Complete Genome Sequence of Methanobrevibacter smithii Strain KB11, Isolated from a Korean Fecal Sample.

The archaeon Methanobrevibacter smithii is a major colonizer of the human gut. Methanobrevibacter smithii strain KB11 was newly isolated from a Korean fecal sample. Here, we present the complete genome sequence of strain KB11 and a brief comparison with that of M. smithii type strain ATCC 35061T.

GENOME ANNOUNCEMENT

Methanobrevibacter is a fastidious archaeal microorganism and obligate anaerobe. It can be cultivated in a pressurized anaerobic atmosphere of 80% hydrogen and 20% carbon dioxide (1, 2). Among Methanobrevibacter species, M. smithii is a near-ubiquitous resident of the human intestinal microbiome (3). The prevalence of methanogens in humans has been reported to be dependent on the age of the human host; populations increase gradually throughout childhood, reaching a maximum abundance level in adults (3, 4). Methanobrevibacter smithii may impact human health (5, 6), but its beneficial effect is still questionable. In the course of an investigation into the diversity of methanogens in the human gut, feces were collected with an anaerobic sampling system (7) and were maintained under strict anaerobic conditions, as previously described (8). A methanogenic strain, KB11, was purified from the feces of a healthy 43-year-old Korean male. This is the first human gut methanogen isolated from South Korea.

The genomic DNA of KB11 was extracted as previously described (2). Complete genome sequencing was carried out using Illumina MiSeq and PacBio RS II platforms, as recommended by the manufacturers, at ChunLab, Inc. (Seoul, Republic of Korea). A hybrid assembly was performed using SPAdes v3.9.0 (http://cab.spbu.ru/software/spades/) from a total of 1.98 Gb MiSeq reads (average length, 192.6 bp) and 850 Mb of PacBio RS II filtered subreads (mean length, 8,534 bp; N50, 11,609 bp), generated by HGAP 2.0. The largest contig (1.81-Mb long) was cut into pieces and joined using the CLC Genomics Workbench v9.5.1 (Qiagen Bioinformatics, Aarhus, Denmark), allowing the finalized sequence to begin with the dnaA gene. Self-corrected PacBio long reads were used for fragment joining and confirmation of the circular structure of the chromosomal contig. Residual errors were corrected by three successive rounds of MiSeq read mapping and consensus sequence extraction. Genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/) and the Rapid Annotations using Subsystems Technology (RAST) server (9). To the best of our knowledge, this is the first reported publicly available complete genome sequence of Methanobrevibacter smithii isolated from a human gut (M. smithii ATCC 35061T was isolated from a sewage digester [10]). The KB11 genome has a 1,805,545-bp chromosome (31.2% G+C), which is 47,615 bp smaller than that of ATCC 35061T. Despite the overall similarity, we found an inversion (699958 to 1484782) in the ATCC 35061T chromosome that led to C-term truncation in the DNA helicase UvrD (Msm_0731). It is also noteworthy that an adhesin-like protein (Msm_0173, 2,879 amino acids [aa]) in ATCC 35061T has 17 DUF11 domains (pfam01345), while the KB11 homolog is disrupted with a frameshift (BK798_03360). A KB11-specific region (500216 to 523396) was also found to accommodate genes encoding hypothetical proteins, a type I restriction-modification system, and transposases.

This additional genome information may be used to improve our understanding of the genetic diversity of human gut-associated M. smithii within individuals. This knowledge will enhance studies concerning the archaeal gut microbiota and human physiology, especially with respect to human health and disease.

Accession number(s).

The complete genome sequences of Methanobrevibacter smithii KB11 have been deposited in DDBJ/ENA/GenBank under the accession number CP017803.