Should You Do a Gut Microbiome Test? No — Here’s Why

Posted on March 18, 2026 by gutsandgrowth

J McCreary. MedPage Today; 2/26/26. Open Access! Same Stool Sample, Different Results in Gut Microbiome Tests

An excerpt:

“Direct-to-consumer gut microbiome tests produced markedly different results — even when analyzing the same stool sample, researchers found.

Identical fecal samples sent via 21 home-testing kits to seven anonymized direct-to-consumer testing companies yielded a wide variation in reported bacterial abundance and in the health assessments generated from those data, reported Stephanie L. Servetas, PhD, of the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, and colleagues in Communications Biology.

In some cases, there was not even agreement among kits produced by the same company…

When researchers compared 18 commonly reported microbial genera across companies, no single provider aligned with the consensus profile for all 18. Across the full dataset, 1,208 unique taxa were reported, but only three genera appeared in every company’s results…

The authors said the discrepancies likely stem from differences in sample processing, sequencing methods, bioinformatics pipelines, reference databases, reporting thresholds, and quality control standards…

“These tests have become popular, partly because people, I think, are increasingly interested in health and wellness, and partly because the gut microbiome has been linked — at least in the public imagination — to the idea that you can improve a whole range of conditions through diet and lifestyle changes,” said co-author Diane Hoffmann, MS, JD, of the University of Maryland in Baltimore.

“There’s been a lot of hype around that, but the hype doesn’t really match the evidence. These tests often have limited evidence behind them, especially when it comes to informing clinical decisions or even basic dietary recommendations,” she added. “So the marketing can be questionable, and consumers can end up misinterpreting or over-trusting results that aren’t very reliable.”

Related article from Houston Methodist Hospital (2024): Should You Do a Gut Microbiome Test? Key point: “While these tests seem to be effective in mapping the gut microbiome, there is currently no benchmark for what a ‘normal’ gut microbiome looks like. So the question becomes what to do with the results…microbiomes are highly variable — even normal, healthy ones. This makes it incredibly challenging to define the patterns or signatures that suggest a microbiome has become imbalanced. Plus, the at-home steps for correcting microbiome imbalance aren’t established either.”

My take: It is uncomfortable informing families that these gut microbiome tests have little clinical value because there is not a proper way to interpret the results. In addition, this study shows that the tests from one place to another produce wildly different results.

While one’s microbiome is important, we still don’t understand what exactly is a normal microbiome.

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Highway to El Chalten and Mount Fitz Roy, Argentina

Extent of Eosinophilic Esophagitis and Response to PPI Therapy

Posted on March 17, 2026 by gutsandgrowth

DA Hartnett et al. Clin Gastroenterol Hepatol 2026; 24: 375-384. Open Access! Distribution of Esophageal Eosinophilia as a Predictor of Proton Pump Inhibitor Response in Eosinophilic Esophagitis

Methods: This was a retrospective cohort study of newly diagnosed adult patients with EoE — All patients received ≥8-week PPI trial and underwent repeat biopsies to assess response. There were including 66 with isolated distal and 200 with proximal/diffuse disease. 86% of patients received twice daily PPI therapy (73% in those with isolated distal disease and 87% in the diffuse/isolated proximal disease.

Key findings:

PPI response was higher among patients with isolated distal disease:

histologic remission [<15 eosinophils/hpf post-PPI]: 63.6% vs 44.5%; P = .01
deep remission [<6 eosinophils/hpf]: 54.5% vs 31.0%; P = .001
symptom improvement: 92.4% vs 81.0%; P = .03).

The discussion noted that there has been limited studies of EoE distribution and response to treatment. “Godat et al observed that the distribution of esophageal eosinophilia had no impact on clinicohistologic remission rates (defined as ≤2 on a scale of 0–10 for dysphagia/odynophagia in the last 7 days and a peak eosinophil count <5 eos/hpf) in patients treated with budesonide orodispersible tablets.¹⁹“

“The generally higher PPI response with isolated/predominant distal disease suggests that acid suppression and improved mucosal barrier function likely play a key role in how PPI may lead to EoE remission…prior studies have demonstrated no correlation between findings on ambulatory pH monitoring and PPI response in EoE.²⁵ Therefore, the differential response to PPI based on eosinophil distribution phenotypes may be due to more than comorbid GERD alone.”

