Context-Dependent Competition in a Model Gut Bacterial Community

Abstract

Understanding the ecological processes that generate complex community structures may provide insight into the establishment and maintenance of a normal microbial community in the human gastrointestinal tract, yet very little is known about how biotic interactions influence community dynamics in this system. Here, we use natural strains of Escherichia coli and a simplified model microbiota to demonstrate that the colonization process on the strain level can be context dependent, in the sense that the outcome of intra-specific competition may be determined by the composition of the background community. These results are consistent with previous models for competition between organisms where one competitor has adapted to low resource environments whereas the other is optimized for rapid reproduction when resources are abundant. The genomic profiles of E. coli strains representing these differing ecological strategies provide clues for deciphering the genetic underpinnings of niche adaptation within a single species. Our findings extend the role of ecological theory in understanding microbial systems and the conceptual toolbox for describing microbial community dynamics. There are few, if any, concrete examples of context-dependent competition on a single trophic level. However, this phenomenon can have potentially dramatic effects on which bacteria will successfully establish and persist in the gastrointestinal system, and the principle should be equally applicable to other microbial ecosystems.

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

“…Many host-specific factors have been studied, including host species, genotype, diet and health (Rawls et al, 2006;Turnbaugh et al, 2006;Benson et al, 2010;Goodrich et al, 2014), as well as microbe-specific factors, including mutualistic and competitive interactions (de Muinck et al, 2013;Levy and Borenstein, 2013). While the list of potential factors is long, they can be divided into two major categories: selective processes, in which microbes establish and thrive in an environment (in this case the host itself) due to differences in their relative ecological fitness; and neutral processes, which include the dynamics of passive dispersal (for example, sampling individuals from a source pool of available colonists) and the effects of ecological drift (the stochastic loss and replacement of individuals; Chase and Myers, 2011).…”

Understanding Microbiome Data: A Primer for Clinicians

“…and interactions between all of these actors. Interactions between microorganisms are beginning to be depicted through predatorprey models [5] and/or context-dependent competition [6] . Co-evolution of microorganisms and host provide a beneficial symbiotic relationship; thus, besides the biotic interactions that influence community dynamics, symbiotic events occur between microorganisms and host determinants shaping the microbial community as well as the local conditions [7,8] .…”

Biotic interactions and temporal dynamics of the human gastrointestinal microbiota

“…In vitro studies of GI bacteria have even shown that strain-level dynamics can be determined by interactions with very distantly related taxa (de Muinck et al, 2013). This suggests that the dynamics can be modulated by biotic interactions across taxonomic levels.…”

“…In the case of the GI microbiota, this is, in general, not a viable option as most species are non-cultivable (Zoetendal et al, 2004). Also, the form of a pairwise interaction may depend upon the environmental context in which it takes place (de Muinck et al, 2013), making extrapolation from laboratory experiments to natural systems problematic.…”