A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota

Abstract

The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.

The importance of host physical niches for the stability of gut microbiome composition

“…The specificity of a beneficial host-microbe association is determined by both the host and the microbe, and there are various degrees of specificity with different mechanisms [11,13,15,19,28]. When the host constructs a physical niche that selectively binds with molecular specificity certain bacteria to the exclusion of others, this represents one of the highest degrees of host control [13,32]. By requiring such a high degree of specificity in a physical niche, a host can recruit specific bacteria from the highly diverse pool in the environment without falling vulnerable to pathogen invasion of the niche.…”

“…This physical barrier and the constricted region together prevent invasion by external bacteria [64]. The niche in the Drosophila foregut also has a pouch-like element, called the crop, but it is not sealed off from invading bacteria [32,66,67]. Instead, the bacteria physically adhere to the wall of the niche.…”

“…The assays rely on the fly's consumption of germ-free food to push unstable colonizers out of the gut. While flies typically feed on microbe-rich food, the gut clearing approaches that identified stable colonizers both used food with maintained sterility to prevent the reintroduction of bacteria [32,66,67]. Gut clearance techniques have been established in mammals with the similar goal to isolate the stable colonizers [71].…”

“…To test the robustness of colonization, perturbation assays have been employed. In flies, a pulse-chase technique was developed to push out unstably adhered cells and measure the kinetics of the population turnover as a half-life [32]. This revealed a half-life on the order of weeks for a subpopulation of bacteria in the physical niche.…”

When the microbiome shapes the host: immune evolution implications for infectious disease

“…In this way, host immune signalling is uniquely activated by the presence of pathogens, but less so by mutualists, despite the same immune architecture sensing MAMPs common to both bacteria [5]. This physical separation of mutualist microbes from the surveilling elements of the systemic immune response is a common strategy of insects with obligate symbionts, which have evolved specialized immune-competent tissues in which they house their beneficial microbes [14][15][16].…”