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Draft genome sequence of Senegalimassilia sp. KGMB 04484 isolated from healthy Korean human feces
Korean J. Microbiol 2019;55(2):160-163
Published online June 30, 2019
© 2019 The Microbiological Society of Korea.

Kook-Il Han1, Se Won Kang1, Ji-Sun Kim1, Keun Chul Lee1, Mi Kyung Eom1, Min Kuk Suh1, Han Sol Kim1, Seung-Hwan Park1, Ju Huck Lee1, Jam-Eon Park1, Byeong Seob Oh1, Seung Yeob Yu1, Seung-Hyeon Choi1, Dong Ho Lee2, Hyuk Yoon2, Byung-Yong Kim3, Je Hee Lee3, and Jung-Sook Lee1,4,*

1Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea,
2Seoul National University Bundang Hospital, Seongnam 13620, Republic of Korea,
3ChunLab, Inc., Seoul 06725, Republic of Korea,
4University of Science and Technology (UST), Daejeon 34113, Republic of Korea
Correspondence to: E-mail: jslee@kribb.re.kr; Tel.: +82-63-570-5618; Fax: +82-63-570-5609
Received February 14, 2019; Revised March 13, 2019; Accepted March 20, 2019.
Abstract

Senegalimassilia sp. KGMB 04484 was isolated from fecal samples obtained from a healthy Korean. The whole-genome sequence of Senegalimassilia sp. KGMB 04484 was analyzed using the PacBio Sequel platform. The genome comprises a 2,748,041 bp chromosome with a G+C content of 61.18%, 2,300 total genes, 2,139 protein-coding gene, 21 rRNA genes, and 51 tRNA genes. Also, we found that strain KGMB 04484 had some genes for hydrolysis enzyme, fatty acid biosynthesis and metabolism in its genome based on the result of genome analysis. Those genes of KGMB 04484 may be related to regulation of human health and digest.

Keywords : Senegalimassilia sp. KGMB 04484, cellulase, fatty acid, feces
Body

Human gut microbiome is the complex community of microorganisms that live in the digestive tracts. The majority of the bacteria reside in the colon, with estimates of about 1011-14 cells/g bacteria (Sender et al., 2016). The four major bacterial phyla in the human gut are Actinobacteria, Bacteroidetes, Proteobacteria, and Firmicutes (Khanna and Tosh, 2014). The gut microbiome products, such as short-chain fatty acids (SCFAs) and membrane proteins, may affect host metabolism by regulating digestion, inflammation, and other functions (Cuevas-Sierra et al., 2019). Strain KGMB 04484 was isolated during the investigation of the bacterial diversity of Korean gut microbiome. On the basis of the phylogenetic, phenotypic, and chemotaxonomic characteristics, strain KGMB 04484T (= KCTC 15721T = CCUG 72347T) was found to belong to a novel species as a member of the genus Senegalimassilia within the family Coriobacteriaceae of Actinobacteria.

The genus Senegalimassilia was first proposed by Lagier et al. (2013). Senegalimassilia species have been isolated from the fecal flora of a healthy Senegalese subject [Senegalimassilia anaerobia (Lagier et al., 2013)]. The genus Senegalimassilia are Gram-positive, anaerobic, indole-negative, and motile coccobacillus bacteria (Lagier et al., 2013). Here, we describe the draft genome sequence and annotation of Senegalimassilia sp. KGMB 04484 isolated from healthy Korean human feces.

The fecal sample was collected from Seoul National University Bundang Hospital, Republic of Korea. The Senegalimassilia sp. KGMB 04484 was grown in Columbia blood agar supplemented with 5% (v/v) horse blood for 3 days at 37°C under a N2/H2/CO2 (86:7:7, by vol) gas mixture. The genomic DNA was extracted using a Wizard genomic DNA purification kit (Promega). Purified genomic DNA sheared to a size of 10 kb using a g-TUBE™ device according to the manufacturer’s instructions (Covaris). Fragmented DNA quantity was analyzed by a Qubit 2.0 fluorometer with a Qubit dsDNA HS Assay Kit (Invitrogen). DNA size was measured by the Agilent 2100 Bioanalyzer with the DNA 12000 assay kit (Agilent). Single-Molecule Real-Time (SMRT) bell library was prepared according to the manufacturer’s instructions (Pacific Biosciences) without a non-size selection. Genome sequencing was performed using a Pacific Biosciences Sequel (Pacific Biosciences) with 2.0 sequencing chemistry and 600 min movies.

