The aerobic, Gram-positive, psychrotolerant bacterium Kurthia sibirica was first isolated from the stomach and intestinal contents of the Magadan mammoth recovered from the permafrost in eastern Siberia in 1977. K. sibirica was sequenced, and the predicted genome size is 3,496,665 bp, with 36.42% G+C content

Goen, Abigail E.

Kelley, Carolyn

MacLea, Kyle S.

Silverwood, Tyler

Trachtenberg, Ariel M.

Underriner, Aria

English

UNH Scholars' Repository

University of New Hampshire University of New Hampshire Scholars' Repository Faculty Publications 8-9-2018 Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154T Abigail E. Goen University of New Hampshire, Manchester Tyler Silverwood Seacoast School of Technology Aria Underriner Seacoast School of Technology Ariel M. Trachtenberg University of New Hampshire, Manchester Carolyn Kelley Seacoast School of Technology See next page for additional authors Follow this and additional works at: https://scholars.unh.edu/faculty_pubs Recommended Citation Goen, Abigail E.; Silverwood, Tyler; Underriner, Aria; Trachtenberg, Ariel M.; Kelley, Carolyn; and MacLea, Kyle S., "Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154T" (2018). Microbiology Resource Announcements. 704. https://scholars.unh.edu/faculty_pubs/704 This Article is brought to you for free and open access by University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Faculty Publications by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact nicole.hentz@unh.edu. Authors Abigail E. Goen, Tyler Silverwood, Aria Underriner, Ariel M. Trachtenberg, Carolyn Kelley, and Kyle S. MacLea This article is available at University of New Hampshire Scholars' Repository: https://scholars.unh.edu/faculty_pubs/704 Draft Genome Sequence of the Psychrotolerant BacteriumKurthia sibirica ATCC 49154TAbigail E. Goen,a Tyler Silverwood,c Aria Underriner,c Ariel M. Trachtenberg,a Carolyn Kelley,c Kyle S. MacLeaa,b,daBiology Program, University of New Hampshire, Manchester, New Hampshire, USAbBiotechnology Program, University of New Hampshire, Manchester, New Hampshire, USAcBiomedical Science and Technology Program, Seacoast School of Technology, Exeter, New Hampshire, USAdDepartment of Life Sciences, University of New Hampshire, Manchester, New Hampshire, USAABSTRACT The aerobic, Gram-positive, psychrotolerant bacterium Kurthia sibiricawas first isolated from the stomach and intestinal contents of the Magadan mam-moth recovered from the permafrost in eastern Siberia in 1977. K. sibirica was se-quenced, and the predicted genome size is 3,496,665 bp, with 36.42% GC content.Kurthia sibirica strain 13-2T (ATCC 49154, CCM 3477, VKM B-1549) is an aerobicGram-positive bacterium, motile via flagella, from the Planococcaceae family. Thisstrain was initially isolated from the intestinal contents and stomach of the Magadanmammoth that had recently been removed from the permafrost in eastern Siberia in1977 by Belikova and colleagues (1, 2). Other species in the Kurthia genus have beenisolated from a variety of meats and meat products and spoiled food, as well as fromthe feces of certain domestic animals (3–5), and have been identified as pathogens (6).Members of the Kurthia genus are Gram-positive aerobes that do not fermentglucose. They are usually motile with peritrichous flagella and form regular, un-branched rods with rounded ends. In older cultures, these bacteria form coccoid-likecells due to fragmentation of rods (1). K. sibirica differs from other Kurthia species in thatit has high-vitamin nutritional requirements, cannot grow in a 7% NaCl environment,exhibits phosphatase activity, synthesizes a yellow pigment, has low DNA-DNA hybrid-ization (45%) compared with that of Kurthia zopfii and Kurthia gibsonii, and lackscoccoid formation in older cultures (1). K. sibirica can also grow in pH ranges of 5.5 to9.5 and is able to produce acid from fructose and glycerol but not from ethanol orribose (1).K. sibirica ATCC 49154T in lyophilized form was purchased from the ATCC (Manassas,VA, USA). It was rehydrated in tryptic soy broth and incubated in a shaking incubatorat 25°C for 48 hours. Two drops of inoculated broth were spread onto tryptic soy agarand incubated at 26°C. A single colony was selected and plated onto brain heartinfusion (BHI) agar and struck for isolates, one colony of which was then used toinoculate BHI broth and to obtain genomic DNA (gDNA) using the Qiagen DNA minikit(Valencia, CA, USA). A double-stranded DNA (dsDNA) broad-range assay kit (DeNovix,Wilmington, DE, USA) was used to check the integrity of the DNA. Purified gDNA wasfragmented and tagged with sequence adapters using a Nextera DNA library prep kit(Illumina, San Diego, CA, USA) and subsequently sequenced on an Illumina HiSeq 2500instrument (Hubbard Center for Genome Studies, Durham, NH, USA). With