A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria

TLDR

Lachnospiraceae, a highly abundant Firmicutes family in mammalian guts, is linked to obesity and colon cancer protection through butyrate production, yet its ecological roles and evolutionary history remain largely unexplored. The study examined 30 Lachnospiraceae genomes to elucidate the origins of butyrate production and other ecological adaptations. The authors analyzed 30 genomes and metagenomes, identifying environment‑specific functional signatures such as endospore‑formation genes in human gut strains but not in other lineages. Less than half of the 30 Lachnospiraceae genomes encode butyrate‑producing genes, a trait likely acquired via lateral gene transfer, while gut‑associated strains uniquely carry endospore‑formation genes absent in other lineages, illustrating that niche adaptation arises from both gene loss and horizontal transfer.

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 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 many 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, whereas 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 to an ecological niche and acquisition of defining functional roles within a microbiome can arise through a combination of both habitat-specific gene loss and LGT.