Draft genome sequences of Butyrivibrio hungatei DSM 14810 (JK 615^T) and Butyrivibrio fibrisolvens DSM 3071 (D1^T)

Butyrivibrio is commonly found in the rumen of wild and domesticated ruminant animals (1, 2). Butyrivibrio spp. are anaerobic, Gram-negative curved rods with a single flagellum, and they ferment rumen oligosaccharides and monosaccharides into butyrate, an essential source of energy for the host (1, 3, 4). Butyrivibrio fibrisolvens DSM 3071 (D1^T) was isolated from cow rumen in the 1950s in Maryland, USA (3), while Butyrivibrio hungatei DSM 14810 (JK 615^T) was isolated from sheep rumen in the 1990s in Mnichovice, Czech Republic (1). Here, we report draft genome sequences of these two Butyrivibrio-type strains as part of the 1000 Microbial Genomes Project (5). These resources will improve our understanding of the complex metabolism and physiology of rumen microbiomes.

Leibniz Institute DSMZ cultured B. fibrisolvens DSM 3071 and B. hungatei DSM 14810 anaerobically at 37°C and 40°C, respectively, using DSMZ Medium 330 broth (https://mediadive.dsmz.de/medium/330) inoculated from an ampoule preserved by freeze-drying. The centrifuged cell pellet from an approximately 50-mL culture was used to extract genomic DNA using Epicentre’s MasterPure Gram-positive DNA Purification Kit. The Joint Genome Institute constructed an Illumina paired-end library with an average insert size of 270 bp. The library was quantified using KAPA Biosystem’s sequencing library qPCR kit and run on a Roche LightCycler 480 real-time PCR instrument. Several libraries were multiplexed and prepared for sequencing using a TruSeq paired-end cluster kit (v.3) and Illumina’s cBot instrument. Sequencing was performed on an Illumina HiSeq 2000 using TruSeq SBS sequencing kits (v.3) following a 2 × 150 indexed run protocol. A total of 8,786,458 reads totaling 1,318.0 Mbp were generated for B. fibrisolvens DSM 3071 and 9,376,984 reads totaling 1,406.5 Mbp were generated for B. hungatei DSM 14810. Reads were quality controlled and trimmed through DUK (v.1.0) (6). Filtered reads were assembled using Velvet (v.1.2.07) (velveth: 63 –shortPaired and velvetg: –very clean yes –exportFiltered yes –min contig lgth 500 –scaf- folding no –cov cutoff 10); 1- to 3-kb simulated paired-end reads were created from Velvet contigs using wgsim (v.1.0) (–e 0–1 100–2 100 –r 0 –R 0 –X 0); and these reads were assembled with simulated read pairs with Allpaths-LG (v.r46652) (PrepareAllpathsInputs: PHRED 64 = 0 PLOIDY = 1 FRAG COVERAGE = 125 JUMP COVERAGE = 25 LONG JUMP COV = 50, RunAllpath- sLG TARGETS = standard) (7–9). Gene annotation was performed using Prodigal (v.2.5), with manual curation via GenePRIMP (v.1.0) (10, 11). Predicted coding sequences were translated and used to search National Center for Biotechnology Information nr, UniProt, TIGRFam, Pfam, KEGG, COG, and InterPro (12–18). tRNAScanSE (v.1.3.1) was used to identify tRNA genes, while rRNA genes were found using SILVA (v.123) (19, 20) (Table 1).

Both B. fibrisolvens DSM 3071 and B. hungatei DSM 14810 metabolize cellobiose (2, 3), and accordingly, their genomes contain many predicted beta glucosidases (GH1 and GH3 domains). However, DSM 3071 can metabolize polysaccharides such as carboxymethyl cellulose, while DSM 14810 cannot (1). This activity is likely attributable to one or more of the eight predicted cellulases in the DSM 3071 genome, compared to three proteins with cellulase domains (GH5/8/9/44/48) in the DSM 14810 genome (Table 1).

The work (proposal DOI: https://doi.org/10.46936/10.25585/60000886) was conducted by the US Department of Energy, Joint Genome Institute (JGI) (https://ror.org/04xm1d337), a DOE Office of Science User Facility that is supported by the Office of Science of the US Department of Energy operated under contract no. DE-AC02-05CH11231. This announcement was largely prepared by undergraduate students, and we gratefully acknowledge JGI for initiating and supporting it as an educational project (the “Adopt-a-Genome” Project).