Abstract
Limosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.
Highlights
Limosilactobacillus reuteri is a Gram-positive bacterial symbiont that has been recently reclassified from Lactobacillus reuteri (Zheng et al, 2020)
To predict the phylogenetic features of L. reuteri in metagenome samples, we profiled the composition of Genome-Based Strain Types (GSTs)
(1) As shown in Supplementary Figure 2, our phylogenetic tree is similar to a previously published tree (Duar et al, 2017; Yu et al, 2018), which makes it possible to assign our GSTs to host-specific lineages reported before and to profile metagenome samples with those lineages (Figures 2C,E)
Summary
Limosilactobacillus reuteri is a Gram-positive bacterial symbiont that has been recently reclassified from Lactobacillus reuteri (Zheng et al, 2020). Host-Association of Limosilactobacillus reuteri previously been studied through amplified-fragment length polymorphism, multi-locus sequence analysis, and core-genome phylogeny (Oh et al, 2010; Wegmann et al, 2015; Yu et al, 2018). These studies identified genetically distinct subpopulations that highly correlate with their host, indicating a stable host-symbiont relationship. The transfer from one individual host to another could simultaneously occur in different host populations, resulting in distinct phylogenetic lineages, even in the same host species (Wegmann et al, 2015)
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