Abstract
BackgroundButyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting energy from the diet. Within these genera, 5 rumen species have been classified (B. fibrisolvens, B. hungatei, B. proteoclasticus, P. ruminis and P. xylanivorans); nonetheless, the phylogeny and evolution of these genera is still unclear. Given the recent increase in available genomes, a re-investigation of the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio is timely.ResultsWe show, using both a 16S rDNA and 40 gene marker phylogenetic tree, that 6 species, namely 1. P. ruminis, 2. P. xylanivorans, 3. B. fibrisolvens, 4. Butyrivibrio sp., 5. B. hungatei, and 6. B. proteclasticus likely exist. Pangenome analysis at 100% core definition showed a high abundance of accessory genes (91.50 to 99.34%) compared with core genes (0.66 to 8.50%), illustrating possession of very open genomes. Across the 71 genomes, 870 COGs (clusters of orthologous genes) were shared by all taxa, suggesting evolution through speciation from a common ancestor. Further analysis of Carbohydrate-Active Enzymes (CAZymes) genes show that most are within the accessory genome and orthologous in descent with numerous within-family CAZyme isoforms apparent, CAZyme family tree lineages show that these isoforms largely group according to the 6 species, suggesting extensive horizontal gene transfer within these families.ConclusionsWe show the extensive genomic variation found within Butyrivibrio, and to a lesser extent, Pseudobutyrivibrio. and demonstrate the existence of a new Butyrivibrio species. The Butyrivibrio and Pseudobutyrivibrio genomes are very open with very low % core genomes and high % accessory genomes., and possess a number of GH isoforms that we hypothesise facilitate metabolic plasticity and resilience under dietary perturbations. This study utilizes all currently available genomes and consequently provides a major advancement in our understanding of these important anaerobic bacteria.