Bacterial Strategies of Host Colonization

Our environment exposes us to a vast array of microorganisms some of which populate our microbiomes. Research on microbiome assembly has largely focused on host features that dictate habitability, but bacterial features that promote colonization of a host, especially in non-pathogenic organisms, remain poorly understood. In the August issue of Cell Host & Microbe, Robinson et al. investigate bacterial strategies of host colonization and identify a mechanism by which bacteria use chemically regulated motility to promote rapid immigration into the host.

To identify bacterial traits that promote bacterial colonization of the host, Robinson and colleagues carried out an evolution passaging experiment in germ free (GF) zebrafish. Generation zero was inoculated with a zebrafish gut commensal isolate Aeromonas veronii and subsequent generations were treated with the pooled gut-associated Aer01 populations from the previous generation. This process was repeated for 20 generations following which genomes of isolates from different passages were sequenced and compared to the genome of the ancestral strain. One A. veronii gene commonly mutated in evolved isolates that outcompeted the ancestral isolate for host colonization is a gene the authors named spdE.

Structural evidence showed that spdE encodes a diguanylate cyclase enzyme with two functional domains: a tandem PAS/double Cache (tPAS/dCache) domain in the periplasm and a GGDEF (diguanylate cyclase) domain in the cytoplasm. Biochemical experiments revealed that the tPAS/dCache domain binds the amino acid proline—and to a lesser extent valine and isoleucine. SpdE appears to be involved in production of the second messenger cyclic diguanylate (c-di-GMP) as inhibition via ligand binding or deletion (ΔspdE) resulted in decreased intracellular c-di-GMP. Inhibition of SpdE also increased cell motility, reduced biofilm formation, and offered a competitive advantage for host colonization. Importantly, the authors found that the amino-acid ligands of SpdE act as chemoattractants for A. veronii cells. This motility response to SpdE ligand availability worked independent from chemotaxis (movement along a chemical gradient) as proline was still somewhat capable of attracting a chemotaxis defective strain (ΔcheA). Furthermore, reduced immigration into the host observed in ΔcheA compared to WT strains was rescued upon inhibition of SpdE, suggesting that even in the absence of chemotaxis, SpdE provides an advantage for host colonization.

Finally, the authors sought to determine the source of these environmental SpdE ligands. Compared to GF fish-conditioned flask media (FC-FM), A. veronii cells in conventionally reared FC-FM showed a trend toward increased motility and reduced biofilm formation, thus suggesting that the presence of a complex microbiota increased availability of SpdE ligands. Supernatant from GF fish treated with a bacterial collagenase to free proline from the amino-acid rich host protein collagen also increased cell motility, offering a potential mechanism by which the gut microbiota augments environmental SpdE ligands.

Taken together, Robinson et al. showed that host-emitted amino acid cues produced by the resident microbiota inhibit SpdE production of c-di-GMP which, in turn, promotes increased bacterial motility and enhanced colonization of the host. This work not only revealed a novel mechanism of bacterial chemokinesis that seems to optimize bacterial chemotactic tracking and movement toward a host, but also provides new insight into the principal of microbial succession. In their experiments using CR fish, the authors noted a high amount of variability in A. veronii motility responses. This was likely due to variation in the composition of host microbial communities and their different functional capacities for liberating proline from host sources. Zebrafish containing microbiomes with less microbial collagenase activity, for instance, would emit lower concentrations of amino acids into the environment. This would reduce the capacity for A. veronii to colonize the host, thus offering evidence of how a host’s microbial community history can impact new species colonization. Future work in other model organisms will be of great interest for understanding the contribution of bacterial chemokinesis to host colonization under non-aquatic living conditions.