Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum

Abstract

Molecular biology approaches were employed to examine the genetic diversity of bacteria from the Cytophaga/Flexibacter/Bacteroides (CFB) phylum in the rumen of cattle. By this means we were able to identify cultured strains that represent some of the larger CFB clusters previously identified only by PCR amplification and sequencing. Complete 16S rDNA sequences were obtained for 16 previously isolated rumen strains, including the type strains of Prevotella ruminicola, P. bryantii, P. brevis and P. albensis to represent a wide range of diversity. Phylogenetic analysis of cultured strains revealed the existence of three clusters of ruminal CFB: (i) a cluster of Prevotella strains, which have been found only in the rumen, including the two type strains, P. brevis GA33(T) and P. ruminicola 23(T); (ii) Prevotella spp. that cluster with prevotellas from other ecological niches such as the oral cavity and which include the type strains, P. bryantii B(1)4(T) and P. albensis M384(T); (iii) two Bacteroides spp. strains clustering with B. forsythus of oral origin. In order to establish whether the cultivated isolates cover the whole range of ruminal CFB genetic diversity, 16S rRNA gene sequences were amplified and cloned from DNA extracted from the same rumen samples (one cow in Slovenia, one in Scotland and three in Japan). Sequencing and phylogenetic analysis of 16S rRNA genes confirmed the existence of two superclusters of ruminal Prevotella, one exclusively ruminal and the other including non-ruminal species. In the case of ruminal Bacteroides spp., however, phylogenetic analysis revealed the existence of three new superclusters, one of which has as yet no cultivable counterpart. Interestingly, these Bacteroides clusters were represented almost exclusively by clone libraries from the Japanese cattle and only three sequences were from the European cattle. This study agrees with previous analyses in showing that rumen Prevotella/Bacteroides strains exhibit a remarkable degree of genetic diversity and suggests that different strain groupings may differ greatly in their recovery by cultural methods. The most important conclusion, however, is that cultured strains can be identified that represent some of the larger clusters previously identified only by PCR amplification and sequencing.

Composition and Similarity of Bovine Rumen Microbiota across Individual Animals

“…The high abundance of this genus is interesting from an ecological point of view: it might be the result of a metabolic niche that is wide enough to be occupied by bacteria that have similar metabolic capabilities, due to genetic relatedness or to high genetic variability that enables members of this genus to occupy different ecological niches within the rumen. Indications from previous studies imply the latter, as members of this genus are considered to exhibit a remarkable degree of genetic diversity [18], [19], [20]. Nevertheless, these two possibilities need to be further examined and distinguished.…”

Relationship between the Rumen Microbiome and Residual Feed Intake-Efficiency of Brahman Bulls Stocked on Bermudagrass Pastures

“…Even though Prevotella may be the most abundant genus observed, cultured species only accounted for a small fraction of the total Prevotella population [33], [35]. Cultivated Prevotella strains display highly varied genetic divergence [36] suggesting uncultured Prevotella also have diverse functions. Prevotella species have a documented role in metabolism of starch, hemicellulose, pectin, and peptide or protein catabolism [37]–[40].The whole genome of a P. ruminicola and P. bryantii strain were sequenced to evaluate their genetic similarity [41].…”

Molecular diversity of rumen bacterial communities from tannin-rich and fiber-rich forage fed domestic Sika deer (Cervus nippon) in China

“…Considering the genetic diversity of Prevotella spp. [27,42], it is assumed that the tolerance to tannins of domestic Sika deer may be related to the abundance of Prevotella spp. in the OL group.…”