Lactobacillus fermentum SRCM103285 was isolated from Korean rice wine, makgeolli. Here, we report the complete genome sequence of L. fermentum SRCM103285. Strain SRCM 103285 showed 99.87% of 16S rRNA gene similarity and 99.17% of OrthoANIu value with L. fermentum B1 28
T. The complete genome sequence was obtained by using PacBio RS II platform. Strain SRCM103285 has single circular chromosome of 1,905,587 bp and the G + C contents is 52.3%. The genome contains 1,864 coding sequences, 15 rRNA genes, and 58 tRNA genes. There are at least five genes involved in acetate fermentation and five alcohol tolerance genes.
Keywords: Lactobacillus fermentum, SRCM103285, complete genome sequence, fermentation
Makgeolli is a traditional Korean rice wine that brewed with steamed rice and nuruk, fermenting agent used to make alcohol in a Korean traditional way. Nuruk is made by breeding koji mold by floating grains such as wheat or steamed beans (Aidoo et al., 2006). Even after brew, makgeolli still contains micro-
organisms, especially lactate-producing bacteria, derived from nuruk due to its unique brewing method (Song and Park, 2003).
We isolated a L. fermentum strain designated SRCM103285 from makgeolli by using MRS agar medium at 20°C. The strain was deposited in the Korean Culture Center of Microorganisms (KCCM) with the accession number of KCCM 12742P.
Strain SRCM103285 was closely related to Lactobacillus fermentum B1 28
Tthrough 16S rRNA gene similarity value, 99.87%. Lactobacillus fermentum is an economically important species of lactic acid bacterium used in fermented food (Yeung et al., 2002) and probiotics (Maldonado et al., 2012). The members of L. fermentum are known to produce short-chain fatty acids (SCFA) vigorously (Kahouli et al., 2015). In this report, we investigate the genome of strain SRCM103285, focusing on SCFA production and alcohol resistance.
Genomic DNA was extracted using the Fast DNA
TMSpin Kit for Soil (MP Bio) and checked by 1% agarose gel electrophoresis and quantified by a QuantiFluor
TM(Promega).
The complete genome of strain SRCM103285 was sequenced using the PacBio RS II platform (Pacific Biosciences) with a 20 kb SMRTbell
TMtemplate at Macrogen Inc. and the reads were
Korean Journal of Microbiology (2020) Vol. 56, No. 3, pp. 337-339 pISSN 0440-2413
DOI https://doi.org/10.7845/kjm.2020.0054 eISSN 2383-9902
Copyright ⓒ 2020, The Microbiological Society of Korea
Complete genome sequence of Lactobacillus fermentum SRCM103285 isolated from Korean rice wine, makgeolli
Woorim Kang
1†, Seong-Yeop Jeong
2†, In-seong Cha
1, Min Seok Cho
1, Do-Youn Jeong
2, Byung-Yong Kim
1, and Je Hee Lee
1*
1
ChunLab, Inc., Seoul 06725, Republic of Korea
2
Microbial Institute for Fermentation Industry (MIFI), Sunchang 56048, Republic of Korea
한국 막걸리 막걸리에서 분리 한 Lactobacillus fermentum SRCM103285의 전장 유전체
강우림
1†･ 정성엽
2†･ 차인성
1･ 조민석
1･ 정도연
2･ 김병용
1･ 이제희
1*
1
천랩,
2발효미생물산업진흥원
(Received June 15, 2020; Revised September 2, 2020; Accepted September 3, 2020)
†
These authors contributed equally to this work.
*For correspondence. E-mail: [email protected];
Tel.: +82-2-875-2501; Fax: +82-2-875-7250
338 ∙ Kang et al.
미생물학회지 제56권 제3호
assembled using HGAP version 2.3. The genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (https://www.ncbi.nlm.nih.gov/genome/annotation_
prok/) with the best-placed reference protein set and GeneMarkS methods.
We obtained the complete genome sequence of strain SRCM103285 that has a single circular chromosome of 1,905,587 bp with 52.3% G + C contents. The genome of strain SRCM103285 contains 1,864 coding sequences (CDSs), 15 rRNA genes, and 58 tRNA genes.
Genome-derived 16S rRNA gene sequence of strain SRCM 103285 was compared to other type strains, including the members of Lactobacillus using EzBioCloud server (Yoon et al., 2017a). Genomic relatedness between strain SRCM103285 and L. fermentum B1 28
Twas evaluated with average nucleotide identify (ANI) calculator (Yoon et al., 2017b).
OrthoANIu value between strain SRCM103285 and L.
fermentum B1 28
Twas 99.17%.
Acetate is one of the most representative bacterial SCFAs (LeBlanc et al., 2017). Pyruvate, made from glucose through glycolysis, is decarboxylated by pyruvate dehydrogenase (PDH) to acetyl-CoA and acetyl-CoA is used for acetate production by acetate kinase (Zaunmüller et al., 2006). Four pyruvate dehydrogenase related genes (pdhA, pdhB, pdhC, and ldhA) and an acetate kinase gene (ackA) were found from the genome of strain SRCM103285. Furthermore, strain SRCM 103285 potentially utilize ethanol as an energy source and produce acetate as a by-product. Ethanol is catabolized to acetate through acetaldehyde by alcohol dehydrogenase and acetaldehyde dehydrogenase (Arndt et al., 2008). We found two alcohol dehydrogenase genes (adh) and an acetaldehyde dehydrogenase gene (adhE) in the genome of strain SRCM 103285.
As a member of makgeolli ecosystem, strain SRCM103285 should have alcohol resistance to survive. One of the most representative strategies for alcoholic stress is suppressing the metabolism through the stalling of the ribosome, and RelA/
SpoT family, NusA, and GppA are related genes (Haft et al., 2014). We found these genes in the genome of strain SRCM 103285. Also, members of the genus Lactobacillus, especially, are known to replace fatty acids in the cell membrane with long-chain to gain alcohol tolerance (Gold et al., 1992). We
found two genes that encode Beta-ketoacyl synthase, which is involved in the synthesis of long-chain fatty acid. Taken together, strain SRCM103285 is expected to ribosome stalling and convert cell membrane composition to long-chain fatty acid to resist ethanol in the makgeolli ecosystem.
Nucleotide sequence accession number
The complete genome sequence of Lactobacillus fermentum SRCM103285 was deposited at NCBI under the GenBank accession no. CP035054.
적 요
Lactobacillus fermentum SRCM103285은 막걸리로부터 분리되었다. SRCM103285와 유전적으로 가장 가까운 균주는 L. fermentum B1 28
T이며, 16S rRNA 유전자 분석에서 99.87%
일치도를 보였다. Lactobacillus fermentum SRCM103285의 유 전체는 PacBio RS II 플랫폼을 사용해 분석하였다. SRCM 103285의 유전체는 1,905,587 bp의 크기로, GC 비율은 52.3%
이다. 유전체는 15개의 rRNA, 58개의 tRNA 유전자가 포함된 1,864개의 단백질 코딩 유전자를 갖는 것으로 확인되었다.
SRCM103285는 최소 8개 이상의 아세트산 대사관련 유전자 와 6개 이상의 알코올 내성 유전자를 보유하고 있을 것으로 추 정된다.
Acknowledgments
This research was supported by the Ministry of Trade, Industry & Energy (MOTIE), Korea Institute for Advancement of Technology (KIAT) and Establishment of Infrastructure for Industrialization of Korean Useful Microbes (R0004073).
References
