Unravelling habitat adaptation in the Lactobacillaceae

Species within the Lactobacillaceae are found in a multiplicity of ecological niches. However, lifestyles of lactobacilli are diverse and vary in the degree of host specificity, and it is difficult to determine the exact niches and the mechanisms underlying habitat adaptations. Here we present a machine learning tool named aurora that can identify allochthonous strains and lineages that are adapted to a particular habitat and determine the genes responsible for this adaptation. We validated aurora with two species with well-established but contrasting lifestyles: Limosilactobacillus reuteri, a host-adapted species composed of lineages that have become highly specialized to particular hosts, and Lactiplantibacillus plantarum, a generalist species without specific genomic signatures marking adaptations (a “nomadic” lifestyle). aurora successfully classified L. reuteri strains as autochthonous for rodents, poultry, porcine, primate, and human, and identified genes that underlie genotype-habitat associations, such as L-Ala-D/L-Glu epimerase, cobalt/nickel transport system, and a passive transporter to maintain Mg2+ homeostasis in rodent strains. In contrast, L. plantarum strains were identified as allochthonous to the habitats they were isolated from, confirming its status as a generalist species capable of shifting between habitats. Having successfully validated aurora, we now plan to apply the tool to other species of Lactobacillaceae to comprehensively map colonization/association factors for different habitats. In conclusion, aurora allows the determination of autochthony and genes that underpin habitat adaptation, and therefore provides information of paramount importance to unravel the ecological success and functional diversity of this group.