A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic

Orlane Patrascu,Christel Béra-Maillet,Anne-Laure Abraham,Hervé M Blottière,Christophe Klopp,Joël Doré,Marion Leclerc,Emmanuelle Le Chatelier,Fabienne Béguet-Crespel,Bernard Henrissat,Nicolas Terrapon,Ludovica Marinelli

doi:10.1038/srep40248

Abstract

The digestion of dietary fibers is a major function of the human intestinal microbiota. So far this function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using easily accessible fecal material. However, microbial fermentations, supported by the presence of short-chain fatty acids, are suspected to occur in the upper small intestine, particularly in the ileum. Using a fosmid library from the human ileal mucosa, we screened 20,000 clones for their activities against carboxymethylcellulose and xylans chosen as models of the major plant cell wall (PCW) polysaccharides from dietary fibres. Eleven positive clones revealed a broad range of CAZyme encoding genes from Bacteroides and Clostridiales species, as well as Polysaccharide Utilization Loci (PULs). The functional glycoside hydrolase genes were identified, and oligosaccharide break-down products examined from different polysaccharides including mixed-linkage β-glucans. CAZymes and PULs were also examined for their prevalence in human gut microbiome. Several clusters of genes of low prevalence in fecal microbiome suggested they belong to unidentified strains rather specifically established upstream the colon, in the ileum. Thus, the ileal mucosa-associated microbiota encompasses the enzymatic potential for PCW polysaccharide degradation in the small intestine.

Highlights

To cite this version: Orlane Patrascu, Fabienne Beguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, AnneLaure Abraham, et al
In order to explore the fibrolytic systems of these microorganisms, 20,000 metagenomic clones were screened for their plant cell wall (PCW) polysaccharides degrading capacity
Using functional metagenomic screening in E. coli, our study demonstrated that the human ileal ecosystem harbors an enzymatic machinery able to perform catabolism of complex and diversified PCW polysaccharides from dietary fibres

Summary

Introduction

To cite this version: Orlane Patrascu, Fabienne Beguet-Crespel, Ludovica Marinelli, Emmanuelle Le Chatelier, AnneLaure Abraham, et al. The digestion of dietary fibers is a major function of the human intestinal microbiota. This function has been attributed to the microorganisms inhabiting the colon, and many studies have focused on this distal part of the gastrointestinal tract using accessible fecal material. The human intestine is a long and segmented part of the gastrointestinal (GI) tract, characterized by the small intestine in the proximal part, and the large intestine (colon) in the distal part Both are colonised by a complex and diversified microbial community, the intestinal microbiota, accounting for 102 to 108 bacteria/g in the small intestine depending on duodenum, jejunum or ileum segments[1] and 1011 bacteria/g of content in the colon[2]. The intestinal microbiota is considered as an “organ” with structural alterations regarded as a causal driver or consequence in several diseases[4]

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Conclusion