Ruminococcal cellulosome systems from rumen to human

Abstract

A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R. champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin-coding genes that form part of a gene cluster. Representative R. champanellensis dockerins were tested against putative cohesins, and the results revealed three different cohesin-dockerin binding profiles which implied two major types of cellulosome architectures: (i) an intricate cell-bound system and (ii) a simplistic cell-free system composed of a single cohesin-containing scaffoldin. The cell-bound system can adopt various enzymatic architectures, ranging from a single enzyme to a large enzymatic complex comprising up to 11 enzymes. The variety of cellulosomal components together with adaptor proteins may infer a very tight regulation of its components. The cellulosome system of the human gut bacterium R. champanellensis closely resembles that of the bovine rumen bacterium Ruminococcus flavefaciens. The two species contain orthologous gene clusters comprising fundamental components of cellulosome architecture. Since R. champanellensis is the only human colonic bacterium known to degrade crystalline cellulose, it may thus represent a keystone species in the human gut.

First insight into the faecal microbiota of the high Arctic muskoxen (Ovibos moschatus)

“…Of the shared sequences, uncharacterized genera belonging to Ruminococcaceae (24.9–39.3 %) and Lachnospiraceae (3.9–9.8 %) were dominant (Table 1). Several members related to Ruminococcaceae play a key role in the degradation of recalcitrant polysaccharides such as crystalline cellulose (Rincón et al , 2001; Ben David et al , 2015). Free-ranging muskoxen typically graze on highly lignified plants during winter, which may explain the high proportion of Ruminococcaceae -related constituents observed in this study (Fig.…”

Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

“…Categorizing fibres as prebiotics is complicated by the fact that a diet ary fibre can be a prebiotic in one host but not another. For exam ple, cellulose can be considered a prebiotic in ruminants but not in humans, as the latter's intestinal microbiota only poorly utilize β(1→4) linked d glucose polysacchar ides 35 . Furthermore, a substrate qualify ing as a prebiotic might also depend on the target site.…”

Lysozyme activity of the Ruminococcus champanellensis cellulosome

“…All dockerins from the R. champanellensis scaffoldins (eight in total) were tested, since they represent the main backbones of its cellulosome structures. The four additional selected dockerins belonged to the three dockerin groups (Groups 1, 2 and 3–4) of cohesin–dockerin interactions in this bacterium, as previously defined using bioinformatic‐based criteria (Ben David et al ., ; Morais et al ., ). ScaK, expressed as a full‐length protein (lacking the signal peptide), was able to interact with the ScaG and protein 3939 dockerins (Fig.…”

“…In our previous report (Ben David et al ., ), the ScaK cohesin was expressed as a CBM‐fused cohesin (carbohydrate binding module) but was not found to bind any of the dockerin partners tested. In the present study, we cloned and expressed the ScaK scaffoldin as an intact wild‐type protein, in an attempt to reveal potential cohesin affinity partners and to study the GH25 activity.…”