Diet is a major factor governing the fecal butyrate-producing community structure across Mammalia, Aves and Reptilia

Abstract

Butyrate-producing bacteria have an important role in maintaining host health. They are well studied in human and medically associated animal models; however, much less is known for other Vertebrata. We investigated the butyrate-producing community in hindgut-fermenting Mammalia (n ¼ 38), Aves (n ¼ 8) and Reptilia (n ¼ 8) using a gene-targeted pyrosequencing approach of the terminal genes of the main butyrate-synthesis pathways, namely butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). Most animals exhibit high gene abundances, and clear diet-specific signatures were detected with but genes significantly enriched in omnivores and herbivores compared with carnivores. But dominated the butyrate-producing community in these two groups, whereas buk was more abundant in many carnivorous animals. Clustering of protein sequences (5% cutoff) of the combined communities (but and buk) placed carnivores apart from other diet groups, except for noncarnivorous Carnivora, which clustered together with carnivores. The majority of clusters (but: 5141 and buk: 2924) did not show close relation to any reference sequences from public databases (identity o90%) demonstrating a large 'unknown diversity'. Each diet group had abundant signature taxa, where buk genes linked to Clostridium perfringens dominated in carnivores and but genes associated with Ruminococcaceae bacterium D16 were specific for herbivores and omnivores. Whereas 16S rRNA gene analysis showed similar overall patterns, it was unable to reveal communities at the same depth and resolution as the functional gene-targeted approach. This study demonstrates that butyrate producers are abundant across vertebrates exhibiting great functional redundancy and that diet is the primary determinant governing the composition of the butyrate-producing guild.

Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine

“…Further emphasizing the need to more fully characterize this family, and in agreement with previous gene-targeted studies (17,37), we detected many OTUs with low identity to both confirmed sequences and cultured organisms. This work reveals many gaps in our knowledge of the but gene family.…”

“…Butyrate is centrally important to colonic homeostasis and is present in every vertebrate gut system studied to date (37). The butyrate-producing microbiota has been implicated in host health in many different disease models (35,(38)(39)(40)(41)(42)(43)(44)(45)(46)(47), resulting in increased interest in studying this community.…”

“…7 and 8). Additionally, because of the degeneracy of this primer set, spurious off-target amplification and incorrectly sized PCR products regularly occur with these primers, necessitating the inclusion of a gel extraction step in sequencing library prep (17,37).…”

“…These primers were designed to amplify a wide range of but-like sequences, acknowledging that they would amplify closely related non-but genes. The primers were used to elucidate the diversity of but gene sequences in humans and many other vertebrate species via Roche's 454 pyrosequencing (17,37). The in silico processing pipeline they describe attempts to remove some of the non-but sequences by eliminating those that closely match reference sequences that reside outside the phylogenetic cluster formed by functionally confirmed But-encoding genes.…”

Relationship of Enhanced Butyrate Production by Colonic Butyrate-Producing Bacteria to Immunomodulatory Effects in Normal Mice Fed an Insoluble Fraction of Brassica rapa L

“…The main human colonic butyrate producers belong to two groups of Gram-positive firmicutes: Faecalibacterium prausnitzii in the Clostridium leptum (or clostridial cluster IV) cluster, and Eubacterium rectale/Roseburia spp. in the Blautia coccoides (formerly Clostridium coccoides, clostridial cluster XIVa) (12-15), whereas there are other butyrate-producing groups that have been detected in humans (16)(17)(18).Vegetables belonging to the Brassica genus (Brassicaceae family) contain a number of nutrients with health-promoting properties, such as anticancer actions (19) and effects on cholesterol metabolism (20). These vegetables (Brassica oleracea L. [kale, cabbage, and broccoli], and Brassica rapa L. [turnip]) are unique in that they are rich sources of fiber, carotenoids, and foliate, as well as polyphenols and sulfur-containing compounds (21).…”