My take: While the pathophysiology of how PPIs work for EoE is unclear, it appears that the response to PPIs is better with in those with isolated distal EoE. The difference in response may have been even more pronounced if both groups had a similar percentage of receiving twice daily PPI treatment.

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How Long Should a pH Probe Last to Accurately Diagnose Gastroesophageal Reflux

Posted on March 16, 2026 by gutsandgrowth

RI Rusu et al. Clin Gastroenterol Hepatol 2026; 24: 365-374. Open Access! The Optimal Duration of pH Monitoring: Testing the Validity of Lyon 2.0 Recommendations for Wireless pH Measurement

Background: “The Lyon 2.0 consensus recommends 96-hour wireless pH studies for gastroesophageal reflux disease (GERD) diagnosis…Ninety-six-hour monitoring is not always possible, either for technical reasons (eg, early detachment of the pH sensor) or for practical and financial reasons (48-hour studies are routine and cost-efficient in many centers).”

Methods: Data from 944 patients (16-85 years) with 4-day recordings (Bravo capsule) was reviewed. Patients were classified at 24, 48, and 72 hours against the 96-hour reference standard. Acid exposure time (AET) <4% was conclusively negative, and AET >6% was conclusively positive for GERD.

Key findings:

With longer duration, more patients were able to be diagnosed with GERD and fewer patients were in the indeterminate group. The proportion of patients with inconclusive results (AET 4%–6%) reduced from 113 of 944 at 24 hours to 40 of 113 at 96 hours (35% of subgroup; P = .02)
Only 3 of 60 patients with LA grade B esophagitis demonstrated physiologic reflux burden across all 96 hours of recording (which indicates that for significant reflux esophagitis, pH monitoring is not needed in most cases)

In the associated editorial (pg 306-308), the authors note that “the minimum duration for an effective study seems to be 3 days, because ~90% of conclusively positive studies identified over 4 days would be detected with 72 hours of recording. However, to achieve this, a 4-day study would need to be planned because of potential data loss, reported in almost a third of the cases in this and prior cohorts.”
“96-hour wireless monitoring is optimal for ruling out GERD when the pretest likelihood of reflux is low, especially when empiric PPI therapy is ineffective.”

My take: pH probe tests have many limitations. This study reinforces the need for longer studies in many patients when the findings would be equivocal with shorter duration studies.

Related blog post:

Prospective Study: Acute Gastroenteritis Increases Risk of Disorders of Gut-Brain Interaction

Posted on March 15, 2026 by gutsandgrowth

A Palorath et al. Am J Gastroenterol 2026; 121: 242-247. Acute Gastroenteritis Is a Risk Factor for the Development of Disorders of Gut-Brain Interaction in Children

Methods: A prospective, controlled, cohort study. Children (1-15 years) with recent AGE (cases) and siblings (controls) were followed for 6 months. We assessed DGBIs using a validated questionnaire (QPGS IV) per Rome criteria. Patients with underlying GI disorders (eg. Celiac, IBD, recent abdominal surgery) were excluded.

Key findings:

Among children without a history of DGBI before the AGE, 6 (12.2%) cases vs 0 control were diagnosed with DGBI (P = 0.01) at follow-up at 3 months
At 6 months, 5 cases (1 lost to follow-up) vs 0 control had persistent DGBI (P = 0.03)
Severity of AGE was correlated with PI-DGBI. Severe AGE included abdominal pain, ED consullt, and need for IV fluids

My take: It is well-known that previous AGE increases the risk of PI-DGBIs, especially irritable bowel syndrome. However, this is the first prospective cohort study showing this association between AGE and DGBIs in a nonoutbreak setting. In addition, it correlates the risk of DGBI with the severity of AGE.

