose research focuses on this interface.

And bacteriophages — viruses that infect and kill bacteria — are highly abundant in the gut. “Bacteriophages begin to colonize our GI [gastrointestinal] tract at the same time we develop our own microbiome shortly after birth, and from that time on, they interact with the bacteria in our GI tract, shaping [and being shaped by] the bacterial species we carry with us,” said Robert (Chip) Schooley, MD, distinguished professor of medicine at the University of California San Diego School of Medicine.

“We’ve been talking about things that affect the gut microbiome — diet, genetics, immune response — but probably the biggest influence on what grows in the GI tract are bacteriophages,” said Schooley, co-director of the Center for Innovative Phage Applications and Therapeutics, in a session on the extra-bacterial gut ecosystem.

Among the current questions: How can phages be used to manipulate the gut microbiome and influence GI-related diseases? And how can the pathogenic potential of commensal fungi be limited?

 

‘New life’ for Phage Therapy

Bacteriophages represent a promising approach for the treatment of multidrug resistant bacterial pathogens in an era of increasing resistance and a dried-up antibiotic discovery pipeline, Schooley said. (In 2019, an estimated 4.95 million deaths around the world were associated with bacterial antimicrobial resistance, and by 2050, it has been forecast that this number will rise to an estimated 8.22 million deaths.)

But in addition to suppressing bacterial pathogens causing direct morbidity, phage therapy has the potential to suppress bacteria believed to contribute to chronic diseases, he said. “We have proof-of-concept studies about the ability of phage to modulate bacteria in the digestive tract,” and an increasing number of clinical trials of the use of phages in GI and other diseases are underway, he said.

Phages were discovered just over a century ago, but phage therapy was widely abandoned once antibiotics were developed, except for in Russia and the former Eastern Bloc countries, where phage therapy continued to be used.

Phage therapy “got new life” in the West, Schooley said, about 10-15 years ago with an increasing number of detailed and high-profile case reports, including one in which a UC San Diego colleague, Tom Patterson, PhD, contracted a deadly multidrug resistant bacterial infection in Egypt and was eventually saved with bacteriophage therapy. (The case was the subject of the book The Perfect Predator).

Since then, as described in case reports and studies in the literature, “hundreds of people have been treated with bacteriophages here and in Europe,” most commonly for pulmonary infections and infections in implanted vascular and orthopedic devices, said Schooley, who coauthored a review in Cell in 2023 that describes phage biology and advances and future directions in phage therapy.

The use of bacteriophages to prevent systemic infections during high-risk periods — such as during chemotherapeutic regimens for hematological regimens — is an area of interest, he said at the meeting.

In research that is making its way to a clinical trial of patients undergoing allogeneic hematopoietic stem cell transplant (HSCT), researchers screened a library of phages to identify those with broad coverage of Escherichia coli. Using tail fiber engineering and CRISPR technology, they then engineered a combination of the four most complementary bacteriophages to selectively kill E coli — including fluoroquinolone-resistant strains that, in patients whose GI tracts are colonized with these strains, can translocate from the gut into the bloodstream, causing sepsis, during chemotherapeutic regimens for HSCT.

In a mouse model, the CRISPR-enhanced four-phage cocktail (SNIPR001) led to a steady reduction in the E coli colony counts in stool, “showing you can modulate these bacteria in the gut by using bacteriophages to kill them,” Schooley said. Moreover, the CRISPR enhancement strengthened the phages’ ability to break up biofilms, he said, showing “that you can engineer bacteriophages to make them better killers.” A phase 1b/2a study is being planned.

 

Other Niches for Therapeutic Phages, Challenges

Bacteriophages also could be used to target a gut bacterium that has been shown to attenuate alcoholic liver disease. Patients with alcoholic hepatitis “have a gut microbiome that is different in distribution,” Schooley said, often with increased numbers of Enterococcus faecalis that produce cytolysin, an exotoxin that exacerbates liver injury and is associated with increased mortality.

In published research led by investigators at UC San Diego, stool from cytolysin-positive patients with alcoholic hepatitis was found to exacerbate ethanol-induced liver disease in gnotobiotic mice, and phage therapy against cytolytic E faecalis was found to abolish it, Schooley shared.

Research is also exploring the potential of phage therapy to selectively target adherent invasive E coli in Crohn’s disease, and Klebsiella pneumoniae in the gut microbiome as an exacerbator of inflammatory bowel disease (IBD), he said.

