Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients

Abstract

The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition. Based on signature taxa, CD microbiotas clustered into 2 distinct metacommunities, indicating individual variability in CD microbiome structure. Metacommunity-specific functional shifts in CD showed enrichment in producers of the pro-inflammatory hexa-acylated lipopolysaccharide variant and a reduction in the potential to synthesize short-chain fatty acids. Disruption of ecological networks was evident in CD, coupled with reduction in growth rates of many bacterial species. Short-term exclusive enteral nutrition elicited limited impact on the overall composition of the CD microbiota, although functional changes occurred following treatment. The microbiotas in CD patients can be stratified into 2 distinct metacommunities, with the most severely perturbed metacommunity exhibiting functional potentials that deviate markedly from that of the healthy individuals, with possible implication in relation to CD pathogenesis.

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

“…Survey of human metagenomic data sets. Available cohorts of human gut metagenomic sequence data (National Center for Biotechnology Information projects PRJNA422434 [87], PRJEB10878 [88], PRJEB12123 [89], PRJEB12124 [90], PRJEB15371 [91], PRJEB6997 [92], PRJDB3601 [93], PRJNA48479 [94], PRJEB4336 [95], PRJEB2054 [96], PRJNA392180 [51], and PRJNA527208 [97]) were searched for the presence of 1,3GUL nucleotide sequences from B. fluxus (12.5 kb), B. thetaiotaomicron (12.6 kb), and B. uniformis (14.5 kb) using the following workflow. Each 1,3GUL nucleotide sequence was used separately as a template, and then magic-blast v1.5.0 (98) was used to recruit raw Illumina reads from the available metagenomic data sets with an identity cutoff of 97%.…”

Extensive transfer of genes for edible seaweed digestion from marine to human gut bacteria

“…Available cohorts of human gut metagenomic sequence data (National Center for Biotechnology Information projects: PRJNA422434 45 , PRJEB10878 46 , PRJEB12123 47 , PRJEB12124 48 , PRJEB15371 49 , PRJEB6997 50 , PRJDB3601 51 , PRJNA48479 52 , PRJEB4336 53 , PRJEB2054 54 , PRJNA392180 55 , and PRJNA527208 56 were searched for the presence of CGN/POR/AGAR degrading PUL nucleotide sequences from Bt 37371 , Bo 12C04 , Bp 17135 , Bu NP1 , Bx 18-002P and Faecalicatena spp. using the following workflow: Each PUL nucleotide sequence was used separately as a template and then magic-blast v1.5.0 57 was used to recruit raw Illumina reads from the available metagenomic datasets with an identity cutoff of 97%.…”

Interplay between food and gut microbiota in health and disease

“…The fiber-derived fermentation products including the SCFAs butyrate, propionate and acetate contribute to a variety of positive health effects both locally in the intestine and systemically. For example, in animal models of inflammatory bowel disease, where reduced levels of SCFAs in the feces associate with disease severity , and in humans, where lack of bacteria with potential for SCFA production is a signature of Crohn's disease patients (He et al, 2017).…”