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Complete genome sequence of Lachnospiraceae bacterium KGMB03038 (=KCTC 15821) isolated from healthy Korean feces
Korean J. Microbiol 2019;55(3):289-292
Published online September 30, 2019
© 2019 The Microbiological Society of Korea.

Ji-Sun Kim1, Se Won Kang1, Kook-Il Han1, Keun Chul Lee1, Mi Kyung Eom1, Min Kuk Suh1, Han Sol Kim1, Ju Huck Lee1, Seung-Hwan Park1, Jam-Eon Park1, Byeong Seob Oh1, Seung Yeob Yu1, Seung-Hyeon Choi1, Seoung Woo Ryu1, 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 August 7, 2019; Revised August 21, 2019; Accepted September 1, 2019.
Abstract
Lachnospiraceae bacterium KGMB03038 (=KCTC 15821) belonging to the class Clostridia in phylum Firmicutes, was isolated from a stool sample of a healthy Korean. Herein, we report the complete genome sequence of strain KGMB03038 analyzed using the PacBio Sequel platform. The genome comprises of 3,334,474 bp with G + C content of 47.8%, which includes 3,099 predicted protein-coding genes, 12 ribosomal RNAs, 54 transfer RNAs, and 4 ncRNAs. Genome analysis revealed that strain KGMB03038 possesses a number of genes involved in hydrolysis of carbohydrates, including mono-, di-, and oligo-saccharides, and biosynthesis of various amino acids.
Keywords : Lachnospiraceae, KGMB03038, carbohydrate, human feces
Body

The human gastrointestinal tract contains a diverse microbial community such as bacteria, virus, archaea and eukarya. This microbial community plays a pivotal role in human health and disease. In particular, the family Lachnospiraceae has been known as major players in the human gut (Manson et al., 2008) because of their ability to produce secondary metabolites such as short chain fatty acids (SCFAs). The designation of the family Lachnospiraceae was first proposed by Rainey (2009). The family Lachnospiraceae is a phylogenetically and morphologically heterogeneous taxon of the class Clostridia in phylum Firmicutes. The members of the family are anaerobic, fermentative, chemoorganotrophic, and some have potential hydrolytic activity such as pectin methylesterase, pectate lyase, xylanase, galactosidase, and glucosidase. The digestive tract of humans or animals is a major habitat for most members and some have been isolated from the oral cavity and soil. On the basis of phylogenetic analysis of 16S rRNA gene sequence, Lachnospiraceae bacterium KGMB03038 was closely related to Merdimonas faecis BR31T (94.3% 16S rRNA gene similarity) and formed a distinct genus-level lineage within the family Lachnospiraceae. This result indicated that strain KGMB03 038 represents a novel species within the novel genus belonging to family Lachnospiraceae of the class Clostridia.

Lachnospiraceae bacterium KGMB03038 was isolated from a healthy Korean feces. The fresh stool sample was collected in anaerobic pouch from Seoul National University Bundang Hospital. The isolation and cultivation of bacteria were performed in the anaerobic chamber (Coy Laboratory Products Inc.) filled with 86% N2, 7% CO2, and 7% H2. The fecal sample suspended in 0.85% saline solution was serially diluted and spread onto Eggerth-Gagnon (EG) agar [2.4 g lab-lemco meat extract, 10 g proteose peptone No. 3, 5 g yeast extract, 4 g Na2HPO4, 1.5 g D-(+)-glucose, 0.5 g soluble starch, 0.2 g L-cystine, 0.5 g L-cysteine, 50 ml horse blood per 1 L; pH 7.6].

Genomic DNA was extracted from cells grown on EG medium as described previously (Chun and Goodfellow, 1995). The genomic DNA of strain KGMB03038 was sequenced using the Pacific Biosciences Sequel platform using a 10 kb Single-Molecule Real-Time (SMRT) bell library by Chun Lab, Inc. De novo genome assembly was performed with the Hierarchical Genome Assembly Process (HGAP4) pipeline in the SMRT Analysis version 4.0 (GUI) using default parameters. Potential contamination in genome assembles was inspected by the Contamination Estimator by 16S (ContEst 16S) and CheckM tools (Lee et al., 2017). The protein coding sequences (CDS) were predicted by prodigal (Hyatt et al., 2010) and the CRISPRs were searched using PILER-CR (Edgar, 2007) and CRISPR Recognition Tool (CRT) (Bland et al., 2007). The annotation of each CDS was performed using the National Center for Biotechnology Information (NCBI)’s Prokaryotic Genome Annotation Pipeline 2.0 (PGAP) (Tatusova et al., 2016).

