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. 2016 Dec 1;4(6):e01338-16. doi: 10.1128/genomeA.01338-16

Genome Sequence of the Acetogenic Bacterium Butyribacterium methylotrophicum DSM 3468T

Frank R Bengelsdorf a, Anja Poehlein b, Bettina Schiel-Bengelsdorf a, Rolf Daniel b, Peter Dürre a,✉
PMCID: PMC5137411  PMID: 27908997

Abstract

Butyribacterium methylotrophicum DSM 3468T is an acetogenic methylotrophic, anaerobic, carbon monoxide–oxidizing bacterium that produces acetate, butyrate, and butanol. The genome consists of a single chromosome (4.3 Mb) and harbors 3,989 predicted protein-encoding genes.

GENOME ANNOUNCEMENT

Butyribacterium methylotrophicum DSM 3468T is a Gram-positive, motile bacterium that was isolated from a sewage digester in Marburg (Gemany) by Zeikus et al. in 1980 (1). This autotrophic acetogen can reduce H2 + CO2 and CO using the Wood-Ljungdahl pathway and produces acetate, butyrate, and butanol (2). In general, the metabolic features of B. methylotrophicum appear to be similar to those of Eubacterium limosum ATCC 8486T (3), and phylogenetic analysis of the 16S rRNA gene sequences also indicated a close relationship between both strains (4, 5). B. methylotrophicum and related strains harbor metabolic characteristics, which make these organisms ideal candidates for a syngas fermentation process (6), although B. methylotrophicum was provisionally classified as a risk level 2 organism by the Deutsche Sammlung von Mikroorganismen und Zellkulturen.

Extracted DNA was used to generate Illumina shotgun paired-end sequencing libraries, which were sequenced with a MiSeq instrument and the MiSeq reagent kit version 3, as recommended by the manufacturer (Illumina, San Diego, CA, USA). Quality filtering using Trimmomatic version 0.32 (7) resulted in 4,256,529 paired-end reads with an average read length of 301 bp. The assembly was performed with the SPAdes genome assembler software version 3.5.0 (8). The assembly resulted in 27 contigs (>500 bp) and an average coverage of 94-fold. The assembly was validated and the read coverage determined with QualiMap version 2.1 (9). The draft genome of B. methylotrophicum DSM 3468 consists of a single chromosome (4.3 Mb) with an overall GC content of 47.5%. Automatic gene prediction and identification of rRNA and tRNA genes was performed using the software tool Prokka (10). The draft genome contained nine rRNA genes, 55 tRNA genes, 2,890 protein-encoding genes with function prediction, and 1,099 genes coding for hypothetical proteins.

Genes encoding enzymes of the methyl and carbonyl branches of the Wood-Ljungdahl pathway are conserved within acetogenic bacteria (11). Correspondingly, the genome of B. methylotrophicum harbors a gene cluster that is highly similar to the respective cluster of E. limosum ATCC 8486T and harbors genes encoding the Rnf complex. A comparative genome analysis of the strains E. limosum ATCC 8486T (12) and E. limosum KIST612 (13) with B. methylotrophicum DSM 3468 revealed high average nucleotide identities of 94.6% and 99.7%, respectively. The threshold range for species differentiation is 95 to 96% (14). A further comparison revealed that the genome of strain DSM 3468 (4,256,529 bp) is smaller than that of ATCC 8486T (4,370,113 bp) and of similar size to KIST612 (4,276,902 bp), indicating that B. methylotrophicum is a distinct species compared to E. limosum ATCC 8486T.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number MIMZ00000000. The version described in this paper is the first version, MIMZ01000000.

ACKNOWLEDGMENTS

Work was supported by grants from the BMBF Gas-Fermentation project (FKZ 031A468A), the ERA-IB 5 project CO2CHEM (FKZ 031A566A), and the MWK-BW project Nachhaltige und effiziente Biosynthesen (AZ 33-7533-6-195/7/9). We thank Kathleen Gollnow and Frauke-Dorothee Meyer for technical support.

Footnotes

Citation Bengelsdorf FR, Poehlein A, Schiel-Bengelsdorf B, Daniel R, Dürre P. 2016. Genome sequence of the acetogenic bacterium Butyribacterium methylotrophicum DSM 3468T. Genome Announc 4(6):e01338-16. doi:10.1128/genomeA.01338-16.

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