And investigators in Japan, he noted, have reported that bacteriophage therapy against K pneumoniae can ameliorate liver inflammation and disease severity in primary sclerosing cholangitis.

Challenges in the therapeutic use of phages include the narrow host range of phages and an uncertain predictive value of in vitro phage susceptibility testing. “We don’t know yet how to do resistance testing as well as we do with antibiotics,” he said.

In addition, most phages tend to be acid labile, requiring strategies to mitigate inactivation by gastric acid, and there are “major knowledge gaps” relating to phage pharmacology. “We also know that adaptive immune responses to phages can but often doesn’t impact therapy, and we want to understand that better in clinical trials,” Schooley said.

Phages that have a “lysogenic” lifestyle — as opposed to lytic phages which are used therapeutically — can contribute to antibiotic resistance by facilitating the interchange of bacterial resistance genes, he noted.

 

A Window Into the Mycobiome

The human gut mycobiome is primarily composed of fungi in the Saccharomyces, Candida, and Malassezia genera, with Candida species dominating. Fungal cells harbor distinct immune-stimulatory molecules and activate distinct immune pathways compared with bacteria and other members of the microbiome, said Ost, assistant professor in the immunology and microbiology department of CU Anschutz.

Some fungi, including those in the Candida genus, activate adaptive and innate immune responses that promote metabolic health and protect against infection. A recently published study in Science, for instance, demonstrated that colonization with C dubliniensis in very young mice who had been exposed to broad-spectrum antibiotics promoted “the expansion and development of beta cells in the pancreas” in a macrophage dependent manner, improving metabolic health and reducing diabetes incidence, she shared.

On the one hand, fungi can “exacerbate and perpetuate the pathogenic inflammation that’s found in a growing list of inflammatory diseases” such as IBD. And “in fact, a lot of the benefits and detriments are driven by the exact same species of fungi,” said Ost. “This is particularly true of Candida,” which is a “lifelong colonizer of intestinal microbiota that rarely causes disease but can be quite pathogenic when it does.”

A 2023 review in Nature Reviews Gastroenterology & Hepatology coauthored by Ost describes the role of commensal fungi in intestinal diseases, including IBD, colorectal cancer, and pancreatic cancer.

The pathogenic potential of commensal fungi is largely dependent on its strain, its morphology and its expression of virulence factors, researchers are learning. Ost has studied C albicans, which has been associated with intestinal inflammation and IBD. Like some other Candida species, C albicans are “fascinating shape shifters,” she said, transitioning between a less pathogenic “yeast” morphology and an elongated, adhesive “hyphae” shape that is more pathogenic.

It turns out, according to research by Ost and others, that the C albicans hyphal morphotype — and the adhesins (sticky proteins that facilitate adherence to epithelial cells) and a cytolytic toxin it produces — are preferentially targeted and suppressed by immunoglobulin A (IgA) in the gut.

“Our gut is protected by a large quantity of IgA antibodies…and these IgA interact with the microbiota and play a big role in what microbes are there and the biology of the microbes,” Ost said. Indeed, symptomatic IgA deficiency in humans has been shown to be associated with C albicans overgrowth.

Leveraging the hyphal-specific IgA response to protect against disease seems possible, she said, referring to an experimental anti-Candida fungal vaccine (NDV-3A) designed to induce an adhesin-specific immune response. In a mouse model of colitis, the vaccine protected against C albicans-associated damage. “We saw an immediate IgA response that targeted C albicans in the intestinal contents,” Ost said.

C glabrata, which has also been associated with intestinal inflammation and IBD, does not form hyphae but — depending on the strain — may also induce intestinal IgA responses, she said in describing her recent research.

Ost reported having no disclosures. Schooley disclosed being a consultant for SNIPR Biome, BiomX, Locus, MicrobiotiX, Amazon Data Monitoring Committee: Merck.

A version of this article appeared on Medscape.com.

WASHINGTON, DC — Research on the gut microbiome — and clinical attention to it — has focused mainly on bacteria, but bacteriophages and fungi play critical roles as well, with significant influences on health and disease, experts said at the Gut Microbiota for Health (GMFH) World Summit 2025.

