Population dynamics of microbiota bacteria lead morphogenetic variations, phenotypic pathogenesis shifts and antimicrobial resistance expression

Abstract

The wide and essential role of the gut microbiota includes fending off pathogens, enabling nutrient generation, metabolism and absorption, participating in the development of immune and nervous system and more. Although correlational research has given us an insight on the microbiota composition, a mechanistic understanding of microbial population coordination and dynamics and its impact on the host health remains a key challenge. For example, the process that leads commensal microbiota players to become pathogens, and the factors that limit the establishment of incoming healthy bacteria (probiotics) have not been fully elucidated. Likewise, the critical involvement of micronutrients on microbial selection is at its infancy.
The primary aim of this PhD Thesis was to investigate the differential prevalence of a subset of bacterial species commonly encountered in the gut as commensal or as pathogens to better understand bacterial population dynamics and competition. Specifically, we aimed to elucidate bacterial population dynamics in response to an underrated but emerging potential pathogen, Serratia marcescens, and external factors such as the micronutrient zinc. To study such a complex ecosystem, we used a bottom-up approach of in vitro co-culture competition experiments with pairs of bacterial species (Escherichia coli, Serratia marcescens, Pseudomonas aeruginosa, Proteus vulgaris, Klebsiella aerogenes, Staphylococcus aureus, Enterococcus faecalis, Lactobacillus plantarum and Streptococcus salivarius). A rich microbiological media was used as a surrogate for the postprandial intestine.
While no difference in prevalence was observed in pairwise competitions between strains of E. coli and S. marcescens, we have identified a novel phenomenon where S. marcescens in co-culture with E. coli exhibited a differential spatial geometric distribution on solid media with the appearance of a “bull’s eye” pattern. The pattern only and consistently appeared in well-defined conditions (cell density, temperature, nutrients). This morphogenetic pattern was accompanied by phenotypic changes that affected virulence and antimicrobial resistance, a novel and cutting-edge finding that may help to design effective intervention tools to treat infectious diseases and tackle antibiotic resistance. The phenomenon was mathematically modelled, and the outcome suggested the need to increase model complexity thus informing biological research going forward. We also observed that P. aeruginosa prevailed over some Gram-positive cocci (S. aureus and S. streptococcus) and S. marcescens, and that Lactobacillus plantarum inhibited the growth of selected Gram-negatives.
Our results established proof of concept regarding bacterial behaviours and morphogenetic variations that can be harnessed to explore genome-wide changes and related virulence and pathogenesis mechanisms, and may enrich the microbiota-linked prevention and infections management.