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Oral Integrin Inhibitor for Moderate to Severe Ulcerative Colitis

Posted on March 13, 2026 by gutsandgrowth

BE Sands et al. Clin Gastroenterol Hepatol 2026; 23: 525-534. Open Access! A Phase 2 Study of MORF-057, an Oral α4β7 Integrin Inhibitor in Moderately to Severely Active Ulcerative Colitis

Background: MORF-057 is an orally administered small-molecule drug that inhibits α4β7 integrin-mediated recruitment of α4β7-expressing lymphocytes to the gut. It has a similar target as vedolizumab, a monoclonal anti-integrin antibody used to treat ulcerative colitis (approved in 2014), but it requires parenteral administration.

Methods: This open-label, phase 2a, single-arm, multicenter trial (EMERALD-1) comprised a 6-week screening period, a 52-week active treatment period (including a 12-week induction period and 40-week maintenance period), and a 4-week safety follow-up period. Of the 35 participants enrolled in the main cohort, 18 participants received 100 mg of oral MORF-057 twice daily for the entire treatment period.

The primary efficacy endpoint was a change in the Robarts Histopathology
Index (RHI) score from baseline to week 12. “RHI was chosen as the primary efficacy assessment because it is an objective measure that can be assessed in a blinded fashion, which was critical given the open label study design. RHI also allows for a deeper, more quantitative probe than endoscopy.”

Key findings:

MORF-057 was well tolerated, and no treatment-emergent serious adverse events were
observed
At week 12, participants (n= 35) exhibited a mean change from baseline in RHI
score of ‒6.4 (standard deviation, 11.2). Additionally, 22.9% of participants (8/35) achieved
RHI remission (RHI score ≤3)
In participants with evaluable data (n=18), the effects of MORF-057 on pharmacokinetics, pharmacodynamics, and clinical efficacy were achieved at week 12 and remained consistent to week 52

Symptomatic remission based on whether patient was advanced therapy (AT)-naive or AT-experienced

My take: This small open label study shows that an oral medication targeting α4β7 integrin has potential as an effective therapy for ulcerative colitis. If effective, then it would be important to understand how it compares to vedolizumab.

Related blog post: In Trials: An Oral IL-23 Antagonist Peptide

Chronic Nonbacterial Osteomyelitis Associated with Pediatric Inflammatory Bowel Disease

Posted on March 12, 2026 by gutsandgrowth

M Matar et al. J Pediatr Gastroenterol Nutr. 2026;82:487–494. Chronic nonbacterial osteomyelitis associated with pediatric inflammatory bowel disease: : A multicenter retrospective study from the Paediatric inflammatory bowel disease Porto Group of ESPGHAN

Methods: Retrospective study with 45 pediatric patients with inflammatory bowel disease (n=32 with Crohn’s disease, n=8 with ulcerative colitis, n=5 with IBD-U)

Key findings:

CNO presented in 15 patients (33%) within 3 months of IBD diagnosis, and in additional 20 (44%) patients after IBD diagnosis; in 10 (22%) patients CNO preceded the diagnosis of IBD with a median time 46 (25–248) weeks
11 (24%) subjects displayed at least one additional extra-intestinal manifestations, including arthritis (6, 13%), erythema nodosum (4, 9%), sacro-ileitis (2, 4%), psoriasis (1, 2%), and pyoderma gangrenosum (1, 2%).
Complications occurred in six patients and included vertebral collapse, bone fracture, and bone deformity. In eight (18%) subjects vertebral collapse was present already at the time of diagnosis.
“While in most patients, diagnosis of CNO was associated with either clinical or laboratory indices of active IBD, especially CD, in some cases, the intestinal disease was quiescent.”
“All patients achieved remission of CNO at some point during follow-up, which may support the hypothesis that anti-TNF treatment is unlikely to promote CNO development and does not reinforce the theory of a paradoxical effect that has been suggested by Cordesse et al.²²“

My take: This is a useful review highlighting the association of CNO with both active disease and quiescent IBD. The authors argue that their data does not support the development of CNO as a paradoxical effect. I disagree with this premise. Many of the extraintestinal manifestations, that anti-TNF agents can treat, rarely can be caused by them. Besides CNO, paradoxical reactions to anti-TNF agents have included the development of rheumatoid arthritis, psoriasis, hidradenitis suppurativa and autoimmune liver disease.

