Effect of Exclusion Diets on Symptom Severity and the Gut Microbiota in Patients With Irritable Bowel Syndrome

BACKGROUND & AIMS: Altered fecal microbiota have been reported in irritable bowel syndrome (IBS), although studies vary, which could be owing to dietary effects. Many IBS patients may eliminate certain foods because of their symptoms, which in turn may alter fecal microbiota diversity and composition. This study aimed to determine if dietary patterns were associated with IBS, symptoms, and fecal microbiota differences reported in IBS. METHODS: A total of 346 IBS participants and 170 healthy controls (HCs) completed a Diet Checklist reflecting the diet(s) consumed most frequently. An exclusion diet was defined as a diet that eliminated food components by choice. Within this group, a gluten-free, dairy-free, or low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols diet was further defined as restrictive because they often are implicated in reducing symptoms. Stool samples were obtained from 171 IBS patients and 98 HCs for 16S ribosomal RNA gene sequencing and microbial composition analysis. RESULTS: Having IBS symptoms was associated with consuming a restrictive diet (27.17% of IBS patients vs 7.65% of HCs; odds ratio, 3.25; 95% CI, 1.66–6.75; P value = .006). IBS participants on an exclusion or restrictive diet reported more severe IBS symptoms (P = .042 and .029, respectively). The composition of the microbiota in IBS patients varied depending on the diet consumed. IBS participants on an exclusion diet had a greater abundance of Lachnospira and a lower abundance of Eubacterium (q value, <.05), and those on a restrictive diet had a lower abundance of Lactobacillus (q value, <.05). CONCLUSIONS: Restrictive diets likely are consumed more by IBS patients than HCs to reduce GI symptom severity. Dietary patterns influence the composition of the fecal microbiota and may explain some of the differences between IBS and HCs.

IBS patients between the ages of 18 and 69 years in our research database were screened consecutively for possible inclusion in this study. The majority of patients in the research database were recruited through community advertisements for physiologic or treatmentrelated clinical studies by the University of California Los Angeles G. Oppenheimer Center for Neurobiology of Stress and Resilience, and a lesser proportion of patients were recruited for research studies directly through the general GI clinics at University of California Los Angeles. All participants were recruited during the time periods between July 2013 and June 2019. Patient data from previous physiologic studies was used if patients met the inclusion criteria for this study. Of note, microbiome data from only a small subset of HCs (n ¼ 25) was published previously in studies assessing obesity, food addiction, and the brain-gut axis. 1,2 No microbiome data from IBS patients had been published previously, and no previous studies in our research database had focused on the effect of diet on the gut microbiota. This study was approved by the Institutional Review Board at the University of California Los Angeles, which allowed for the repurposing of previously collected data.
All participants underwent a medical history and physical examination. IBS participants were included in our study if they met Rome III or Rome IV criteria, depending on the year of recruitment, and were subclassified as having IBS-C, IBS-D, IBS-M, or IBS unclassified. IBS participants were excluded if they had any current organic disease that also could contribute to chronic abdominal pain (ie, inflammatory bowel disease, active peptic ulcer disease, diverticulitis, and so forth), had an overlapping dominant functional disorder such as functional dyspepsia, had any active psychiatric disease, or were on chronic opioid medications. HCs were included if they had no history of GI symptoms or an organic GI disease, and were excluded if they had any active psychiatric disease or were on chronic opioid medications. Both HCs and IBS participants who submitted stool samples for microbiota analysis were excluded if they had received antibiotics within the previous 3 months. Only a very small percentage of IBS participants (2.6%) and HCs (1.18%) reported the use of probiotics. Analyses were performed both with including and excluding these participants on probiotics, and there was no significant effect of probiotic use on our overall findings. Therefore, the participants on probiotics were included in the final analysis.

Diet Checklist
If participants did not believe that the diet they consumed most frequently was reflected by the choices of a standard American diet, modified American diet, Mediterranean diet, Paleo diet, vegan diet, vegetarian diets, gluten-free diet, dairy-free diet, or the low FOD-MAP diet, the option was given to select "other," and describe the components of their individual diet in regard to consumption of meat, dairy, eggs, fruits, vegetables, and grains. If a participant selected "other," their comments regarding intake of food components were reviewed individually, as was that participant's 24-hour diet diary that reflected every food component consumed in the 24-hour period before stool submission for microbiota analysis. After review of the dietary comments and 24-hour diet diaries, participants who selected "other" then were reclassified into the diet category that was most reflective of their individual diet. This then was verified against the participant's responses on the DHQ-II, a food frequency questionnaire.
If a participant selected 2 diets on the Diet Checklist, one of which fell into the standard category and one of which fell into the exclusion category, that participant ultimately was characterized as being on an exclusion diet. When available, 24-hour diet diaries were examined for participants on an exclusion diet to confirm compliance. If a participant's 24-hour diet diary was not consistent with their self-reported exclusion diet from the Diet Checklist, that participant's responses to the DHQ-II were reviewed and the diet was reclassified as appropriate.
Our institution's Diet Checklist also was validated internally against the standardized DHQ-II and each patient's 24-hour diet recall of all foods consumed in a 24hour period before submitting a stool sample for microbiome analysis. The Food Patterns Equivalents Database from the DHQ-II, which converts foods and beverages in the Food and Nutrient Database for Dietary Studies to 37 United States Department of Agriculture Food Pattern components, was used for validation. Compliance with an exclusion diet on the Diet Checklist (dairy-free, Paleo, vegetarian, or vegan) was defined as 3 or fewer dietary indiscretions per month. This cut-off value was determined to be applicable to real-life compliance scenarios after consultation with a registered GI dietician at the University of California Los Angeles. For example, if a patient stated on their Diet Checklist that they consumed a dairy-free diet, but review of their DHQ-II showed 4 episodes of dairy intake in a 1-month period, this person was determined to not actually follow a dairy-free diet.
Using this methodology, only 2 (7.4%) subjects who indicated that they were on a Paleo diet on the Diet Checklist were nonadherent based on their DHQ-II responses, 0 (0.0%) subjects who indicated that they were on a vegan diet were nonadherent based on their DHQ-II responses, 1 subject (4.5%) who reported being on a standard vegetarian diet was nonadherent based on his or her DHQ-II responses, 0 (0.0%) subjects who indicated that they were on an ovovegetarian, lactovegetarian, or ovolactovegetarian diet were nonadherent based on their DHQ-II responses, and 1 subject who reported consuming a dairy-free diet was nonadherent based on his or her DHQ-II responses. These subjects were reclassified into the diet category that best matched their eating patterns based on their DHQ-II responses and 24-hour diet recall. Validation was unable to be performed for the gluten-free diet and low FODMAP diet because the DHQ-II does not specifically assess consumption of gluten or distinguish between foods that are low or high in FODMAPs. For the 4 subjects who were not compliant with their indicated diet on the Diet Checklist, we then reviewed their individual Diet Checklist, DHQ responses, and 24hour diet diary if available. Subjects' diets were reclassified into the diet category that best reflected the diet they consumed.

March 2022
Exclusion Diets and the Gut Microbiota e477 Supplementary Figure 3.