Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease

Abstract

Aims: To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions. Methods and Results: Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule and LOS-related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs. Conclusions: Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E. coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment. Significance and Impact of the Study: This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies.

Gut resistome presents a unique biome signature in chronic multi-symptom illness patients and links persistent pro-inflammatory phenotype in a mouse model reversible by fecal microbiota transfer

“…Also, IBD phenotype is known to be associated with microbiome dysbiosis which led to upregulation of antibiotic resistance [64], a condition also observed in GW-CMI veterans [65]. We have shown a direct association between gastrointestinal, systemic and neuronal inflammation observed in GW-CMI pathology and diversity of AGFs and resistant drug classes in a mouse model.…”

Integrated 16S rDNA Gene Sequencing and Untargeted Metabolomics Analyses to Investigate the Gut Microbial Composition and Plasma Metabolic Phenotype in Calves With Dampness-Heat Diarrhea

“…Lachnoclostridium is associated with the production of short-chain fatty acids in the gut ( 54 ), and its significant decrease in DHD calves may be related to the significant changes in unsaturated fatty acid metabolism pathways. Subdoligranulum has also been found to be significantly decreased in a lot of intestinal diseases ( 55 , 56 ). In this study, the correlation network analysis showed that DHD was associated with changes in the relevant structure and possible interaction structure of the intestinal microbiota.…”

Classification of the Occurrence of Dyslipidemia Based on Gut Bacteria Related to Barley Intake

“…Although the energy source and mechanism of Subdoligranulum and its involvement in dyslipidemia are unclear, it is known to produce butyrate, which improves lipid metabolism ( 39 , 40 ). A clinical study in Taiwan and China has reported that Subdoligranulum is depleted in patients with inflammatory bowel disease, suggesting that it may be a helpful bacteria ( 41 , 42 ).…”