The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid

Abstract

Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.

Keywords: Butyrivibrio fibrisolvens; INBov1; cow rumen; genome sequencing.

Fig. 1.

(a) Top: visualization using the program Mauve [18] of scaffolds placed by Soma in the optical restriction map (70 % map coverage). Bottom: structure of the genome sequence after manual placing of scaffolds with NEBcutter (95 % map coverage). (b) Final genomic sequence of B. fibrisolvens (4 398 850 bp, complete genomic structure with 96 % of identified bases) after using GapCloser. Gap length is shown (gap regions smaller than 10 bases are not shown).

Fig. 2.

Circular visualization of the B. fibrisolvens INBov1 chromosome. The image shows (from outside to centre): genes on the forward strand, genes on the reverse strand (coding sequences in blue, tRNAs in red, rRNAs in purple). The G+C content is in black with peaks indicating higher or lower values than the average G+C content (peaks out/inside, respectively). There are four noticeable peaks inside that correspond to the largest gap regions, as shown in Fig. 1. The inner circle shows the GC skew. Positive values correspond to green peaks, indicating that the amounts of guanines are enriched in the top strand versus the amount of cytosines in the bottom strand. Purple peaks represent the opposite.

Fig. 3.

Circular visualization of the chromid sequence (pINBov266) in Cgview. The location of parB, hbs and repA genes are shown by red circles. The upper circle shows that these genes are located in a region where the GC skew switches the nucleotide frequency polarity. The lower circle corresponds to the blast hits of the genes parB (red), hbs (blue) and repA (green).