Whole genome sequencing by the PacBio platform produced a total of 46,321 reads with an average length of 3,288 bp and genome coverage depth, about 383. As described in Table 1, the complete genome of strain KGMB03038 consists of a single circular 3,334,474 bp chromosome with G + C content of 47.8%. No functional plasmid was detected in genome. The genome is predicted to contain 3,099 coding sequences (CDSs), 12 rRNAs (5S, 16S, 23S), 54 tRNAs, and 4 ncRNA genes. A total of 2,924 genes were functionally assigned to categories based on clusters of orthologous group (COG) assignments and the categorized genes were presented in the circular representation with color codes (Fig. 1). Among them, major categories were following as: “unknown function” (S, 37.3%), “amino acid transport and metabolism” (E, 8.7%), “transcription” (K, 8.2%), “replication, recombination and repair” (L, 6.9%), and “carbohydrate transport and metabolism” (G, 6.4%). Genome analysis revealed that strain KGMB03038 possesses putative enzymes for a variety of carbohydrates metabolism. The genome sequence contains key enzymes in glycerol metabolism (glycerol kinase and glycerol dehydrogenase) and D-sorbitol metabolism (aldose reductase and sorbitol dehydrogenase). This strain also possesses α-/β-galactosidase, galactokinase, α-glucosidase, xylanase, α-amylase, and amylosucrase, which hydrolyze mono-, di-, and oligo-saccharides such as galactose, maltose, sucrose, xylan, and starch. In addition, genome contains enzymes related with biosynthesis of various amino acid such as alanine, glycine, serine, threonine, cysteine, valine, lysine, arginine, phenylalanine, tyrosine, tryptophan and selenocompound. Overall, the genome analysis suggests that strain KGMB03038 is able to break down various kinds of mono-, di-, and oligo-saccharides, and biosynthesizes amino acids in human gut, indicating that this novel Lachnospiraceae bacterium KGMB03038 will contribute to human health promotion.

General genomic features of Lachnospiraceae bacterium KGMB 03038

Attribute Value
Genome assembly
 Assembly method SMRT Analysis version 4.0 (HGAP4)
 Genome coverage 382.92X
Genome features
 Genome size (bp) 3,334,474
 G+C content (%) 47.8
 No. of contig 1
 Total genes 3,275
 Protein coding CDS 3,099
 Genes assigned to COGs 2,924
 rRNA genes (5S, 16S, 23S) 12 (4, 4, 4)
 tRNA genes 54
 ncRNA genes 4
 Pseudogenes 106
 GenBank accession NZ_CP041667

Fig. 1.

Complete genome map of Lachnospiraceae bacterium KGMB03038. From the center to the outside: GC skew (red and green), G + C content (yellow and blue), CDS on the forward strand (colored by COG categories), CDSs on the reverse strand (colored by COG categories), and RNA genes (rRNAs-red and tRNAs-blue).



Nucleotide sequence accession number

Lachnospiraceae bacterium KGMB03038 has been deposited in the Korean Collection for Type Cultures under accession number, KCTC 15821. The GenBank/EMBL/DDBJ accession number for the genome sequence of Lachnospiraceae bacterium KGMB03038 is NZ_CP041667.

References
  1. Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, and Hugenholtz P. 2007. CRISPR recognition tool (CRT):a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Biofinformatics 18, 209.
    Pubmed CrossRef
  2. Chun J, and Goodfellow M. 1995. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int. J. Syst. Bacteriol 45, 240-245.
    Pubmed CrossRef
  3. Edgar RC. 2007. PILER-CR:fast and accurate identification of CRISPR repeats. BMC Bioinformatics 8, 18.
    Pubmed CrossRef
  4. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, and Hauser LJ. 2010. Prodigal:prokaryotic gene recognition and translation initiation site identification. BMC Biofinformatics 11, 119.
    Pubmed CrossRef
  5. Lee I, Chalita M, Ha SM, Na SI, Yoon SH, and Chun J. 2017. ContEst16S:an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol 67, 2053-2057.
    Pubmed CrossRef
  6. Manson JM, Rauch M, and Gilmore MS. 2008. The commensal microbiology of the gastrointestinal tract. Adv. Exp. Med. Biol 635, 15-28.
    Pubmed CrossRef
  7. Rainey FA. 2009. Family V. Lachnospiraceae fam. nov., pp. 921.In De Vos P, Garrity GM, Jones D, Krieg NR, and Ludwig W, et al (eds.) Bergey's Manual of Systematic Bacteriology, 2nd edn, Springer, New York, USA.
  8. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44, 6614-6624.
    Pubmed CrossRef


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