the HiSeq2500 instrument, we generated 250-bp paired-end read sequences, which werebioinformatically trimmed prior to assembly and gene analysis using Trimmomaticto remove aberrant or mistagged fragments (7). These trimmed reads were thenassembled using SPAdes version 3.11.1 with default settings (8). A total of 3,843,530reads making up 960,882,500 bp of sequence were assembled into 79 total contigsafter removal of small contigs and contaminants. This represents 274 average cov-Received 7 June 2018 Accepted 10 July2018 Published 9 August 2018Citation Goen AE, Silverwood T, Underriner A,Trachtenberg AM, Kelley C, MacLea KS. 2018.Draft genome sequence of the psychrotolerantbacterium Kurthia sibirica ATCC 49154T.Microbiol Resour Announc 7:e00841-18.https://doi.org/10.1128/MRA.00841-18.Editor Karen G. Lloyd, University of Tennesseeat KnoxvilleCopyright © 2018 Goen et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Kyle S. MacLea,Kyle.MacLea@UNH.edu.T.S. and A.U. contributed equally to this work.GENOME SEQUENCEScrossmVolume 7 Issue 5 e00841-18 mra.asm.org 1 on November 15, 2019 at UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://mra.asm.org/Downloaded from erage of a total sequence length of 3,496,665 bp. The largest contig was 361,432 bp,with an N50 value of 138,251 bp and a GC content of 36.42%. The assembled contigswere annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) pro-cess (9) and found to have a total of 3,400 genes, 3,250 protein-coding sequences, 69pseudogenes, 7 rRNAs, and 69 tRNAs.Data availability. The Kurthia sibirica ATCC 49154T whole-genome shotgun se-quence (WGS) project has been deposited in DDBJ/ENA/GenBank under accessionnumber QFVR00000000. The version described in this paper is the first version,QFVR01000000.ACKNOWLEDGMENTSSequencing and bioinformatics analysis were undertaken at the Hubbard Center forGenome Studies at UNH, supported by NH-INBRE, with the kind assistance of KelleyThomas, Toni Westbrook, and Stephen Simpson. K.S.M. acknowledges Thomas Kulik,UNH Manchester, for his eminently useful translation (2) from the original Russian ofBelikova et al., published in Mikrobiologiia in 1986 (1). That translation has beendeposited in GitHub (https://github.com/KyleMacLea/Kurthia-sibirica) to allow otherscientists to access it. K.S.M. further dedicates this work to the memory of RobertDouglas MacLea (1942–2018). This work was a project of the Microbiology Educationthrough Genome Annotation-New Hampshire (MEGA-NH) program.The Department of Life Sciences at UNH Manchester provided funds for purchasingthe bacterial strain. Sequencing costs were supported by New Hampshire-INBREthrough an Institutional Development Award (IDeA) (P20GM103506) from the NationalInstitute of General Medical Sciences of the NIH. The funders had no role in studydesign, data collection and interpretation, or the decision to submit the work forpublication.REFERENCES1. Belikova VA, Cherevach NV, Kalakutskiı˘ LV. 1986. New species of bacteriain the genus Kurthia–Kurthia sibirica sp. nov. Mikrobiologiia 55:831–835.2. Kulik T, MacLea KS. 2017. Translation of Kurthia sibirica, a new bacterialspecies of the Kurthia genus, by V.A. Belikova, N.V. Cherevach, L.V. Kala-kutski. Mikrobiologija 55:831–835. Published in 1986.3. Belikova VL, Cherevach NV, Baryshnikova LM, Kalakutskiı˘ LV. 1980. Mor-phologic and physiologic-biochemical characteristics of Kurthia zopfii.Mikrobiologiia 49:64–69.4. Gardner GA. 1969. Physiological and morphological characteristics ofKurthia zopfii isolated from meat products. J Appl Bacteriol 32:371–380.https://doi.org/10.1111/j.1365-2672.1969.tb00986.x.5. Holzapfel WH. 1992. Culture media for non-sporulating Gram-positivefood spoilage bacteria. Int J Food Microbiol 17:113–133. https://doi.org/10.1016/0168-1605(92)90110-O.6. Pancoast SJ, Ellner PD, Jahre JA, Neu HC. 1979. Endocarditis due to Kurthiabessonii. Ann Intern Med 90:936–937. https://doi.org/10.7326/0003-4819-90-6-936.7. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer forIllumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-sembly algorithm and its applications to single-cell sequencing. J ComputBiol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.9. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Ciufo S, Li W. 2013.Prokaryotic Genome Annotation Pipeline. In The NCBI handbook, 2nd ed.National Center for Biotechnology Information, Bethesda, MD.Goen et al.Volume 7 Issue 5 e00841-18 mra.asm.org 2 on November 15, 2019 at UNIVERSITY OF NEW HAMPSHIRE LIBRARYhttp://mra.asm.org/Downloaded from 

Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154T

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Draft Genome Sequence of the Psychrotolerant Bacterium Kurthia sibirica ATCC 49154T

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