==== Front Microbiol Resour Announc Microbiol Resour Announc ga mra MRA Microbiology Resource Announcements 2576-098X American Society for Microbiology 1752 N St., N.W., Washington, DC MRA01093-20 10.1128/MRA.01093-20 Genome Sequences Draft Genome Sequence of a Novel Methylobacterium brachiatum Strain Isolated from Human Skin Cremers Geert a Kenyon Angelique a Gubbels Niels a Jansen Matthijs a van Alen Theo A. a https://orcid.org/0000-0003-1833-8731Berben Tom a https://orcid.org/0000-0003-1990-9030Op den Camp Huub J. M. a a Department of Microbiology, IWWR, Radboud University, Nijmegen, The Netherlands Thrash J. Cameron EditorUniversity of Southern California Address correspondence to Huub J. M. Op den Camp, h.opdencamp@science.ru.nl.Citation Cremers G, Kenyon A, Gubbels N, Jansen M, van Alen TA, Berben T, Op den Camp HJM. 2020. Draft genome sequence of a novel Methylobacterium brachiatum strain isolated from human skin. Microbiol Resour Announc 9:e01093-20. https://doi.org/10.1128/MRA.01093-20. 10 12 2020 12 2020 9 50 e01093-2021 9 2020 13 11 2020 Copyright © 2020 Cremers et al.2020Cremers et al.This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Methylobacterium brachiatum MBRA is an aerobic alphaproteobacterium isolated from the human skin on methanol-containing minimal medium. The genome was sequenced using Illumina and Nanopore technology, and the genome was assembled using Unicycler. M. brachiatum MBRA possesses two xoxF genes, one mxaF/mxaI, and a complete serine pathway. ABSTRACT Methylobacterium brachiatum MBRA is an aerobic alphaproteobacterium isolated from the human skin on methanol-containing minimal medium. The genome was sequenced using Illumina and Nanopore technology, and the genome was assembled using Unicycler. M. brachiatum MBRA possesses two xoxF genes, one gene pair, mxaF and mxaI, and a complete serine pathway. EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)https://doi.org/10.13039/100010663669371Op den Camp Huub J. M. Berben Tom cover-dateDecember 2020 ==== Body ANNOUNCEMENT Methanol is a by-product of plant (1) and healthy human metabolism (2). Facultative methylotrophic bacteria from the genera Methylobacterium and Methylorubrum have been isolated from the plant phyllosphere (1), soil (3), and the human body (4–6). Methylobacterium brachiatum was first isolated from a water sample from a food processing plant in Japan (7). Here, we present a draft genome of M. brachiatum MBRA, which we isolated from human skin as part of a laboratory course. Strain MBRA was isolated by placing a human thumb (Nijmegen area, The Netherlands) on solid mineral salt medium (MSM) containing (per liter) 15 g agar, 1.5 g KH2PO4, 7.9 g Na2HPO4·2H2O, 0.8 g NH4Cl, 0.1 g MgSO4·7H2O, 0.5% methanol, 1 ml 1,000× SL10 trace element solution (8), 0.1 ml 10 mM CeCl3 solution, and 0.02 ml 50 mM nitrilotriacetic acid (NTA) solution (medium pH set at 6.8). After growing at room temperature for 1 week, a single colony was picked and restreaked onto an MSM plate. After 5 d at 25°C, biomass was scraped from the plate, and DNA was isolated using a DNeasy PowerSoil kit (Qiagen, Venlo, The Netherlands). Long-read sequencing was performed with the MinION R9 flow cell (FLO-MIN106; Nanopore, Oxford, UK), according to the manufacturer’s protocol, using unsheared DNA (no size selection) and NEBNext formalin-fixed, paraffin-embedded (FFPE) repair mix (M6630), a ligation sequencing kit (SQK-LSK109), the NEBNext end repair/dA-tailing module (E7546), a flow cell priming kit (EXP-FLP001), NEB Blunt/TA ligase master mix (M0367), the NEBNext quick ligation module E6056, and barcode kit EXPNBD104. MiSeq sequencing (Illumina, San Diego, CA, USA) was performed with the Nextera XT kit according to the manufacturer’s protocol. All DNA was measured using a Qubit fluorometer (Thermo Fisher Scientific, Waltham, MA, USA). The quality of the 2,329,486 paired-end Illumina reads (average, 253 bp) was checked using CLC Genomics Workbench v12 (Qiagen Aarhus A/S, Denmark). Read error correction was performed using SPAdes v3.13 (9) in the Unicycler v0.4.4 (10) pipeline, so no trimming was completed prior to assembly. Nanopore reads were base called and demultiplexed using Guppy v3.0.7 (minimum length, 3,000 bp), leaving 129,787 reads with an average length of 8,234 bp for assembly. Assembly using reads from both methods in Unicycler (10) resulted in 25 contigs with an N50 value of 1,578,407 bp. Eight contigs were manually binned by GC content (GC content, ∼69%) and Illumina read-based coverage (coverage, ∼50×) (Table 1). Unicycler also identified five circular high-copy-number small contigs, most likely plasmids. The completeness of the genome was checked using CheckM v1.0.11, indicating 97.2% completeness at the Rhizobiales level and 0% contamination (11). Average nucleotide identity (ANI) analysis by JSpeciesWS v3.6.1 (12) placed the genome at 97.9% similarity to M. brachiatum. The genome was annotated using Prokka v1.12 (13) and manually curated. Default parameters for all programs were used except where otherwise noted. TABLE 1 Characteristics of the Methylobacterium brachiatum MBRA genome sequence and plasmids Characteristic Data for: Genome Plasmid 1 Plasmid 2 Plasmid 3 Plasmid 4 Plasmid 5 Size (bp) 6,459,278 53,490 48,251 45,734 24,909 16,067 DNA GC content (%) 69.4 61.4 68.0 64.9 67.0 56.1 No. of contigs 8 1 1 1 1 1 N50 (bp) 1,573,792 53,490 48,135 45,734 24,910 16,067 Circular No Yes Yes Yes Yes Yes Total no. of genes 6,236 57 60 64 25 23 Protein coding density (%) 84.5 85.6 88.9 85.7 84.5 84.9 No. of rRNA genes 15 0 0 0 0 0 No. of tRNA genes 67 0 0 0 0 1 Coverage (×)a 50 107 117 149 194 296 a Based on MiSeq reads. The genome sequence of strain MBRA reflects its facultative methylotrophic lifestyle. For growth on methanol, the genome encodes two lanthanide-dependent XoxF-type methanol dehydrogenases and a calcium-dependent MxaFI type (14), together with the recently discovered lanM gene (15) and the full serine pathway for carbon assimilation (1). Strain MBRA harbors a glycolysis pathway and a near-complete tricarboxylic acid (TCA) cycle. In addition, the genes for both dissimilatory and assimilatory nitrate reduction were present. Data availability. This whole-genome shotgun sequencing project has been deposited in ENA under accession number PRJEB35543. The assembled genome (13 contigs) is deposited under accession numbers CACTHX010000001 through CACTHX010000013. The versions described in this paper are the first versions. The raw reads are available under SRA accession numbers ERX3765083 and ERX3765085. ACKNOWLEDGMENT H.J.M.O.D.C. and T.B. were supported by the European Research Council Advanced Grant VOLCANO 669371. ==== Refs REFERENCES 1. 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