A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
By A. B. Hall, Moran Yassour, J. Sauk, Ashley Garner, Xiaofang Jiang, Timothy D. Arthur, G. Lagoudas, Tommi Vatanen, Nadine Fornelos, R. Wilson and 12 more. Genome Medicine, 2017
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BackgroundInflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.MethodsWe performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.ResultsWe found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.ConclusionsThis study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
Subfields: Clinical Biochemistry, Food Science, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/ebd40a986e5b71f56f697496f688d8f364af57ad
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Citations in the corpus
- Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19 (2021, neutral): “R. gnavus and R. torques in the gut have been reported to co-occur with inflammatory bowel disease, 34 35 and B. dorei and B. vulgatus are implicated in several inflammatory gut diseases such as irritable bowel disease and ulcerative colitis.”
- Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide (2019, background): “gnavus levels peak at 69% of the gut microbiota (3).”
- Role of gut microbiota in type 2 diabetes pathophysiology (2020, background): “Potentially detrimental microbes in T2D (pathobionts), like Fusobacterium nucleatum and Ruminococcus gnavus can increase several inflammatory cytokines, albeit in other inflammatory diseases [103,104].”
- Human gut microbiota in health and disease: Unveiling the relationship (2022, background): “nucleatum positive cancer, indicating that the gut microbiome may be a significant mediator between dietary and colorectal cancer interactions (Hall et al., 2017).”