Spatial and Temporal Features of the Growth of a Bacterial Species Colonizing the Zebrafish Gut

Abstract

The vertebrate intestine is home to microbial ecosystems that play key roles in host development and health. Little is known about the spatial and temporal dynamics of these microbial communities, limiting our understanding of fundamental properties, such as their mechanisms of growth, propagation, and persistence. To address this, we inoculated initially germ-free zebrafish larvae with fluorescently labeled strains of an Aeromonas species, representing an abundant genus in the zebrafish gut. Using light sheet fluorescence microscopy to obtain three-dimensional images spanning the gut, we quantified the entire bacterial load, as founding populations grew from tens to tens of thousands of cells over several hours. The data yield the first ever measurements of the growth kinetics of a microbial species inside a live vertebrate intestine and show dynamics that robustly fit a logistic growth model. Intriguingly, bacteria were nonuniformly distributed throughout the gut, and bacterial aggregates showed considerably higher growth rates than did discrete individuals. The form of aggregate growth indicates intrinsically higher division rates for clustered bacteria, rather than surface-mediated agglomeration onto clusters. Thus, the spatial organization of gut bacteria both relative to the host and to each other impacts overall growth kinetics, suggesting that spatial characterizations will be an important input to predictive models of host-associated microbial community assembly.

The Gut Microbiome: Connecting Spatial Organization to Function

“…Fluorescent protein expression has been used successfully to study several pathogens (Arena et al, 2015; Muller et al, 2012) and commensals (Amar et al, 2011; Jemielita et al, 2014), although such in vivo bacterial localization studies require some persistence of the strain within the community. Moreover, to engineer protein expression within such a strain requires that the species be culturable and genetically tractable.…”

The biogeography of polymicrobial infection

“…As with in vitro biofilms, pathogenic microorganisms that are in aggregates have enhanced virulencerelated phenotypes, including accelerated growth 42 , increased stress resistance 43,44 , immune evasion 38,45–47 and transmission 37,48 . Therefore, it is important for the host to physically disperse these populations to successfully eliminate them.…”

A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development

“…Following development of the gut tube within the sterile embryo, the intestine of the emergent larva becomes open to the environment at both the mouth and the vent by 3.5 dpf, allowing for inoculation by environmental microbes (Bates et al, 2006). Within the larval gut, bacteria proliferate rapidly, such that a single species in mono-association can reach the luminal carrying capacity within several hours (Jemielita et al, 2014). …”