Common occurrence of antibacterial agents in human intestinal microbiota

Abstract

Laboratory experiments have revealed many active mechanisms by which bacteria can inhibit the growth of other organisms. Bacteriocins are a diverse group of natural ribosomally synthesized antimicrobial peptides produced by a wide range of bacteria and which seem to play an important role in mediating competition within bacterial communities. In this study, we have identified and established the structural classification of putative bacteriocins encoded by 317 microbial genomes in the human intestine. On the basis of homologies to available bacteriocin sequences, mainly from lactic acid bacteria, we report the widespread occurrence of bacteriocins across the gut microbiota: 175 bacteriocins were found to be encoded in Firmicutes, 79 in Proteobacteria, 34 in Bacteroidetes, and 25 in Actinobacteria. Bacteriocins from gut bacteria displayed wide differences among phyla with regard to class distribution, net positive charge, hydrophobicity and secondary structure, but the α-helix was the most abundant structure. The peptide structures and physiochemical properties of bacteriocins produced by the most abundant bacteria in the gut, the Firmicutes and the Bacteroidetes, seem to ensure low antibiotic activity and participate in permanent intestinal host defense against the proliferation of harmful bacteria. Meanwhile, the potentially harmful bacteria, including the Proteobacteria, displayed highly effective bacteriocins, probably supporting the virulent character of diseases. These findings highlight the eventual role played by bacteriocins in gut microbial competition and their potential place in antibiotic therapy.

Structured environments fundamentally alter dynamics and stability of ecological communities

“…In the classic LV model, interaction mechanisms and fitness differences are combined into a single parameter that characterizes competition as an effective carrying capacity for the focal species relative to the density of a competitor; hence there is no differentiation between, e.g., competition for resources and toxin-mediated killing. Here, we extend the classic LV framework to reflect "active competition," where passive competition for space and nutrients (affecting carrying capacity) is decoupled from active competition mechanisms that directly impact growth rate, such as Type VI secretion system mediated killing or bacteriocin production (21,22), giving the system of partial differential equations (PDEs)…”

Structured environments fundamentally alter dynamics and stability of ecological communities

“…competition for space and toxin-mediated killing. Here, we extend the classic framework to reflect ‘active competition’, where passive competition for space and nutrients (affecting carrying capacity) is decoupled from active competition mechanisms that directly impact growth rate, such as T6SS mediated killing or bacteriocin production (16, 17), giving the partial differential equation (PDE)…”

Single strain control of microbial consortia

“…Here we suggest bacteriocins, secreted anti-microbial peptides, as such a mechanism and detail the construction and characterisation of a control system that uses them. A wide range of bacteriocins are produced in natural microbial communities such as the human intestinal microbiota [13] where they play an important role in niche competition [23]. We have previously demonstrated the ability of the bacteriocin microcin-V to improve plasmid maintenance [14]; a challenge which includes preventing competitive exclusion.…”