Abnormal composition of intestinal bacteria —“dysbiosis”— is characteristic of Crohn’s disease. Disease treatments include dietary changes and immunosuppressive anti-TNFα antibodies as well as ancillary antibiotic therapy but their effects on microbiota composition are undetermined. Using shotgun metagenomic sequencing, we analyzed fecal samples from a prospective cohort of pediatric Crohn’s disease patients starting therapy with enteral nutrition or anti-TNFα antibodies and reveal the full complement and dynamics of bacteria, fungi, archaea and viruses during treatment. Bacterial community membership was associated independently with intestinal inflammation, antibiotic use, and therapy. Antibiotic exposure was associated with increased dysbiosis, whereas dysbiosis decreased with reduced intestinal inflammation. Fungal proportions increased with disease and antibiotic use. Dietary therapy had independent and rapid effects on microbiota composition distinct from other stressor-induced changes and effectively reduced inflammation. These findings reveal that dysbiosis results from independent effects of inflammation, diet, and antibiotics and shed light on Crohn disease treatments.

Some of the most common symptoms of the inflammatory bowel diseases (IBD, which include ulcerative colitis and Crohn’s disease) are abdominal pain, diarrhea, and weight loss. It is therefore not surprising that clinicians and patients have wondered whether dietary patterns influence the onset or course of IBD. The question of what to eat is among the most commonly asked by patients and among the most difficult to answer by clinicians. There are therefore substantial variations in dietary behaviors of patients and recommendations for them, although clinicians do not routinely endorse specific diets for patients with IBD. Dietary clinical trials have been limited by their inability to include a placebo control, contamination of study groups, and inclusion of patients receiving medical therapies. Further challenges include accuracy of information on dietary intake, complex interactions between foods consumed, and differences in food metabolism among individuals. We review the roles of diet in the etiology and management of IBD, based on plausible mechanisms and clinical evidence. Researchers have learned much about the effects of diet on the mucosal immune system, epithelial function, and the intestinal microbiome; these findings could have significant practical implications. Controlled studies of patients receiving enteral nutrition and observations made from patients on exclusion diets have shown that components of whole foods can have deleterious effects for patients with IBD. Additionally, studies in animal models suggested that certain nutrients can reduce intestinal inflammation. In the future, engineered diets that restrict deleterious components but supplement beneficial nutrients could be used to modify the luminal intestinal environment of patients with IBD—these might be used alone or in combination with immunosuppressive agents, or as salvage therapy for patients who do not respond or lose responsiveness to medical therapies. Stricter diets might be required to induce remission, whereas more sustainable exclusion diets could be used to maintain long-term remission.

Background There are insufficient data to make firm dietary recommendations for patients with inflammatory bowel disease (IBD). Yet patients frequently report that specific food items influence their symptoms. In this study, we describe patients’ perceptions about the benefits and harms of selected foods and patients’ dietary patterns. Methods CCFA Partners is an ongoing internet-based cohort study of patients with IBD. We used a semi-quantitative food frequency questionnaire to measure dietary consumption patterns and open-ended questions to elicit responses from patients about food items they believe ameliorate or exacerbate IBD. We categorized patients into four mutually exclusive disease categories: CD without an ostomy or pouch (CD), UC without an ostomy or pouch (UC), CD with an ostomy (CD-ostomy), and UC with a pouch (UC-pouch). Results Yogurt, rice, and bananas were more frequently reported to improve symptoms whereas non-leafy vegetables, spicy foods, fruit, nuts, leafy vegetables, fried foods, milk, red meat, soda, popcorn, dairy, alcohol, high-fiber foods, corn, fatty foods, seeds, coffee, and beans were more frequently reported to worsen symptoms. Compared to CD patients, CD-ostomy patients reported significantly greater consumption of cheese (odds ratio (OR) 1.56, 95% CI 1.03–2.36), sweetened beverages (OR 2.14, 95% CI 1.02–1.03), milk (OR 1.84, 95% CI 1.35–2.52), pizza (OR 1.57, 95% CI 1.12–2.20), and processed meats (OR 1.40; 95% CI 1.04–1.89). Conclusions Patients identified foods that they believe worsen symptoms and restricted their diet. Patients with ostomies ate a more liberal diet. Prospective studies are needed to determine whether diet influences disease course.