Fungi account for < 1% of the total genetic material in the microbiome but 1%-2% of its total biomass. “Despite their relative rarity, they have an important and outsized influence on gut health” — an impact that results from their unique interface with the immune system, said Kyla Ost, PhD, of the Anschutz Medical Campus, University of Colorado, in Denver, whose research focuses on this interface.

And bacteriophages — viruses that infect and kill bacteria — are highly abundant in the gut. “Bacteriophages begin to colonize our GI [gastrointestinal] tract at the same time we develop our own microbiome shortly after birth, and from that time on, they interact with the bacteria in our GI tract, shaping [and being shaped by] the bacterial species we carry with us,” said Robert (Chip) Schooley, MD, distinguished professor of medicine at the University of California San Diego School of Medicine.

“We’ve been talking about things that affect the gut microbiome — diet, genetics, immune response — but probably the biggest influence on what grows in the GI tract are bacteriophages,” said Schooley, co-director of the Center for Innovative Phage Applications and Therapeutics, in a session on the extra-bacterial gut ecosystem.

Among the current questions: How can phages be used to manipulate the gut microbiome and influence GI-related diseases? And how can the pathogenic potential of commensal fungi be limited?

 

‘New life’ for Phage Therapy

Bacteriophages represent a promising approach for the treatment of multidrug resistant bacterial pathogens in an era of increasing resistance and a dried-up antibiotic discovery pipeline, Schooley said. (In 2019, an estimated 4.95 million deaths around the world were associated with bacterial antimicrobial resistance, and by 2050, it has been forecast that this number will rise to an estimated 8.22 million deaths.)

But in addition to suppressing bacterial pathogens causing direct morbidity, phage therapy has the potential to suppress bacteria believed to contribute to chronic diseases, he said. “We have proof-of-concept studies about the ability of phage to modulate bacteria in the digestive tract,” and an increasing number of clinical trials of the use of phages in GI and other diseases are underway, he said.

Phages were discovered just over a century ago, but phage therapy was widely abandoned once antibiotics were developed, except for in Russia and the former Eastern Bloc countries, where phage therapy continued to be used.

Phage therapy “got new life” in the West, Schooley said, about 10-15 years ago with an increasing number of detailed and high-profile case reports, including one in which a UC San Diego colleague, Tom Patterson, PhD, contracted a deadly multidrug resistant bacterial infection in Egypt and was eventually saved with bacteriophage therapy. (The case was the subject of the book The Perfect Predator).

Since then, as described in case reports and studies in the literature, “hundreds of people have been treated with bacteriophages here and in Europe,” most commonly for pulmonary infections and infections in implanted vascular and orthopedic devices, said Schooley, who coauthored a review in Cell in 2023 that describes phage biology and advances and future directions in phage therapy.

The use of bacteriophages to prevent systemic infections during high-risk periods — such as during chemotherapeutic regimens for hematological regimens — is an area of interest, he said at the meeting.

In research that is making its way to a clinical trial of patients undergoing allogeneic hematopoietic stem cell transplant (HSCT), researchers screened a library of phages to identify those with broad coverage of Escherichia coli. Using tail fiber engineering and CRISPR technology, they then engineered a combination of the four most complementary bacteriophages to selectively kill E coli — including fluoroquinolone-resistant strains that, in patients whose GI tracts are colonized with these strains, can translocate from the gut into the bloodstream, causing sepsis, during chemotherapeutic regimens for HSCT.

In a mouse model, the CRISPR-enhanced four-phage cocktail (SNIPR001) led to a steady reduction in the E coli colony counts in stool, “showing you can modulate these bacteria in the gut by using bacteriophages to kill them,” Schooley said. Moreover, the CRISPR enhancement strengthened the phages’ ability to break up biofilms, he said, showing “that you can engineer bacteriophages to make them better killers.” A phase 1b/2a study is being planned.

 

Other Niches for Therapeutic Phages, Challenges

Bacteriophages also could be used to target a gut bacterium that has been shown to attenuate alcoholic liver disease. Patients with alcoholic hepatitis “have a gut microbiome that is different in distribution,” Schooley said, often with increased numbers of Enterococcus faecalis that produce cytolysin, an exotoxin that exacerbates liver injury and is associated with increased mortality.

In published research led by investigators at UC San Diego, stool from cytolysin-positive patients with alcoholic hepatitis was found to exacerbate ethanol-induced liver disease in gnotobiotic mice, and phage therapy against cytolytic E faecalis was found to abolish it, Schooley shared.