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QI Project: Increasing H Pylori Eradication

Posted on March 11, 2026 by gutsandgrowth

KR Arellanos et al (Senior Author S Bonilla). JPGN Reports. 2026;7:19–27. Standardizing a protocol for Helicobacter pylori gastric biopsy culture: From implementation to sustained practice

Background: “The availability of antibiotic susceptibility data is essential for understanding local and regional resistance patterns and for informing future guidelines on optimal treatment regimens for children.” This quality improvement project report documents how “using a standardized checklist, in combination with educational initiatives for staff physicians and collaborative efforts with endoscopy and laboratory teams, were effective strategies to increase the use of gastric biopsy culture as a diagnostic tool for H. pylori infection and, to a lesser extent, to improve culture yield in patients with positive histology.”

Key steps:

Standardized checklist for biopsy collection used by nurses
Standardized transport protocol
Prompt refridgeration/transportation
Using a single lab for testing (Mayo clinic)

Key findings:

There was a consistent increase in culture positivity for H pylori and this was associated with improved eradication rates
Overall, antimicrobial resistance was highest for metronidazole (27.5%) and clarithromycin (18.7%), and lower for rifampin (12.2%), levofloxacin (10.1%), and amoxicillin (4.3%). Only one isolate showed resistance to tetracycline

Discussion: “Among the various interventions implemented during the QI project, the one that appears to have contributed most significantly to the dramatic improvement in culture yield among patients with H. pylori-positive histology was the consolidation of specimen processing to a single specialty laboratory [Mayo clinic].” Specific logistics included using a simple sterile container with saline-moistened tissue for collection and sending samples to specialty lab on the same day as collection.

My take: During this project, there was improved use of gastric culture and in culture yield. This resulted in meaningful improvement for patients. However, without clinical leadership to implement these changes, there will continue to be suboptimal eradication rates at other centers.

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IBAT Inhibitor for Xanthomas in Alagille Syndrome

Posted on March 10, 2026 by gutsandgrowth

G Bora et al. JPGN Reports. 2026;7:1–5. Open Access! Maralixibat for the treatment of severe xanthomas in two children with Alagille syndrome: Case reports

Key findings:

Maralixibat (MRX) resulted almost complete resolution of severe, debilitating xanthomas and clinically meaningful improvements in pruritus/serum bile acid levels.
Clinical scratch score in Case 1 dropped from baseline of 4 to 2 after MRX; in Case 2, it dropped from 3 to 1 after MRX
Serum bile acids in Case 1 dropped from baseline of 468 micromol/L to 206 after MRX; in Case 2 it dropped from 57 to 25 after MRX
This case report involved two patients with ALGS and unusual manifestations of xanthomatosis, including one patient with airway xanthomas and a second patient with severe, diffuse xanthomas

From Figure 1 showing airway and skin changes in case 1:

Rigid bronchoscopy before (C) and then 18 months after maralixibat (E)

Discussion:

“The ICONIC study by Gonzales et al. showed significant improvements in xanthomas in participants treated with maralixibat by 48 weeks, based on overall reductions in the Clinician Xanthomas Score, with further improvements in patients treated for longer durations. Xanthoma reduction was associated with improved quality of life and levels of TC.⁴ This report reviewed real-world experience in two patients with ALGS and characterized the extent of their improvement after treatment with maralixibat.”

My take: This report provides convincing evidence that maralixibat was associated with reversing severe xanthomas in these two patients with Alagille syndrome.

