Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization

Abstract

Many intestinal pathogens, including Clostridioides difficile, use mucus-derived sugars as crucial nutrients in the gut. Commensals that compete with pathogens for such nutrients are therefore ecological gatekeepers in healthy guts, and are attractive candidates for therapeutic interventions. Nevertheless, there is a poor understanding of which commensals use mucin-derived sugars in situ as well as their potential to impede pathogen colonization. Here, we identify mouse gut commensals that utilize mucus-derived monosaccharides within complex communities using single-cell stable isotope probing, Raman-activated cell sorting and mini-metagenomics. Sequencing of cell-sorted fractions reveals members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae, and Bacteroidaceae families. Using this information, we assembled a five-member consortium of sialic acid and N-acetylglucosamine utilizers that impedes C. difficile’s access to these mucosal sugars and impairs pathogen colonization in antibiotic-treated mice. Our findings underscore the value of targeted approaches to identify organisms utilizing key nutrients and to rationally design effective probiotic mixtures.

Metabolic adaption to extracellular pyruvate triggers biofilm formation inClostridioides difficile

“…Thus, we tested if mucus-derived sugars potentiate DOC-induced biofilm formation. Mucus is typically broken down into different hexose sugars including glucose, GlcNAc, fucose, Neu5Ac, galactose and N-acetylgalactosamine (GalNAc) and GlcNac and Neu5Ac acquisition is important for C. difficile growth in the intestinal tract (Ng et al, 2013; Pereira et al, 2020). We tested the effect of these sugars on biofilm formation.…”

“…Depending on the composition of the microbiota, C. difficile could encounter favourable conditions that would include sub-inhibitory concentrations of DOC, and availability of specific amino acids, mucus-derived sugars, and pyruvate (Abbas and Zackular, 2020; Girinathan et al, 2020; Pereira et al, 2020). Under these favourable conditions, sub-inhibitory concentration of DOC would trigger a metabolic adaptation in C. difficile to use the available metabolites produced by the microbiota.…”

“…GlcNac and Neu5Ac acquisition is important for C. difficile growth in the intestinal tract (Ng et al, 2013;Pereira et al, 2020). We tested the effect of these sugars on biofilm formation.…”

“…Once ingested from the surrounding environment or food, spores germinate in the ileum and then vegetative cells colonize the caecum (Crobach et al, 2018; Lim et al 2020). Successful colonization relies on the disruption of the host’s microbiota (Abbas and Zackular, 2020; Ghimire et al 2020; Girinathan et al, 2020; Pereira et al, 2020). The microbiota protects against C. difficile infection by producing metabolites including deoxycholic acid (DOC) and short chain fatty acids (SCFA) (Buffie et al, 2015; Studer et al 2016; McDonald et al, 2018; Sobach et al 2018; Seekatz et al, 2018).…”

Gut microbiota dynamics in carnivorous European seabass (Dicentrarchus labrax) fed plant-based diets

“…Although carbohydrates-metabolism has been exhaustively studied in different microorganisms, including gut ones, and there is enough genomic information (both from individual microorganisms and metagenomics studies) confirming that gut microorganisms possess the necessary enzymatic tools to metabolize different NSPs, it is not known which of these organisms are indeed capable of such metabolizing jobs within the complex context of natural gut communities and if metabolic pathways, capabilities and preferences determined in vitro will be replicated inside the gut. A sophisticated and targeted-approach was recently employed to reveal microbes within the mouse complex gut community with the capacity to utilize mucosal sugars 86 . Similar studies are needed to exploit specific NSP-microbiota interactions in aquaculture fish to fully unveil the underlying mechanisms determining the fate of specific NSP and its effect on fish performance, fish health and nutrient digestibility 39 .…”