Korean Journal of Microbiology (2019) Vol. 55, No. 3, pp. 296-299 pISSN 0440-2413DOI https://doi.org/10.7845/kjm.2019.9092 eISSN 2383-9902Copyright ⓒ 2019, The Microbiological Society of Korea

건강한 한국인 분변으로부터 분리된 Bacteroides sp. KGMB 02408 균주의

유전체 염기서열 초안

유승엽1 ･ 김지선

1 ･ 오병섭

1 ･ 유승우

1 ･ 박승환

1 ･ 강세원

1 ･ 박잠언

1 ･ 최승현

1 ･ 한국일

1 ･ 이근철

1 ･ 엄미경

1 ･ 서민국

1 ･

김한솔1 ･ 이동호

2 ･ 윤혁

2 ･ 김병용

3 ･ 이제희

3 ･ 이정숙

1,4 ･ 이주혁

1*1한국생명공학연구원 생물자원센터,

2분당서울대학교병원,

3천랩,

4과학기술연합대학원대학교

Draft genome sequence of Bacteroides sp. KGMB 02408 isolated from

a healthy Korean feces

Seung Yeob Yu1, Ji-Sun Kim

1, Byeong Seob Oh

1, Seoung Woo Ryu

1, Seung-Hwan Park

1, Se Won Kang

1, Jam-Eon Park

1,

Seung-Hyeon Choi1, Kook-Il Han

1, Keun Chul Lee

1, Mi Kyung Eom

1, Min Kuk Suh

1, Han Sol Kim

1, Dong Ho Lee

2,

Hyuk Yoon2, Byung-Yong Kim

3, Je Hee Lee

3, Jung-Sook Lee

1,4, and Ju Huck Lee

1*

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

(Received August 13, 2019; Revised September 4, 2019; Accepted September 4, 2019)

*For correspondence. E-mail: juhuck@kribb.re.kr;

Tel.: +82-63-570-5634; Fax: +82-63-570-5609

The genus of Bacteroides has been isolated from vertebrate

animal feces. Bacteroides sp. KGMB 02408 was isolated from

fecal samples obtained from a healthy Korean. The whole-

genome sequence of Bacteroides sp. KGMB 02408 was

analyzed using the PacBio Sequel platform. The genome

comprises a 5,771,427 bp chromosome with a G + C content of

39.50%, 5,005 total genes, 18 rRNA genes, and 74 tRNA

genes. Furthermore, we found that strain KGMB 02408 had

some genes for oxidoreductases and menaquinone biosynthesis

in its genome based on the result of genome analysis.

Keywords: Bacteroides sp. KGMB 02408, human feces, mena-

quinone

Various symbiotic microorganisms exist in the human

intestine. Gram-negative Bacteriodetes accounts for a large

proportion of intestinal microorganisms in healthy adults, most

of which are Bacteroides, Alistipes, and Prevotella (The

Human Microbiome Project Consortium, 2012). The genus

Bacteroides was first proposed by Castellani and Chalmers

(1919). Members of the genus Bacteroides are Gram-negative,

non-spore-forming, rod-shaped, non-motile and strictly anae-

robic bacteria, and comprise more than 92 species (Paster et al.,

1994; Smith et al., 2006). As a remarkable genus within the

Bacteroidetes phylum, Bacteroides species are one of the most

numerous groups of microbiota found in gastrointestinal tract

and feces (109–10

11 cells/g) of humans and animals, suggesting

their strong adaptation in the gut (Finegold et al., 1983). They

have various biochemical mechanisms to adopt and survive in

the intestinal environment; for example, reducing oxygen level

in the gut, degrading and fermenting organic substances pre-

sent in the colon, and causing host to produce certain food

Draft genome sequence of Bacteroides sp. KGMB 02408 ∙ 297

Korean Journal of Microbiology, Vol. 55, No. 3

Table 1. General features of Bacteroides sp. KGMB 02408

Property Value

Genome assembly

Assemble method SMRT Analysis version 4.0

Genome coverage 85.22X

Genome features

Genome size (bp) 5,771,427

G + C content (%) 39.50

No. of contigs 53

rRNA genes (5S, 16S, 23S) 18 (6, 5, 7)

tRNA genes 74

Open reading frame 5,005

CDS assigned by COG 4,162

GenBank Accession No. BHWB01000000

source such as fucosylated glycoprotein consumed by other

microorganisms (Wexler et al., 2007; Xu et al., 2007).

