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Aeromonas salmonicida is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies (pectinolytica) and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (Recurvirostra avosetta), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known A. salmonicida subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical A. salmonicida psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host Dictyostelium discoideum amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that A. salmonicida can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive A. salmonicida’s natural environment.

The bacterial species Aeromonas salmonicida officially has five subspecies. A large majority of the currently available sequences come from Aeromonas salmonicida subsp. salmonicida, which causes furunculosis in salmonids. We present the genomic sequences of four Aeromonas salmonicida subsp. achromogenes strains. This will help increase the robustness of genomic analyses for this subspecies.

It is becoming increasingly clear that wild animals have never existed without symbiotic interactions with microbiota. Therefore, investigating relationships between microbiota and their host is essential towards a full understanding of how animal evolve and adapt to their environment. The Lake Whitefish (Coregonus clupeaformis) is a well-documented model for the study of ecological speciation, where the dwarf species (limnetic niche specialist) evolved independently and repeatedly from the normal species (benthic niche specialist). In this study, we compared the transient intestinal microbiota among five wild sympatric species pairs of whitefish as well as captive representatives of dwarf and normal species and their reciprocal hybrids reared in identical controlled conditions. We sequenced the 16s rRNA gene V3-V4 regions of the transient intestinal microbiota present in a total of 185 whitefish to (i) test for parallelism in the transient intestinal microbiota among sympatric pairs of whitefish, (ii) test for transient intestinal microbiota differences among dwarf, normal and both hybrids reared under identical conditions and (iii) compare intestinal microbiota between wild and captive whitefish. A significant effect of host species on microbiota taxonomic composition was observed in the wild when all lakes where analyzed together, and species effect was observed in three of the five species pairs. In captive whitefish, an influence of host (normal, dwarf and hybrids) was also detected on microbiota taxonomic composition and tens of genera specific to dwarf, normal or hybrids were highlighted. Hybrid microbiota was not intermediate; instead its composition fell outside of that observed in the parental forms and this was observed in both reciprocal hybrid crosses. Interestingly, six genera formed a bacterial core which was present in captive and wild whitefish, suggesting a horizontal microbiota transmission. Although diet appeared to be a major driving force for microbiota evolution, our results suggested a more complex interaction among the host, the microbiota and the environment leading to three distinct evolutionary paths of the intestinal microbiota.