Research is also exploring the potential of phage therapy to selectively target adherent invasive E coli in Crohn’s disease, and Klebsiella pneumoniae in the gut microbiome as an exacerbator of inflammatory bowel disease (IBD), he said.

And investigators in Japan, he noted, have reported that bacteriophage therapy against K pneumoniae can ameliorate liver inflammation and disease severity in primary sclerosing cholangitis.

Challenges in the therapeutic use of phages include the narrow host range of phages and an uncertain predictive value of in vitro phage susceptibility testing. “We don’t know yet how to do resistance testing as well as we do with antibiotics,” he said.

In addition, most phages tend to be acid labile, requiring strategies to mitigate inactivation by gastric acid, and there are “major knowledge gaps” relating to phage pharmacology. “We also know that adaptive immune responses to phages can but often doesn’t impact therapy, and we want to understand that better in clinical trials,” Schooley said.

Phages that have a “lysogenic” lifestyle — as opposed to lytic phages which are used therapeutically — can contribute to antibiotic resistance by facilitating the interchange of bacterial resistance genes, he noted.

 

A Window Into the Mycobiome

The human gut mycobiome is primarily composed of fungi in the Saccharomyces, Candida, and Malassezia genera, with Candida species dominating. Fungal cells harbor distinct immune-stimulatory molecules and activate distinct immune pathways compared with bacteria and other members of the microbiome, said Ost, assistant professor in the immunology and microbiology department of CU Anschutz.

Some fungi, including those in the Candida genus, activate adaptive and innate immune responses that promote metabolic health and protect against infection. A recently published study in Science, for instance, demonstrated that colonization with C dubliniensis in very young mice who had been exposed to broad-spectrum antibiotics promoted “the expansion and development of beta cells in the pancreas” in a macrophage dependent manner, improving metabolic health and reducing diabetes incidence, she shared.

On the one hand, fungi can “exacerbate and perpetuate the pathogenic inflammation that’s found in a growing list of inflammatory diseases” such as IBD. And “in fact, a lot of the benefits and detriments are driven by the exact same species of fungi,” said Ost. “This is particularly true of Candida,” which is a “lifelong colonizer of intestinal microbiota that rarely causes disease but can be quite pathogenic when it does.”

A 2023 review in Nature Reviews Gastroenterology & Hepatology coauthored by Ost describes the role of commensal fungi in intestinal diseases, including IBD, colorectal cancer, and pancreatic cancer.

The pathogenic potential of commensal fungi is largely dependent on its strain, its morphology and its expression of virulence factors, researchers are learning. Ost has studied C albicans, which has been associated with intestinal inflammation and IBD. Like some other Candida species, C albicans are “fascinating shape shifters,” she said, transitioning between a less pathogenic “yeast” morphology and an elongated, adhesive “hyphae” shape that is more pathogenic.

It turns out, according to research by Ost and others, that the C albicans hyphal morphotype — and the adhesins (sticky proteins that facilitate adherence to epithelial cells) and a cytolytic toxin it produces — are preferentially targeted and suppressed by immunoglobulin A (IgA) in the gut.

“Our gut is protected by a large quantity of IgA antibodies…and these IgA interact with the microbiota and play a big role in what microbes are there and the biology of the microbes,” Ost said. Indeed, symptomatic IgA deficiency in humans has been shown to be associated with C albicans overgrowth.

Leveraging the hyphal-specific IgA response to protect against disease seems possible, she said, referring to an experimental anti-Candida fungal vaccine (NDV-3A) designed to induce an adhesin-specific immune response. In a mouse model of colitis, the vaccine protected against C albicans-associated damage. “We saw an immediate IgA response that targeted C albicans in the intestinal contents,” Ost said.

C glabrata, which has also been associated with intestinal inflammation and IBD, does not form hyphae but — depending on the strain — may also induce intestinal IgA responses, she said in describing her recent research.

Ost reported having no disclosures. Schooley disclosed being a consultant for SNIPR Biome, BiomX, Locus, MicrobiotiX, Amazon Data Monitoring Committee: Merck.

A version of this article appeared on Medscape.com.

WASHINGTON, DC — Research on the gut microbiome — and clinical attention to it — has focused mainly on bacteria, but bacteriophages and fungi play critical roles as well, with significant influences on health and disease, experts said at the Gut Microbiota for Health (GMFH) World Summit 2025.