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Disclaimer: This blog, gutsandgrowth, assumes no responsibility for any use or operation of any method, product, instruction, concept or idea contained in the material herein or for any injury or damage to persons or property (whether products liability, negligence or otherwise) resulting from such use or operation. These blog posts are for educational purposes only. Specific dosing of medications (along with potential adverse effects) should be confirmed by prescribing physician. Because of rapid advances in the medical sciences, the gutsandgrowth blog cautions that independent verification should be made of diagnosis and drug dosages. The reader is solely responsible for the conduct of any suggested test or procedure. This content is not a substitute for medical advice, diagnosis or treatment provided by a qualified healthcare provider. Always seek the advice of your physician or other qualified health provider with any questions you may have regarding a condition.

How to Improve the Value of Biologic Infusions: Reduce Lab Testing and Frequency

Posted on March 9, 2026 by gutsandgrowth

T Shah et al. JPGN Reports 2026;1–5. Responsible laboratory surveillance of pediatric patients with inflammatory bowel disease on biologic infusion therapy

This retrospective single-center study with 34 pediatric patients with inflammatory bowel disease examined the laboratory costs (2020-2021) associated with monitoring biologic therapy.

Methods: “Routine laboratory studies were defined as those part of the standardized infusion protocol at SBCH and were obtained with each scheduled infusion. The following laboratory studies were considered routine/standard: complete blood count with differential, basic metabolic panel, liver function tests, amylase, lipase, erythrocyte sedimentation rate, C-reactive protein, vitamin D, iron, ferritin, vitamin B12, folate, urine hCG (if a subject was female). Other laboratory studies that were collected, but not considered routine studies included QuantiFERON-TB, and biologic drug and antibody level.”

Key findings:

The average hospital charge for studies obtained per infusion was $1308.36 with an average annual cost of $9543.44 per patient
Fifteen (6%) instances of change in clinical management were found. “Only a limited subset of the 15 laboratory studies included were utilized in making changes: biologic drug, Vitamin D, and iron level”
During the study, 248 infusions were administered with a “total annual charge amongst all patients in the study was $324,447”

Discussion:

“Our study population had well controlled disease as evident by low PCDAI and PUCAI scores…Our observations suggest the utility of routine laboratory surveillance at each biologic infusion is minimal, favoring decreased testing for IBD patients, especially those in clinical remission.”
“We propose obtaining laboratory tests twice a year, or with every third infusion, for patients with mild disease or in remission based on their disease activity index scores. In our small cohort of patients, this change in practice would reduce the total annual costs by 66% ($214,154.82)”

My take: It has been my practice, for most patients with IBD, to obtain labs with every other infusion (~3 times per year). Typically, I will obtain a CBC/d, CMP and CRP and obtain other labs like Vit D, GGT, Quantiferon Gold and drug level monitoring less frequently. I rarely check Vit B12, ESR, Folate, Amylase, and Lipase.

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Afimkibart for Ulcerative Colitis (TUSCANY-2)

Posted on March 8, 2026 by gutsandgrowth

S Danese et al. The Lancet Gastroenterology & Hepatology 2025; 10: 882 – 895. Anti-TL1A antibody, afimkibart, in moderately-to-severely active ulcerative colitis (TUSCANY-2): a multicentre, double-blind, treat-through, multi-dose, randomised, placebo-controlled, phase 2b trial

Briefly noted:

Methods: “The multicentre, double-blind, treat-through, multi-dose, randomised, placebo-controlled, phase 2b, TUSCANY-2 trial” enrolled 228 people who completed induction. All patients had moderate to severe ulcerative colitis who were treated with either subcutaneous afimkibart (a TNF-like ligand 1A (TL1A)) or placebo. There was a 12-week induction phase followed by a 40-week maintenance phase.

Key findings:

At week 14, the primary endpoint of clinical remission by total Mayo score was reported in 12 (26%) of 47 patients in the afimkibart 50 mg group, 14 (23%) of 60 patients in the afimkibart 150 mg group, and 21 (24%) of 88 patients in the in the afimkibart 450 mg group versus five (12%) of 43 patients in the placebo group
Incidences of treatment-emergent adverse events during induction were similar with placebo and afimkibart
The percentages of remission were higher for every afimkibart dose but this did not reach statistical significance compared to placebo

My take: Further testing is needed to determine whether afimkibart will have a significant place for treatment of inflammatory bowel disease.