Furthermore, they can metabolize starch, pullulan and gly-

cogen in the gastrointestinal tract due to their polysaccharide

utilization gene cluster (Koropatkin et al., 2012). Since the

Bacteroides species possess the abilities and characters men-

tioned above, they can provide favorable gut environment for

other microorganism and maintain host’s gut health and ho-

meostasis. Recently, a novel bacterial strain designated KGMB

02408 was isolated from a healthy Korean feces. On the basis

of the phylogenetic, phenotypic and chemotaxonomic cha-

racteristics, strains KGMB 02408 (= KCTC 15687T = SSUB

10523T) was found to belong to a novel species as a member of

the genus Bacteroides within the family Bacteroidaceae of

Bacteroidia. Here, we described the draft genome sequence

and annotation of Bacteroides sp. KGMB 02408 isolated from

a healthy Korean feces.

The Bacteroides sp. KGMB 02408 was grown in Tryptic

Soy Agar (BD) supplemented with 5% sheep blood (TSAB) in

anaerobic chamber (Coy Laboratory Products) containing 90%

N2, 5% H2, and 5% CO2. To obtain the genomic DNA of strain

KGMB 02408, the grown cells on TSAB plates were collected

by the loop and then a Wizard genomic DNA purification kit

(Promega) was used to extract the genomic DNA. The purified

genomic DNA shearing to a size of 10 kb was done by using a

g-TUBETM device according to the manufacturer’s instructions

(Covaris). Fragmented DNA size was measured by the Agilent

2100 Bioanalyzer with the DNA 12000 assay (Agilent) and

quantity was analyzed by a Qubit 2.0 fluorometer with a Qubit

dsDNA HS Assay Kit (Invitrogen). 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 (HGAP4) pipeline in

the SMRT Analysis version 4.0 using default parameters. Po-

tential contamination in genome assembles were checked by

the Contamination Estimator by 16S (ContEst16S) and CheckM

tools (Li et al., 2015; Parks et al., 2015). The gene prediction

algorithm called Prodigal and tRNAscan-SE were used to

search coding DNA sequences (CDSs) and tRNAs, respectively.

The CRISPRs were found using PILER-CR and CRISPR

Recognition Tool (CRT), and rRNAs and other non-coding

RNAs were searched by covariance model search with in-

ference of Rfam 12.0. Each of the CDSs was annotated by

homology search against Swiss-prot, SEED, EggNOG 4.5, and

KEGG databases.

The Table 1 shows the genome statistics; the draft genome of

Bacteroides sp. KGMB 02408 is composed of a 5,771,427 bp

chromosome with a G + C content of 39.5%. The genome is

showed to contain 5,005 CDSs, 18 rRNAs (5S, 16S, 23S), and

74 tRNAs (Fig. 1). A total of 4,162 genes were functionally

assigned to categories based on clusters of orthologous group

(COG) assignments. The majority of the genes are related to

recombination and repair [348 genes (8.36%)] and cell wall/

membrane/envelope biogenesis [319 genes (7.66%)].

We have identified a variety of genes involved in oxidative-

reductive reaction and menaquinone biosynthesis in the genome.

Interestingly, our previous data showed that strain KGMB

02408 was capable of producing acids from D-xylose by de-

hydrogenase. Moreover, the menaquinone 8 and menaquinone

10 were detected as the major respiratory quinones in KGMB

02408. The genome contains family of the oxidoreductases

such as D-xylose 1-dehydrogenase (NADP) HDHD and xdh

genes. These genes are involved in D-xylose metabolism, pro-

ducing D-xylono-1,5-lactone, NADPH and H+

from D-xylose

and NADP+. The genome sequence also revealed the genes for

quinone biosynthesis such as demethylmenaquinone methyl-

298 ∙ Yu et al.

