Microbial communities in animal guts are composed of diverse, specialized bacterial species, but little is known about how gut bacteria diversify to produce genetically and ecologically distinct entities. The gut microbiota of the honey bee, Apis mellifera , presents a useful model, because it consists of a small number of characteristic bacterial species, each showing signs of diversification. Here, we used single-cell genomics to study the variation within two species of the bee gut microbiota: Gilliamella apicola and Snodgrassella alvi . For both species, our analyses revealed extensive variation in intraspecific divergence of protein-coding genes but uniformly high levels of 16S rRNA similarity. In both species, the divergence of 16S rRNA loci appears to have been curtailed by frequent recombination within populations, while other genomic regions have continuously diverged. Furthermore, gene repertoires differ markedly among strains in both species, implying distinct metabolic capabilities. Our results show that, despite minimal divergence at 16S rRNA genes, in situ diversification occurs within gut communities and generates bacterial lineages with distinct ecological niches. Therefore, important dimensions of microbial diversity are not evident from analyses of 16S rRNA, and single cell genomics has potential to elucidate processes of bacterial diversification. Author Summary Gut microbial communities are often complex, consisting of bacteria from divergent phyla as well as multiple strains of each of the constituent species. But because the composition of these communities is typically assessed using 16S rRNA analyses, little is known about genomic changes associated with in situ diversification of bacterial lineages in animal guts. We undertook a single-cell genomic approach to investigate the diversification within two species of the gut microbiota of honey bees. Each species exhibited a surprisingly high level of genomic variation, despite uniformity in the 16S rRNA sequences. Our data indicate that genetically and ecologically distinct lineages can evolve in the gut of the same host species in the presence of frequent recombination at 16S rRNA genes. These findings parallel observations from mammals, suggesting that in situ diversification of a few bacterial lineages is a common pattern in the evolution of gut communities.
【초록키워드】 Evolution, observations, Variation, 16S rRNA, Lineage, Recombination, Community, Bacteria, gut microbiota, characteristic, Strains, microbial community, rRNA, Bacterial, Analysis, strain, Gut, microbial, ecological niches, honey bees, honey bee, observation, Divergence, genomic region, complex, protein-coding gene, genomic variation, mammals, uniformity, bacterial species, 16S rRNA analyses, 16S rRNA genes, 16S rRNA loci, 16S rRNA sequences, 16S rRNA similarity, coding genes, Gilliamella apicola, gut bacteria, Microbial communities, protein-coding genes, single cell genomics, single-cell genomics, guts, dimension, Host, approach, populations, composed, generate, exhibited, appear, occur, genomic change, single-cell genomic, Snodgrassella alvi, 【제목키워드】 Genomics, Honey, bee, Diversity, honey bee,