Draft genome sequence of Anaerosporobacter sp. nov., strain AGMB01083 isolated from a faeces of Korean cow

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The genus of Anaerosporobacter was isolated from a forest-soil sample. The Anaerosporobacter sp. nov. strain AGMB01083 was isolated from faeces of Korean cow. The strain describes a novel species according to whole-genome sequence of strain AGMB01083 using the Illumina platform. According to the 16S rRNA sequence similarity, the strain AGMB01083 was most closely related to Anaerosporobacter mobilis HY-37-4

^T

(95.7%). The genome assembly consists of a 4,589,105 bp chromosome with a DNA G + C content of 36.2%, 3,981 total genes, 27 rRNA genes, and 70 tRNA genes.

Keywords: Anaerosporobacter sp., draft genome sequence, faeces of Korean cow

The genus Anaerosporobacter was firstly proposed by Jeong et al. (2007), which proposed that Anaerosporobacter mobilis KCTC 5027

^T

(GenBank accession number NZ_FR CP00000000) was classified within the new genus Anaero- sporobacter and assigned to the family Lachnospiraceae. Cells of the species in the genus Anaerosporobacter were strictly

anaerobic rods with erose edges, convex, translucent to opaque, greyish-white in color and slightly smooth (Jeong et al., 2007). During a study aimed at isolating novel bacteria from a faeces of Korean cow for further cattle gut microbiome study. Here, we describe the draft genome sequence of Anaero- sporobacter sp. nov. strain AGMB01083.

A novel bacterial strain designated as strain AGMB01083 was isolated from a faeces of Korean cow (6 months old and 163 kg) which was deposited from the National Institute of Animal Science of Korea. As a result of the 16S rRNA sequencing, the strain AGMB01083 was most closely related to Anaerosporobacter mobilis HY-37-4

^T

(95.7%). The strain AGMB01083 was grown on Reinforced Clostridial Medium (RCM) agar plate within 48 h at 37°C under anaerobic conditions. For anaerobic conditions, an anaerobic chamber (Coy Laboratory Products) containing 90% N

2

, 5% H

2

, and 5%

CO

2

was used.

The genomic DNA was extracted with phenol:chloroform:

isoamylalcohol (Wilson et al., 1990). The quantity and quality of the extracted genomic DNA were measured by PicoGreen and Nanodrop. Genomic DNA was sheared by Covaris LE220

Korean Journal of Microbiology (2020) Vol. 56, No. 2, pp. 180-182 pISSN 0440-2413

DOI https://doi.org/10.7845/kjm.2020.0039 eISSN 2383-9902

Draft genome sequence of Anaerosporobacter sp. nov., strain AGMB01083 isolated from a faeces of Korean cow

Seung-Hyeon Choi, Jam-Eon Park, Ji Young Choi, Se Won Kang, Moon-Soo Rhee, Kang Hyun Lee, Mi-Kyung Lee, Jiyoung Lee, Ju Huck Lee, Jung-Sook Lee, and Seung-Hwan Park*

Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si 56212, Republic of Korea

한우 분변에서 분리된 Anaerosporobacter 속의 신종 균주 AGMB01083의 유전체 염기서열 초안

최승현 ･ 박잠언 ･ 최지영 ･ 강세원 ･ 이문수 ･ 이강현 ･ 이미경 ･ 이지영 ･ 이주혁 ･ 이정숙 ･ 박승환*

한국생명공학연구원 생물자원센터

(Received April 23, 2020; Revised April 28, 2020; Accepted April 28, 2020)

*For correspondence. E-mail: [email protected];

Tel.: +82-63-570-5636; Fax: +82-63-570-5609

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Draft genome sequence of Anaerosporobacter sp. nov. strain AGMB01083 ∙

181 Korean Journal of Microbiology, Vol. 56, No. 2 (Covaris). A DNA library was prepared using a TruSeq Nano

DNA kit (Illumina). The final product was validated using the Agilent Technologies 2100 Bioanalyzer (Agilent Technologies).

