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Here, the draft genome sequences of four different Methanobrevibacter species are presented. Three of the Methanobrevibacter species (M. curvatus, M. cuticularis, and M. filiformis) have been isolated from the termite hindgut, while M. oralis was isolated from human subgingival plaque.
Methanobacteriales, in particular members of the genera Methanobrevibacter, have been shown to be some of the most abundant methanogenic archaea in various intestinal environments, including the human gut (1), the termite hindgut (2), and the ovine and bovine rumen (3). Recent studies have indicated that Methanobrevibacter species may not only be contributing to greenhouse gas emissions from farm animals (4, 5), but may also have effects on human physiology and health (6, 7). It is therefore of great interest to gain a better understanding of how different Methanobrevibacter species have adapted to specific host environments at the molecular level. Genome sequences of Methanobrevibacter species have been obtained so far for strains from the human intestinal tract and the rumen (8,–12), but not from any insect guts or the human oral cavity. Methanobrevibacter oralis DSM7256, isolated from the human subgingival plaque (13), is also the first sequenced representative of all human oral methanogens.
Genomic DNA was ordered by the DSMZ (Braunschweig) or was isolated using the MasterPure complete DNA purification kit (Epicentre, Madison, WI, USA). The extracted DNA was used to generate Illumina-shotgun libraries according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Sequencing was conducted using a MiSeq and MiSeq reagent kit v3 (2 × 300 bp paired end) as recommended by the manufacturer (Illumina). Sequencing resulted in 1,934,710 (M. filiformis), 1,983,778 (M. oralis), 3,298,762 (M. curvatus), and 3,533,158 paired end reads (M. cuticularis), respectively. Trimmomatic 0.32 (14) was used to filter low-quality reads and for clipping of adapter contaminations. The assembly was performed with the SPAdes genome assembler software 3.6.2 (15). Coverages were determined using QualiMap version 2.1 (15, 16) and automatic annotation was performed using the software tool PROKKA (17). General genome features are listed in Table 1.
Sequencing the genomes of the four different Methanobrevibacter genomes provides reference sequences for comparative analyses with other Methanobrevibacter genomes and may reveal adaptive traits of Methanobrevibacter species to different environments. Some characteristic features and differences between Methanobrevibacter species are already apparent from formal description of the type strains, e.g., presence of catalase activity in the three Methanobrevibacter species from the termite hindgut (18, 19). The genome sequences allow the identification of the potential molecular basis of this enzyme activity: A monofunctional heme-depended catalase similar to the enzyme purified from M. arboriphilus (20). The gene encoding this enzyme is present in each of the genomes of the three Methanobrevibacter species isolated from the termite hindgut, but appears to be absent from the genome of M. oralis.
These whole-genome shotgun projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers listed in Table 1. The versions described here are the first versions.
We thank Kathleen Gollnow for technical support.
Citation Poehlein A, Seedorf H. 2016. Draft genome sequences of Methanobrevibacter curvatus DSM11111, Methanobrevibacter cuticularis DSM11139, Methanobrevibacter filiformis DSM11501, and Methanobrevibacter oralis DSM7256. Genome Announc 4(3):e00617-16. doi:10.1128/genomeA.00617-16.