title: 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.
  
  
  OBJECTIVE
  Our intestines are home to vast numbers of microbes that influence many aspects of health and disease. Though we now know a great deal about the constituents of the gut microbiota, we understand very little about their spatial structure and temporal dynamics in humans or in any animal: how microbial populations establish themselves, grow, fluctuate, and persist. To address this, we made use of a model organism, the zebrafish, and a new optical imaging technique, light sheet fluorescence microscopy, to visualize for the first time the colonization of a live, vertebrate gut by specific bacteria with sufficient resolution to quantify the population over a range from a few individuals to tens of thousands of bacterial cells. Our results provide unprecedented measures of bacterial growth kinetics and also show the influence of spatial structure on bacterial populations, which can be revealed only by direct imaging.
authors.affiliation: Department of Physics, University of Oregon, Eugene, Oregon, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Jemielita
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Taormina
authors.affiliation: Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA.
authors.forename: Adam R
authors.initials: AR
authors.lastname: Burns
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Hampton
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
authors.forename: Annah S
authors.initials: AS
authors.lastname: Rolig
authors.affiliation: Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Guillemin
authors.affiliation: raghu@uoregon.edu.
authors.forename: Raghuveer
authors.initials: R
authors.lastname: Parthasarathy
mesh_terms: D000333:Aeromonas / Q000254:growth & development*; D000818:Animals; D058491:Bacterial Load; D041981:Gastrointestinal Tract / Q000382:microbiology*; D021621:Imaging, Three-Dimensional; D008856:Microscopy, Fluorescence; D062211:Spatio-Temporal Analysis; D013194:Staining and Labeling; D015027:Zebrafish / Q000382:microbiology*