Environmental and Gut Bacteroidetes: The Food Connection

Abstract

Members of the diverse bacterial phylum Bacteroidetes have colonized virtually all types of habitats on Earth. They are among the major members of the microbiota of animals, especially in the gastrointestinal tract, can act as pathogens and are frequently found in soils, oceans and freshwater. In these contrasting ecological niches, Bacteroidetes are increasingly regarded as specialists for the degradation of high molecular weight organic matter, i.e., proteins and carbohydrates. This review presents the current knowledge on the role and mechanisms of polysaccharide degradation by Bacteroidetes in their respective habitats. The recent sequencing of Bacteroidetes genomes confirms the presence of numerous carbohydrate-active enzymes covering a large spectrum of substrates from plant, algal, and animal origin. Comparative genomics reveal specific Polysaccharide Utilization Loci shared between distantly related members of the phylum, either in environmental or gut-associated species. Moreover, Bacteroidetes genomes appear to be highly plastic and frequently reorganized through genetic rearrangements, gene duplications and lateral gene transfers (LGT), a feature that could have driven their adaptation to distinct ecological niches. Evidence is accumulating that the nature of the diet shapes the composition of the intestinal microbiota. We address the potential links between gut and environmental bacteria through food consumption. LGT can provide gut bacteria with original sets of utensils to degrade otherwise refractory substrates found in the diet. A more complete understanding of the genetic gateways between food-associated environmental species and intestinal microbial communities sheds new light on the origin and evolution of Bacteroidetes as animals’ symbionts. It also raises the question as to how the consumption of increasingly hygienic and processed food deprives our microbiota from useful environmental genes and possibly affects our health.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

“…Indeed, half of the OTUs specialised on allochthonous DOC belonged to the Flavobacteriaceae and Chitinophagaceae (phylum Bacteroidetes; Table 1). Members of these groups have been reported to degrade complex biopolymers (Kirchman, 2002), as are generated during the degradation of plant material (Thomas et al, 2011). Interestingly, Bacteroidetes were also found to be prominent in the phyllosphere and to be more abundant on conifers than on Angiosperms (Redford et al, 2010;Thomas et al, 2011).…”

Lateral gene transfer between the Bacteroidetes and Acidobacteria: The case of α‐l‐rhamnosidases

“…The latter are an important structural component of plant cell walls and, therefore, a-L-rhamnosidases are among the enzymes required for decomposition of plant debris. The wide occurrence of these enzymes in members of the well-studied phylum Bacteroidetes appears to be logical since this bacterial group is regarded as being specialized in the degradation of high molecular weight organic matter (reviewed in [8]). The abilities to efficiently degrade complex biopolymers and to colonize surfaces determine wide distribution of the Bacteroidetes in various environments, where they play a key role in degradation of plant-derived organic matter, one of the major processes mediated by microorganisms in the global carbon cycle.…”

“…Notably, the most abundant groups of proteins in both families (108 and 57 proteins in GH78 and GH106, respectively) originate from bacteria of the phylum Bacteroidetes (according to CAZy; Table 1). This is not surprising since members of this phylum are known as efficient degraders of various macromolecules including complex polysaccharides [8]. Genomes of these bacteria contain a significant number of genes encoding carbohydrate-processing enzymes [8][9][10][11].…”

Early-Life Sugar Consumption Affects the Rat Microbiome Independently of Obesity

“…For example, an HFD reduces populations in the phylum Bacteroidetes and increases both Firmicutes and Proteobacteria relative to control diets that are 10-15% kilocalories from fat with complex carbohydrates (starch) as the primary carbohydrate source (18,19). Bacteroidetes aid in promoting T cell-mediated immune responses in the host and prevent the overgrowth of more harmful pathogens (20)(21)(22), whereas Proteobacteria and Firmicutes are generally associated with gut dysbiosis (23) and obesity (24), respectively. However, given that rodent HFD models produce obesity and metabolic syndrome, it is unclear whether HFD-mediated gut microbiome alterations are based directly on dietary factors or, rather, are secondary to increased adiposity and associated metabolic derangements.…”