Fungi account for < 1% of the total genetic material in the microbiome but 1%-2% of its total biomass. “Despite their relative rarity, they have an important and outsized influence on gut health” — an impact that results from their unique interface with the immune system, said Kyla Ost, PhD, of the Anschutz Medical Campus, University of Colorado, in Denver, whose research focuses on this interface.

And bacteriophages — viruses that infect and kill bacteria — are highly abundant in the gut. “Bacteriophages begin to colonize our GI [gastrointestinal] tract at the same time we develop our own microbiome shortly after birth, and from that time on, they interact with the bacteria in our GI tract, shaping [and being shaped by] the bacterial species we carry with us,” said Robert (Chip) Schooley, MD, distinguished professor of medicine at the University of California San Diego School of Medicine.

“We’ve been talking about things that affect the gut microbiome — diet, genetics, immune response — but probably the biggest influence on what grows in the GI tract are bacteriophages,” said Schooley, co-director of the Center for Innovative Phage Applications and Therapeutics, in a session on the extra-bacterial gut ecosystem.

Among the current questions: How can phages be used to manipulate the gut microbiome and influence GI-related diseases? And how can the pathogenic potential of commensal fungi be limited?

 

‘New life’ for Phage Therapy

Bacteriophages represent a promising approach for the treatment of multidrug resistant bacterial pathogens in an era of increasing resistance and a dried-up antibiotic discovery pipeline, Schooley said. (In 2019, an estimated 4.95 million deaths around the world were associated with bacterial antimicrobial resistance, and by 2050, it has been forecast that this number will rise to an estimated 8.22 million deaths.)

But in addition to suppressing bacterial pathogens causing direct morbidity, phage therapy has the potential to suppress bacteria believed to contribute to chronic diseases, he said. “We have proof-of-concept studies about the ability of phage to modulate bacteria in the digestive tract,” and an increasing number of clinical trials of the use of phages in GI and other diseases are underway, he said.

Phages were discovered just over a century ago, but phage therapy was widely abandoned once antibiotics were developed, except for in Russia and the former Eastern Bloc countries, where phage therapy continued to be used.

Phage therapy “got new life” in the West, Schooley said, about 10-15 years ago with an increasing number of detailed and high-profile case reports, including one in which a UC San Diego colleague, Tom Patterson, PhD, contracted a deadly multidrug resistant bacterial infection in Egypt and was eventually saved with bacteriophage therapy. (The case was the subject of the book The Perfect Predator).

Since then, as described in case reports and studies in the literature, “hundreds of people have been treated with bacteriophages here and in Europe,” most commonly for pulmonary infections and infections in implanted vascular and orthopedic devices, said Schooley, who coauthored a review in Cell in 2023 that describes phage biology and advances and future directions in phage therapy.

The use of bacteriophages to prevent systemic infections during high-risk periods — such as during chemotherapeutic regimens for hematological regimens — is an area of interest, he said at the meeting.

In research that is making its way to a clinical trial of patients undergoing allogeneic hematopoietic stem cell transplant (HSCT), researchers screened a library of phages to identify those with broad coverage of Escherichia coli. Using tail fiber engineering and CRISPR technology, they then engineered a combination of the four most complementary bacteriophages to selectively kill E coli — including fluoroquinolone-resistant strains that, in patients whose GI tracts are colonized with these strains, can translocate from the gut into the bloodstream, causing sepsis, during chemotherapeutic regimens for HSCT.

In a mouse model, the CRISPR-enhanced four-phage cocktail (SNIPR001) led to a steady reduction in the E coli colony counts in stool, “showing you can modulate these bacteria in the gut by using bacteriophages to kill them,” Schooley said. Moreover, the CRISPR enhancement strengthened the phages’ ability to break up biofilms, he said, showing “that you can engineer bacteriophages to make them better killers.” A phase 1b/2a study is being planned.

 

Other Niches for Therapeutic Phages, Challenges

Bacteriophages also could be used to target a gut bacterium that has been shown to attenuate alcoholic liver disease. Patients with alcoholic hepatitis “have a gut microbiome that is different in distribution,” Schooley said, often with increased numbers of Enterococcus faecalis that produce cytolysin, an exotoxin that exacerbates liver injury and is associated with increased mortality.

