A phylogenomic view of ecological specialization in the Lachnospiraceae, a family of digestive tract-associated bacteria

Several bacterial families are known to be highly abundant within the human microbiome, but their ecological roles and evolutionary histories have yet to be investigated in depth. One such family, Lachnospiraceae (phylum Firmicutes, class Clostridia) is abundant in the digestive tracts of many mammals and relatively rare elsewhere. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of this group with the production of butyric acid, a substance that is important for both microbial and host epithelial cell growth. We examined the genomes of 30 Lachnospiraceae isolates to better understand the phylogenetic relationships and basis of ecological differentiation within this group. Although this family is often used as an indicator of butyric acid production, fewer than half of the examined genomes contained genes from either of the known pathways that produce butyrate, with the distribution of this function likely arising in part from lateral gene transfer. An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possessed genes for endospore formation while other members of this family lacked key sporulation-associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity and bovine rumen. Our analysis demonstrates that despite a lack of agreement between Lachnospiraceae phylogeny and assigned habitat there are several examples of genetic signatures of habitat preference derived from both lateral gene transfer and gene loss.