Phylogenetic distribution of genes encoding β‐glucuronidase activity in human colonic bacteria and the impact of diet on faecal glycosidase activities

Abstract

Bacterial β-glucuronidase in the human colon plays an important role in cleaving liver conjugates of dietary compounds and xenobiotics, while other glycosidase activities are involved in the conversion of dietary plant glycosides. Here we detected an increase in β-glucuronidase activity in faecal samples from obese volunteers following a high-protein moderate carbohydrate weight-loss diet, compared with a weight maintenance diet, but little or no changes were observed when the type of fermentable carbohydrate was varied. Other faecal glycosidase activities showed little or no change over a fivefold range of dietary NSP intake, although α-glucosidase increased on a resistant starch-enriched diet. Two distinct groups of gene, gus and BG, have been reported to encode β-glucuronidase activity among human colonic bacteria. Degenerate primers were designed against these genes. Overall, Firmicutes were found to account for 96% of amplified gus sequences, with three operational taxonomic units particularly abundant, whereas 59% of amplified BG sequences belonged to Bacteroidetes and 41% to Firmicutes. A similar distribution of operational taxonomic units was found in a published metagenome dataset involving a larger number of volunteers. Seven cultured isolates of human colonic bacteria that carried only the BG gene gave relatively low β-glucuronidase activity that was not induced by 4-nitrophenyl-β-D-glucuronide. By comparison, in three of five isolates that possessed only the gus gene, β-glucuronidase activity was induced.

Phylogenetic distribution of three pathways for propionate production within the human gut microbiota

“…The deduced protein sequences of mmdA from V. parvula (accession number ZP_06259922), lcdA from C. propionicum (AEM62994) and pduP and pduQ from R. inulinivorans (ABC25528 and ABC25529) were blasted (tblastn) against the metagenomic data set comprising 124 European individuals (Qin et al, 2010) on the in-house Rowett/ BioSS Beowulf cluster as described before (McIntosh et al, 2012). Matches with at least 50% sequence identity for LcdA and 55% for PduP and PduQ were selected on the basis of the blastp results in the non-redundant (nr) database indicating which identity level is likely to represent a true hit (460% for LcdA, as blastp results with query sequence AEM62994 had at least 60% identity for strains known to carry this pathway, followed by a sharp drop in sequence identity to p43% for other matches; 465% for PduP and PduQ, as blastp results with query sequences ABC25528/9 had at least 73% identity for strains known to carry this pathway, followed by a sharp drop in sequence identity to p58%; for PduP (but not PduQ) two matches of 63% identity were also present in Thermoanaerobacterium spp.).…”

The Human Fecal Microbiota Metabolizes Deoxynivalenol and Deoxynivalenol-3-Glucoside and May Be Responsible for Urinary Deepoxy-Deoxynivalenol

“…This high rate of hydrolysis observed in all 5 volunteers studied suggests that the human microbiota will completely hydrolyze DON-3-glucoside within the normal residence time in the human colon. ␤-Glycosidase activity is common among intestinal bacteria, and most human colonic microbiota will possess this activity (22). The release of DON from D3G suggests that the colonic epithelium will be exposed to significant levels of free DON, as the masked mycotoxin D3G is present at approximately 17% of free DON in cereal samples (8).…”

Functional Metagenomics of Human Intestinal Microbiome β-Glucuronidase Activity

“…A recent study that compared levels of human fecal b-glucuronidase activity with overall community diversity also concluded that b-glucuronidase activity was mostly due to particular taxa rather than the wider community (Flores et al 2012). Interestingly, the phylogenetic relationship of gus genes in known bacteria often did not agree with their relatedness based on the 16S rRNA gene sequence (McIntosh et al 2012), which is commonly used to classify bacteria phylogenetically. Thus, it appears that the gus gene has been obtained by horizontal gene transfer in several bacteria.…”

“…The data were therefore compared to a large metagenomic sequence library of 85 healthy human volunteers (Qin et al 2010), which showed that the vast majority of sequences had indeed been captured by the degenerate PCR approach (McIntosh et al 2012). There were slight differences in relative abundance, which is not surprising considering the difference in technical approach as well as volunteer numbers, but overall both approaches correlated significantly in terms of relative abundance as well as prevalence of different OTUs.…”

“…Human fecal metagenomic sequences can be searched to establish the distribution of b-glucuronidases within the human gut community. Degenerate primers targeting highly conserved regions were designed to amplify both types of b-glucuronidase gene from human fecal DNA (McIntosh et al 2012). This revealed that the gus gene is present in many different phylogenetic groups, whereas the BG gene appears only to be present in bacteria related to Bacteroidetes and Firmicutes.…”