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.

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Although PEN improved clinical symptoms, EEN and anti-TNF were more effective for decreasing mucosal inflammation and improving specific aspects of QOL.

The opportunity for structured, ongoing exercise with peer and professional support, in a suitable venue, is perceived as important to people with COPD in facilitating a physically active lifestyle following pulmonary rehabilitation. This desire for such opportunities may be related to individuals' self-efficacy towards physical activity.

Parents served as a good proxy for quality-of-life ratings in this population of pediatric patients with IBD. The degree of concordance between parent and child scores, however, varied, as observed in the present study in which parents underreported their child's health-related quality of life on the IMPACT-III emotional functioning domain.