Strain matters: host responses reflect symbiont origin in the squid-vibrio symbiosis

Understanding the cause and consequences of bacterial strain variation remains a challenge in the study of symbioses. While the diverse reactions of the host immune system to strain variants have been well studied in pathogenesis, much less is known about how strain variation influences beneficial associations. From the complex vertebrate gut microbiome to the more tractable invertebrate models of symbiosis, the host's cellular and molecular responses to this diversity remain largely a mystery. Here, we explore strain diversity in Vibrio fischeri, the bioluminescent bacterial symbiont of the Hawaiian bobtail squid, Euprymna scolopes. Phylogenetic analyses of the genomes of 62 V. fischeri strains, including 50 light organ-associated and 12 planktonic isolates, revealed several genes that were absent in planktonic strains, but uniformly present in symbiotic ones. To better understand the consequences of this diversity to the host, we selected five light-organ associated strains: three from E. scolopes but having different combinations of colonization factors, one from a congeneric squid host, and one from a marine fish. We colonized juvenile E. scolopes with these strains and, using RNAseq, found that (i) the most similar host transcriptomic responses occurred among the native E. scolopes strains, (ii) intermediate was the strain from the related squid, and (iii) least similar was the fish strain. Importantly, native strains downregulated immune-related genes more than non-native ones. Finally, host development was atypical or delayed when colonized by non-native strains. These experiments point the way to more targeted studies of the mechanisms underlying host responses to symbiont strain diversity.

Variation among strains of a bacterial species is a powerful factor underlying the intensity of host responses during pathogenic infections. Less is known about the cellular and molecular responses of host tissues to differences between the strains present in an animal's normal microbiome. We use a natural, species-specific, symbiosis to explore the influence of strain-level differences on host gene expression and morphogenesis. Analysis of symbiotic strains from squids and fishes, as well as free-living strains, shows that the carriage of colonization determinants, while critical to competitive success among strains of a species, has a minimal effect on the transcriptional response of the host. We provide evidence that a more important driver of normal gene expression during the development of symbiosis is the history of a strain's co-diversification with its host species. Such studies, using simple invertebrate models, allow the recognition of otherwise obscured interactions underlying the more complex microbiomes of vertebrates.