Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn's disease of the terminal ileum

Chiodini, Rodrick J.; Dowd, Scot E.; Barron, James N.; Galandiuk, Susan; Davis, Brian R.; Glassing, Angela

doi:10.1099/jmm.0.000690

Cited by 7 publications

(4 citation statements)

References 22 publications

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“…Methane-producing archaea (methanogens) have been associated with disorders of the gastrointestinal tract and dysbiosis. Methanogens play an important role in digestion, improving polysaccharide fermentation by preventing accumulation of acids, reaction end-products and hydrogen gas [ 173 ].…”

Section: Resultsmentioning

confidence: 99%

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

2021

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Inflammatory bowel disease (IBD) is a chronic relapsing–remitting systemic disease of the gastrointestinal tract. It is well established that the gut microbiome has a profound impact on IBD pathogenesis. Our aim was to systematically review the literature on the IBD gut microbiome and its usefulness to provide microbiome-based biomarkers. A systematic search of the online bibliographic database PubMed from inception to August 2020 with screening in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines was conducted. One-hundred and forty-four papers were eligible for inclusion. There was a wide heterogeneity in microbiome analysis methods or experimental design. The IBD intestinal microbiome was generally characterized by reduced species richness and diversity, and lower temporal stability, while changes in the gut microbiome seemed to play a pivotal role in determining the onset of IBD. Multiple studies have identified certain microbial taxa that are enriched or depleted in IBD, including bacteria, fungi, viruses, and archaea. The two main features in this sense are the decrease in beneficial bacteria and the increase in pathogenic bacteria. Significant differences were also present between remission and relapse IBD status. Shifts in gut microbial community composition and abundance have proven to be valuable as diagnostic biomarkers. The gut microbiome plays a major role in IBD, yet studies need to go from casualty to causality. Longitudinal designs including newly diagnosed treatment-naïve patients are needed to provide insights into the role of microbes in the onset of intestinal inflammation. A better understanding of the human gut microbiome could provide innovative targets for diagnosis, prognosis, treatment and even cure of this relevant disease.

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Section: Resultsmentioning

confidence: 99%

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

2021

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“…Faecal metagenomics, however, lacks the additional dimension provided by biopsies: a measure of the subtle changes MGSs undergo along the intestine. Since certain pathologies, such as Crohn’s disease, are known to develop at specific locations along the intestine 32 – 34 , the ability to detect a pathological dysbiosis at such locations is likely to be fundamental for early diagnosis.…”

Section: Resultsmentioning

confidence: 99%

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Vaga

Lee

et al. 2020

Sci Rep

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Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota only. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities’ compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut mucosal microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.

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“…Faecal metagenomics, however, lacks the additional dimension provided by biopsies: a measure of the subtle changes MGSs undergo along the intestine. Since certain pathologies, such as Crohn's disease, are known to develop at specific locations along the intestine [28][29][30] , the ability to detect a pathological dysbiosis at such locations is likely to be fundamental for early diagnosis.…”

Section: Intrigued By the High Bacteroides Enrichment In All Biopsy Mmentioning

confidence: 99%

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Vaga

Lee

et al. 2019

Preprint

View full text Add to dashboard Cite

Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies to investigate faecal microbiota. This work used shotgun metagenomics of mucosal biopsies to explore the microbial communities compositions of terminal ileum and large intestine in 5 healthy individuals. Functional annotations and genome-scale metabolic modelling of selected species were then employed to identify local functional enrichments. While faecal metagenomics provided a good approximation of the average gut microbiome composition, mucosal biopsies allowed detecting the subtle variations of local microbial communities. Given their significant enrichment in the mucosal microbiota, we highlight the roles of Bacteroides species and describe the antimicrobial resistance biogeography along the intestine. We also detail which species, at which locations, are involved with the tryptophan/indole pathway, whose malfunctioning has been linked to pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting gut microbiota and host pathophysiology.

show abstract

Transitional and temporal changes in the mucosal and submucosal intestinal microbiota in advanced Crohn's disease of the terminal ileum

Cited by 7 publications

References 22 publications

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

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