Studying the host-associated butyrate-producing bacterial community is important, because butyrate is essential for colonic homeostasis and gut health. Previous research has identified the butyryl coenzyme A (CoA):acetate-CoA transferase (EC 2.3.8.3) as a gene of primary importance for butyrate production in intestinal ecosystems; however, this gene family (but) remains poorly defined. We developed tools for the analysis of butyrate-producing bacteria based on 12 putative but genes identified in the genomes of nine butyrate-producing bacteria obtained from the swine intestinal tract. Functional analyses revealed that eight of these genes had strong But enzyme activity. When but paralogues were found within a genome, only one gene per genome encoded strong activity, with the exception of one strain in which no gene encoded strong But activity. Degenerate primers were designed to amplify the functional but genes and were tested by amplifying environmental but sequences from DNA and RNA extracted from swine colonic contents. The results show diverse but sequences from swine-associated butyrate-producing bacteria, most of which clustered near functionally confirmed sequences. Here, we describe tools and a framework that allow the bacterial butyrate-producing community to be profiled in the context of animal health and disease.
IMPORTANCEButyrate is a compound produced by the microbiota in the intestinal tracts of animals. This compound is of critical importance for intestinal health, and yet studying its production by diverse intestinal bacteria is technically challenging. Here, we present an additional way to study the butyrate-producing community of bacteria using one degenerate primer set that selectively targets genes experimentally demonstrated to encode butyrate production. This work will enable researchers to more easily study this very important bacterial function that has implications for host health and resistance to disease. S hort-chain fatty acids (SCFAs) play a central role in the maintenance of colonic homeostasis, which is the delicate balance between the host, its immune system, and the gastrointestinal microbial partners (1). Butyrate in particular has potent effects on host tissues. As with other SCFAs, butyrate is consumed by the host as an energy source; however, unlike the other common SCFAs, such as propionate and acetate, butyrate is the preferred energy source for colonocytes (2) and is rapidly absorbed and used by the colonic epithelium. This rapid oxidation of butyrate reduces local oxygen concentrations, causing the epithelia to become hypoxic and thus limiting the growth of facultative aerobic pathogens, such as Salmonella species (3, 4). In addition, butyrate alters host gene expression to promote immune tolerance to the colonic microbiota and to improve the barrier function of the colonic epithelium. For example, butyrate has been shown to increase the secretion of antimicrobial peptides and mucus as well as the expression of tight junction proteins, thickening and strengthenin...