The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens

Abstract

Cellulose-degrading microorganisms involved in the breakdown of plant cell wall material in the human gut remain rather unexplored despite their role in intestinal fermentation. Microcrystalline cellulose-degrading bacteria were previously identified in faeces of methane-excreting individuals, whereas these microorganisms were undetectable in faecal samples from non-methane excretors. This suggested that the structure and activity of the cellulose-degrading community differ in methane- and non-methane-excreting individuals. The purpose of this study was to characterize in depth this cellulose-degrading community in individuals of both CH(4) statuses using both culture-dependent and molecular methods. A new real-time PCR analysis was developed to enumerate microcrystalline cellulose-degrading ruminococci and used to confirm the predominance of these hydrolytic ruminococci in methane excretors. Culture-dependent methods using cell wall spinach (CWS) residue revealed the presence of CWS-degrading microorganisms in all individuals. Characterization of CWS-degrading isolates further showed that the main cellulose-degrading bacteria belong essentially to Bacteroidetes in non-methane-excreting subjects, while they are predominantly represented by Firmicutes in methane-excreting individuals. This taxonomic diversity was associated with functional diversity: the ability to degrade different types of cellulose and to produce H(2) from fermentation differed depending on the species. The structure of the cellulolytic community was shown to vary depending on the presence of methanogens in the human gut.

Genomics Review of Holocellulose Deconstruction by Aspergilli

“…Polysaccharides are deconstructed and resulting sugars assimilated by all microorganisms that live in soil and forest floors (4). Furthermore, natural decomposition of woody (most of the available biomass) materials remains a recalcitrant process that takes place in soil microbiomes and perhaps employs numerous enzymes derived from not one organism but a whole community of microbes (5).…”

Anaerobic Methyl tert -Butyl Ether-Degrading Microorganisms Identified in Wastewater Treatment Plant Samples by Stable Isotope Probing

“…Two bacterial TRFs (67 bp and 215 bp) were highly enriched in the heavy 13 C fractions, while such enrichment was not seen in the corresponding 12 C fractions with similar buoyant densities ( Fig. 2A and B).…”

“…Assimilation of 13 C-labeled MTBE was detected by comparing TRFLP profiles of DNA derived from labeled treatments with DNA from unlabeled treatments. Specifically, the organisms responsible for 13 C assimilation were identified by the comparison of relative abundances of specific terminal restriction fragments (TRFs) between the labeled and unlabeled gradient fractions (see example TRFLP profiles in Fig. S1 in the supplemental material).…”

“…2A and B). A high (Ͼ30%) relative abundance (RA) of both TRFs was noted in the heavier 13 C fractions, and their RA increased over time, as MTBE was degraded (30% and 70% MTBE degraded). When ϳ30% MTBE had been degraded, the maximum RA of the 215-bp TRF from the samples ([ 13 C]MTBE-amended samples) was ϳ15% in the heavy fractions, and this increased to ϳ50% at the second time point (Fig.…”

“…The current study expands on these investigations by applying DNA-based stable isotope probing (SIP) to determine which organisms are responsible for 13 C label uptake from MTBE in anaerobic MTBE-degrading microcosms under methanogenic conditions. The SIP method is unique in that it can directly identify the microorganisms responsible for contaminant degradation and therefore offers more targeted information than community analysis alone (e.g., TRFLP, ARDRA, 16S rRNA clone libraries).…”