The Microbiome in Inflammatory Bowel Diseases: Current Status and the Future Ahead

By A. Kostic, Ramnik J. Xavier, Dirk Gevers. Gastroenterology, 2014

1,679 citations recorded by the source corpus.

Studies of the roles of microbial communities in the development of inflammatory bowel diseases (IBD) have reached an important milestone. A decade of genome-wide association studies and other genetic analyses have linked IBD with loci that implicate an aberrant immune response to the intestinal microbiota. More recently, profiling studies of the intestinal microbiome have associated pathogenesis of IBD with characteristic shifts in the composition of the intestinal microbiota, reinforcing the view that IBD results from altered interactions between intestinal microbes and the mucosal immune system. Enhanced technologies can increase our understanding of the interactions between the host and its resident microbiota, and their respective roles in IBD, from both a large-scale pathway view and at the metabolic level. We review important microbiome studies of patients with IBD and describe what we have learned about the mechanisms of intestinal microbiota dysfunction. We describe the recent progress in microbiome research from exploratory 16S-based studies, reporting associations of specific organisms with a disease, to more recent studies that have taken a more nuanced view, addressing the function of the microbiota by metagenomic and metabolomic methods. Finally, we propose study designs and methodologies for future investigations of the microbiome in patients with inflammatory gut and autoimmune diseases in general.

Subfields: Genetics, Infectious Diseases, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4ecfbd3c798379249f80baaf10641eedee111dd7

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Citations in the corpus

Integrative omics for health and disease (2018, background): “Nonetheless, it is very clear that patients with diseases, such as inflammatory bowel disease 110,111 , type 2 diabetes 112 and obesity 113,114 , have different microbiome profiles from those of healthy controls.”
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics (2016, background): “…of bacteria and yeast (Supplemental Figure 4), and both CD and C. difficile infection have been reported associated with reduction of faecal bacterial diversity in the patients’ stools (Chang et al., 2008; Antharam et al., 2013; Vincent et al., 2013; Kostic et al., 2014; Norman et al., 2015).”
Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome (2019, background): “individuals and IBD patients in terms of load and diversity has been confirmed [75,76].”
The gut microbiome in health and in disease (2015, background): “Targets of the inflammatory response include the commensal microbiota, and IBD are associated with alterations in the gut microbiota, though it is not clear if microbial changes contribute to disease pathogenesis or develop as a result of local inflammation [42].”
Alterations of the human gut microbiome in multiple sclerosis (2016, methodology): “Filtering was performed using custom Python scripts with the following criteria: (1) only one sequence per species (if the species had more than one sequence, then the longest sequence was chosen); (2) non-environmental species (using key words); (3) no sequences with unclear taxonomic lineage infor”
Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism (2018, background): “Along with reduced CYP11A1 expression (Coste et al., 2007) and decreased glucocorticoid production (Huang et al., 2014), disorders of intestinal steroidogenesis have been associated with IBD.”
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).”