미생물학회지 제55권 제3호

Fig. 1. Graphical circular map of Bacteroides sp. KGMB 02408. From the center to the outside: GC skew (red and green), G + C content (yellow and blue),

CDSs on the reverse strand (colored by COG categories), CDS on the forward strand (colored by COG categories), and RNA genes (rRNAs-red and

tRNAs-blue).

transferase ubiE and 1,4-dihydroxy-2-naphthoate polyprenyl-

transferase menA genes. In particular, the ubiE gene catalyzes

a chemical reaction, generating menaquinol and S-adenosyl-

L-homocysteine from demethylmenaquinol and S-adenosyl-L-

methionine in the last step of menaquinone biosynthesis. In

addition, the genome has isoprenoid synthesis gene such as

isopentenyl-diphosphate Delta-isomerase IdI. This isomeri-

zation is a key step in the biosynthesis of isoprenoids through

the mevalonate pathway and the MEP pathway, hence strain

KGMB 02408 is expected to produce long-chain menaqui-

nones such as menaquinone 8. The draft genome sequence of

Bacteroides sp. KGMB 02408 will contribute to understanding

the physiological functions of Bacteroides sp. KGMB 02408 in

the gut.

Based on the 16S rRNA gene sequence similarity and

average nucleotide identity, the strain KGMB 02408 is most

closely related to Bacteroides faecichinchillae KCTC 15666T

with the values of 96.5%.

Nucleotide sequence accession number

Bacteroides sp. KGMB 02408 has been deposited in the

Korean Collection for Type Cultures under accession number

KCTC 15687. The GenBank/EMBL/DDBJ accession number

for the genome sequence of Bacteroides sp. KGMB 02408 is

BHWB01000000.

적 요

Bacteroides 속 균주들은 척추동물의 분변 등에서 분리된

것으로 알려져 있다. 본 연구에서는 건강한 한국인 분변으로

부터 Bacteroides sp. KGMB 02408 균주를 분리하였으며

PacBio Sequel 플랫폼을 이용하여 Bacteroides sp. KGMB

02408 균주의 유전체서열을 분석하였다. 유전체는 G + C 구

성 비율이 39.5%이고, 5,005개의 유전자와 rRNA 18개 tRNA

74개로 구성되었으며, 염색체의 크기는 5,771,427 bp였다. 또

한, 유전체 분석 결과를 통해 산화-환원 효소와 메나퀴논 생합

성 및 그와 관련된 다양한 유전자를 발견하였다.

Draft genome sequence of Bacteroides sp. KGMB 02408 ∙ 299

Korean Journal of Microbiology, Vol. 55, No. 3

Acknowledgements

This work was supported by the Bio & Medical Technology

Development program (Project No. NRF-2016M3A9F394

7962) 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.

References

Castellani A and Chalmers AJ. 1919. Manual of tropical medicine, pp.

959–960. 3rd ed., Williams Wood & Co., New York.

Finegold SM, Sutter VL, and Mathisen GE. 1983. Normal indigenous

intestinal flora (pp. 3–31) in Human intestinal microflora in

health and disease. Academic Press ISBN 0-12-341280-3.

Koropatkin NM, Cameron EA, Martens EC. 2012. How glycan

metabolism shapes the human gut microbiota. Nat. Rev. Micro-

biol. 10, 323–335.

Li X, Jensen RL, Højberg O, Canibe N, and Jensen BB. 2015.

Olsenella scatoligenes sp. nov., a 3-methylindole- (skatole) and

4-methylphenol- (p-cresol) producing bacterium isolated from

pig faeces. Int. J. Syst. Evol. Microbiol. 65, 1227–1233.

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, and Tyson GW.

2015. CheckM: assessing the quality of microbial genomes

recovered from isolates, single cells, and metagenomes. Genome

Res. 25, 1043–1055.

Paster BJ, Dewhirst FE, Olsen I, and Fraser GJ. 1994. Phylogeny of

Bacteroides, Prevotella, and Porphyromonas spp. and related

bacteria. J. Bacteriol. 176, 725–732.

Smith CJ, Rocha ER, and Paster BJ. 2006. The medically important

Bacteroides spp. in health and disease. In Dworkin M, Falkow S,

Rosenberg E, Schleifer KH, Stackebrandt E, et al. (eds.). The

Prokaryotes: A Handbook on the Biology of Bacteria, 3rd ed.,

Vol. 7, pp. 381–427. Springer, New York, USA.

The Human Microbiome Project Consortium. 2012. Structure,

function and diversity of the healthy human microbiome. Nature

486, 207–214.

Wexler HM. 2007. Bacteroides: the Good, the Bad, and the Nitty-

Gritty. Clin. Microbiol. Rev. 20, 593–621.

Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens

EC, Henrissat B, Coutinho PM, Minx P, Latereille P, et al. 2007.

Evolution of symbiotic bacteria in the distal human intestine.

PLoS Biol. 5, e156.