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

Abstract

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 manymammals and relatively rare else where. Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association ofmany species within the 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 origin of butyric acid capabilities and other ecological adaptations within this group. Butyric acid production-related genes were detected in fewer than half of the examined genomes with the distribution of this function likely arising in part from lateral gene transfer (LGT). An investigation of environment-specific functional signatures indicated that human gut-associated Lachnospiraceae possess genes for endospore formation, where as other members of this family lack key sporulation associated genes, an observation supported by analysis of metagenomes from the human gut, oral cavity, and bovine rumen. Our analysis demonstrates that adaptation toanecological niche and acquisition of defining functional roles withina microbiomecan arise through a combination of both habitat-specific gene loss and LGT. © The Author(s) 2014.