The treatment-naive microbiome in new-onset Crohn's disease.

By Dirk Gevers, S. Kugathasan, L. Denson, Yoshiki Vazquez-Baeza, William W. Van Treuren, Boyu Ren, Emma H. Schwager, Dan Knights, S. Song, Moran Yassour and 22 more. Cell Host and Microbe, 2014

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Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.

Subfields: Genetics, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/6caafd343b71eac80104ead447e00e6a2f9eb976

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Citations in the corpus

Disease-specific Alterations in the Enteric Virome in Inflammatory Bowel Disease (2015, background): “One environmental contributor is thought to be microorganisms that live in the intestine (Gevers et al., 2014; Kostic et al., 2014; Minot et al., 2011; Norman et al., 2014; Virgin, 2014).”
Normalization and microbial differential abundance strategies depend upon data characteristics (2017, background): “Significant changes in certain bacterial species abundances are linked to inflammatory bowel diseases [10], diarrhea [11], obesity [12–14], HIV [15], diet [16], culture, age, and antibiotic use [17], among many other conditions.”
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome (2018, positive): “, 2015), Crohn’s disease (Gevers et al., 2014; Wanget al., 2016), type1 diabetes (Kostic et al.”
Fungal microbiota dysbiosis in IBD (2016, background): “5 However, other microorganism types colonising the human gut have not been thoroughly investigated.”
A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients (2017, background): “[20] cohort may be due to a combination of age (20–66 years here, 3–17 years in Gevers et al.”