Putative Antimicrobial Peptides Within Bacterial Proteomes Affect Bacterial Predominance: A Network Analysis Perspective.

Anastasis Oulas,Christos T Chasapis,Alexios Vlamis-Gardikas,Georges Pierre Schmartz,Umer Z Ijaz,Margarita Zachariou,Marios Tomazou,George M Spyrou

doi:10.3389/fmicb.2021.752674

Abstract

The predominance of bacterial taxa in the gut, was examined in view of the putative antimicrobial peptide sequences (AMPs) within their proteomes. The working assumption was that compatible bacteria would share homology and thus immunity to their putative AMPs, while competing taxa would have dissimilarities in their proteome-hidden AMPs. A network–based method (“Bacterial Wars”) was developed to handle sequence similarities of predicted AMPs among UniProt-derived protein sequences from different bacterial taxa, while a resulting parameter (“Die” score) suggested which taxa would prevail in a defined microbiome. T he working hypothesis was examined by correlating the calculated Die scores, to the abundance of bacterial taxa from gut microbiomes from different states of health and disease. Eleven publicly available 16S rRNA datasets and a dataset from a full shotgun metagenomics served for the analysis. The overall conclusion was that AMPs encrypted within bacterial proteomes affected the predominance of bacterial taxa in chemospheres.

Highlights

In terms of species and population, bacterial communities occur in dynamic equilibria related to environmental factors that drive interspecies competition and coexistence
Microcins are class I bacteriocins with pluripotent inhibitory actions that may act in synergy with the larger colicins for even broader inhibition effects (Baquero et al, 2019)
The database was queried to form networks of bacterial interactions based on the number of common antimicrobial peptide sequences (AMPs)

Summary

Introduction

In terms of species and population, bacterial communities occur in dynamic equilibria related to environmental factors that drive interspecies competition and coexistence. In a close contact intercellular war, they may inject lethal molecules (peptidoglycan hydrolases, phospholipases, pore forming proteins, DNases, RNases, NAD(P)+ hydrolases, and ADP-ribosyltransferase among others), to suppress antagonistic species using the type VI secretion system (Coulthurst, 2019; Ross et al, 2019) Another type of antagonism is the secretion of toxic molecules destined for competitors (Richards et al, 2017). The term describes a broad and Putative Antimicrobial Peptides Affect Bacterial Predominance heterogenous category of molecules that can inhibit bacterial growth while being present in a defined contained environment (chemosphere) (Baquero et al, 2019) They are roughly divided in two categories: one of transmembrane proteins [colicins (Kleanthous, 2010)] and another of peptides (class I bacteriocins) (Riley and Wertz, 2002). Bacteriocins have a narrow target range and are designed to benefit the species that produces them over its closely related competitors

Methods

Results

Conclusion