Host Gut Motility and Bacterial Competition Drive Instability in a Model Intestinal Microbiota

Abstract

30The gut microbiota is a complex consortium of microorganisms with the ability to 31 influence important aspects of host health and development. Harnessing this 'microbial 32 organ' for biomedical applications requires clarifying the degree to which host and 33 bacterial factors act alone or in combination to govern the stability of specific lineages. 34To address this we combined bacteriological manipulation and light sheet fluorescence 35 microscopy to monitor the dynamics of a defined two-species microbiota within the 36 vertebrate gut. We observed that the interplay between each population and the gut 37 environment produced distinct spatiotemporal patterns. Consequently, one species 38 dominates while the other experiences dramatic collapses that are well fit by a 39 stochastic mathematical model. Modeling revealed that bacterial competition could only 40 partially explain the observed phenomena, suggesting that a host factor is also 41 important in shaping the community. We hypothesized the host determinant to be gut 42 motility, and tested this mechanism by measuring colonization in hosts with enteric 43 nervous system dysfunction due to mutation in the Hirschsprung disease locus ret. In 44 mutant hosts we found reduced gut motility and, confirming our hypothesis, robust 45 coexistence of both bacterial species. This study provides evidence that host-mediated 46 spatial structuring and stochastic perturbation of communities along with bacterial 47Zebrafish larvae are highly amenable to gnotobiotic techniques and can be reared 99 germ-free (GF) in large numbers [19]. At four days post-fertilization (dpf) larvae possess 100 an open and functional digestive tract that is permissive to microbial colonization, the 101 timing of which is controlled by adding bacteria to the water column. Importantly, larval 102 zebrafish share many physiological traits with humans, including aspects of innate 103 immunity, neurological development, and intestinal function [20]. Therefore, interactions 104 between zebrafish and their microbial symbionts are expected to reflect analogous 105 interactions that occur in other vertebrates. LSFM, combined with the optical 106 transparency of larval zebrafish, enables three-dimensional visualization of the entire 107 intestine with single-bacterium resolution, rapid image acquisition to avoid blurring due 108 to intestinal motility, and extended live imaging with low phototoxicity [21, 22]. This 109 experimental setup provides an unprecedented opportunity to investigate ecological 110 interactions within the vertebrate intestine at a range of spatial and temporal scales. 111 With this model system we found that an apparent competitive interaction 112 between two species native to the zebrafish gut, Aeromonas veronii and Vibrio 113 cholerae, is characterized by sudden and catastrophic collapses of the Aeromonas 114 population, which appear to be driven by mechanical forces related to host intestinal 115 motility. The differential behavior of these two species can be explained by their ...

Stochastic Assembly Produces Heterogeneous Communities in theC. elegansIntestine

“…Similarly, these parameters may change in value over time (and therefore over the course of an experiment) for individual worms. In addition, the demographics of bacterial growth and death may change as worms age [18,28,29], and excretion from the worm may occur in discrete pulses consisting of many individuals, as recently observed in a zebrafish model [30]. These sources of variation could have profound effects on community composition, particularly in more complex cases where there are higher numbers of colonizing species and 230 where the colonists do not compete neutrally, or where interactions between bacteria and host occur over evolutionary time [31].…”