Genome sequencing was performed using a NovaSeq

^TM

6000

Sequencing System (Illumina) with paired-end read lengths of 151 bp. De novo genome assembly was performed with the St. Petersburg genome assembler (SPAdes) version 3.13.0 (Bankevich et al., 2012). Potential contamination in genome assembles was checked by the Contamination Estimator by 16S (ContEst16S) and CheckM tools (Parks et al., 2015; Lee et al., 2017). The coding DNA sequences (CDSs) and tRNAs were predicted using prodigal and tRNAscan-SE, respectively.

The functional annotation of each CDS was analyzed by homology search against UniProt (UniProt, 2015), KEGG (Kanehisa et al., 2014) databases.

The genome statistics are shown in Table 1. The draft genome of the strain AGMB01083 was consist of a 4,589,105 bp chromosome (55 contigs; N

50

, 164,914 bp; sequencing depth of coverage, 687.6×) with a DNA G + C content of 36.2%. The genome was showed to contain 3,981 CDSs, 27 rRNAs (5S, 16S, 23S), and 70 tRNAs were annotated (Fig. 1).

A total of 2,312 genes were functionally assigned to categories

Table 1. General features of Anaerosporobacter sp. nov. strain AGMB01083

Property Value

Genome assembly

Assemble method SPAdes 3.13.0

Genome coverage 687.6X

Genome features

Genome size (bp) 4,589,105

DNA G + C content (%) 36.2

No. of contigs 55

rRNA genes (5S, 16S, 23S) 27 (8, 10, 9)

tRNA genes 70

Open reading frame 3,981

CDS assigned by COG 2,312

GenBank Accession No. JAAQRO000000000

Fig. 1. Graphical circular map of Anaerosporobacter sp. nov. strain AGMB01083. From outside to the center; ring 1 shows tRNA and rRNA, as well as coding DNA sequences (CDS) on the forward strand and reverse strand from the outside; ring 2 shows G + C% content and ring 3 shows GC skew.

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182

^∙ ^Choiet al.

미생물학회지 제56권 제2호

based on clusters of orthologous group (COG) assignments.

The average nucleotide identity (ANI) value was calculated using the OrthoANI algorithm (Lee et al., 2016). When compared with the closest Anaerosporobacter mobilis HY- 37-4

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, the ANI value was 75.5% which was below the ANI criterion for interspecies identity.

We found genome related to the phosphotransferase system (PTS) used by bacteria to ingest sugars belonging to the Fru family such as fructose PTS system EIIB component (fruA), fructose PTS system EIIA component (fruB) and phosphoenol- pyruvate-protein phosphotransferase (ptsI). The genome con- tained sec-SRP pathway gene among the bacterial secretion system. For example, preprotein translocase subunit (secA, secB, secD, secE, secG, secY, yajC) YidC/Oxa1 family membrane protein insertase (yidC), fused signal recognition particle receptor (ftsY) and signal recognition particle subunit SRP54 (ffh). Also, the genome had several vancomycin resistance gene, such as vancomycin resistance protein (vanW), two- component system, OmpR family, sensor histidine kinase (vanS) and two-component system, OmpR family, response regulator (vanR).

The Anaerosporobacter sp. nov. strain AGMB01083 has been deposited in the Korean Collection for Type Cultures under accession number KCTC 15857.

Nucleotide sequence accession number

The GenBank/EMBL/DDBJ accession number for the genome sequence of Anaerosporobacter sp. nov. strain AGMB01083 is JAAQRO000000000.

적 요

Anaerosporobacter에 속하는 균주는 산림 토양에서 분리 된 것으로 알려져 있다. Anaerosporobacter sp. nov. strain AG MB01083 균주는 한우 분변에서 분리되었다. Illumina 플랫폼 을 이용한 strain AGMB01083의 유전체 서열에 따라 새로운 종을 기술한다. 16S rRNA 서열 유사성에 따르면, AGMB01083 균주는 Anaerosporobacter mobilis HY-37-4

^T

(95.7%)와 가장

밀접한 관련이 있었다. 유전체는 36.6%의 DNA G + C 함량, 3,981개의 유전자, 27개의 rRNA, 70개의 tRNA로 구성되었으 며, 염색체의 크기는 4,589,105 bp 구성되어 있다.

Acknowledgments

This work was supported by the Bio & Medical Technology Development program of the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (MSIT) of the Republic of Korea and a grant from the Korea Research Institute of Bioscience & Biotechnology (KRIBB) Research initiative program.

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