In published research led by investigators at UC San Diego, stool from cytolysin-positive patients with alcoholic hepatitis was found to exacerbate ethanol-induced liver disease in gnotobiotic mice, and phage therapy against cytolytic E faecalis was found to abolish it, Schooley shared.

Research is also exploring the potential of phage therapy to selectively target adherent invasive E coli in Crohn’s disease, and Klebsiella pneumoniae in the gut microbiome as an exacerbator of inflammatory bowel disease (IBD), he said.

And investigators in Japan, he noted, have reported that bacteriophage therapy against K pneumoniae can ameliorate liver inflammation and disease severity in primary sclerosing cholangitis.

Challenges in the therapeutic use of phages include the narrow host range of phages and an uncertain predictive value of in vitro phage susceptibility testing. “We don’t know yet how to do resistance testing as well as we do with antibiotics,” he said.

In addition, most phages tend to be acid labile, requiring strategies to mitigate inactivation by gastric acid, and there are “major knowledge gaps” relating to phage pharmacology. “We also know that adaptive immune responses to phages can but often doesn’t impact therapy, and we want to understand that better in clinical trials,” Schooley said.

Phages that have a “lysogenic” lifestyle — as opposed to lytic phages which are used therapeutically — can contribute to antibiotic resistance by facilitating the interchange of bacterial resistance genes, he noted.

 

A Window Into the Mycobiome

The human gut mycobiome is primarily composed of fungi in the Saccharomyces, Candida, and Malassezia genera, with Candida species dominating. Fungal cells harbor distinct immune-stimulatory molecules and activate distinct immune pathways compared with bacteria and other members of the microbiome, said Ost, assistant professor in the immunology and microbiology department of CU Anschutz.

Some fungi, including those in the Candida genus, activate adaptive and innate immune responses that promote metabolic health and protect against infection. A recently published study in Science, for instance, demonstrated that colonization with C dubliniensis in very young mice who had been exposed to broad-spectrum antibiotics promoted “the expansion and development of beta cells in the pancreas” in a macrophage dependent manner, improving metabolic health and reducing diabetes incidence, she shared.

On the one hand, fungi can “exacerbate and perpetuate the pathogenic inflammation that’s found in a growing list of inflammatory diseases” such as IBD. And “in fact, a lot of the benefits and detriments are driven by the exact same species of fungi,” said Ost. “This is particularly true of Candida,” which is a “lifelong colonizer of intestinal microbiota that rarely causes disease but can be quite pathogenic when it does.”

A 2023 review in Nature Reviews Gastroenterology & Hepatology coauthored by Ost describes the role of commensal fungi in intestinal diseases, including IBD, colorectal cancer, and pancreatic cancer.

The pathogenic potential of commensal fungi is largely dependent on its strain, its morphology and its expression of virulence factors, researchers are learning. Ost has studied C albicans, which has been associated with intestinal inflammation and IBD. Like some other Candida species, C albicans are “fascinating shape shifters,” she said, transitioning between a less pathogenic “yeast” morphology and an elongated, adhesive “hyphae” shape that is more pathogenic.

It turns out, according to research by Ost and others, that the C albicans hyphal morphotype — and the adhesins (sticky proteins that facilitate adherence to epithelial cells) and a cytolytic toxin it produces — are preferentially targeted and suppressed by immunoglobulin A (IgA) in the gut.

“Our gut is protected by a large quantity of IgA antibodies…and these IgA interact with the microbiota and play a big role in what microbes are there and the biology of the microbes,” Ost said. Indeed, symptomatic IgA deficiency in humans has been shown to be associated with C albicans overgrowth.

Leveraging the hyphal-specific IgA response to protect against disease seems possible, she said, referring to an experimental anti-Candida fungal vaccine (NDV-3A) designed to induce an adhesin-specific immune response. In a mouse model of colitis, the vaccine protected against C albicans-associated damage. “We saw an immediate IgA response that targeted C albicans in the intestinal contents,” Ost said.

C glabrata, which has also been associated with intestinal inflammation and IBD, does not form hyphae but — depending on the strain — may also induce intestinal IgA responses, she said in describing her recent research.

Ost reported having no disclosures. Schooley disclosed being a consultant for SNIPR Biome, BiomX, Locus, MicrobiotiX, Amazon Data Monitoring Committee: Merck.

A version of this article appeared on Medscape.com.