The de novo genome assembly was performed with the Hierarchical Genome Assembly Process (HGAP version 4.0, Pacific Biosciences). Pipeline in the SMRT Analysis (version 4.0, Graphical User Interface) using default parameters. Potential contamination in genome assembles were checked by the ContEst16S (Lee et al., 2017). The tRNA was predicted by using tRNAscan-SE (Lowe and Chan, 2016). The CRISPRs were detected using PILER-CR and CRISPR Recognition Tool. The rRNAs and other non-coding RNAs were searched by covariance model search with inference of Rfam 12.0 (Nawrocki et al., 2015). The gene annotation of each CDSs were performed with homology searches against Swiss-prot (Bairoch and Apweiler, 2000), EggNOG 4.5 (Huerta-Cepas et al., 2016), SEED (Aziz et al., 2012), and KEGG databases.

The genome statistics are showed in Table 1. The draft genome of Senegalimassilia sp. KGMB 04484 was composed of a 2,748,041 bp chromosome with a G+C content of 61.18%. The genome features of Senegalimassilia sp. KGMB 04484 are summarized in Fig. 1. The genome is showed to contain 2,139 protein-coding genes, 21 rRNAs (5S, 16S, 23S), and 51 tRNAs were annotated. A total of 2,010 genes were functionally assigned to categories based on clusters of orthologous group (COG) assignments. The majority of the genes are related to energy production and conversion [175 genes (8.7%)] and amino acid transport and metabolism [174 genes (8.6%)].

General features of Senegalimassilia sp. KGMB 04484

PropertyValue
Genome assembly
 Assemble methodSMRT Analysis version 4.0
 Genome coverage153×
Genome features
 Genome size (bp)2,748,041
 G+C content (%)61.18
 No. of contigs2
 Total genes2,300
 Protein-coding genes2,139
 Pseudo genes85
 rRNA genes (5S, 16S, 23S)21 (7, 7, 7)
 tRNA genes51
 CDS assigned by COG2,010
 GenBank accession no.SDPW00000000

Fig. 1.

Graphical circular map of Senegalimassilia sp. KGMB 04484. Marked characteristics are shown from outside to the center; coding DNA sequences (CDS) on forward strand, CDS on reverse strand, tRNA, rRNA, GC content, and GC skew.


We found that various genes involved in hydrolytic enzymes and fatty acid were identified in the genome. The genome revealed the presence of cellulase, which involved in the degradation of cellulose. The genome sequence contained genes for fatty acid biosynthesis and metabolism such as [acyl-carrier-protein] S-malonyltransferase accA, [acyl-carrier-protein] S-malonyltransferase fabD, holo-[acyl-carrier-protein] synthase acpS, β-ketoacyl-[acyl-carrier-protein] synthase III fabH, oxaloacetate decarboxylase oadA, acetyl-CoA carboxylase accC, acyl carrier protein, 3-oxoacyl-[acyl-carrier-protein] reductase fabG, enoyl-CoA hydratase, and 3-hydroxybutyryl-CoA dehydrogenase paaH|hbd|fadB|mmgB gene. The draft genome sequence of Senegalimassilia sp. KGMB 04484 will contribute to understanding the physiological functions of Senegalimassilia sp. KGMB 04484 in the gut.

Based on the 16S rRNA gene sequence similarity and average nucleotide identity, the strain KGMB 04484 is most closely related to Senegalimassilia anaerobia JC110T with the values of 96.49% and 82.74%, respectively.

Nucleotide sequence accession number

Senegalimassilia sp. KGMB 04484 has been deposited in the Korean Collection for Type Cultures under accession number KCTC 15721. The GenBank/EMBL/DDBJ accession number for the genome sequence of Senegalimassilia sp. KGMB 04484 is SDPW00000000.

적 요

본 연구에서는 건강한 한국인 분변으로부터 Senegalimassilia sp. KGMB 04484 균주를 분리하였으며 PacBio Sequel 플랫폼을 이용하여 유전체서열을 분석하였다. 유전체는 G+C 구성 비율이 61.18%이며, 2,300개의 유전자와 2,139개의 단백질 코딩 유전자, 21개의 rRNA 및 51개 tRNA로 구성되었으며, 염색체의 크기는 2,748,041 bp였다. 유전체의 주요 특징은 가수분해효소와 지방산생합성 및 대사에 관련된 유전자를 포함한다. 이러한 유전체의 분석은 KGMB 04484 균주가 사람의 건강 및 소화에 관여할 것으로 여겨진다.

Acknowledgements

This work was supported by the Bio & Medical Technology Development program (Project No. NRF-2016M3A9F3947962) 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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June 2019, 55 (2)
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