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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2024; 52(2): 218-220

https://doi.org/10.48022/mbl.2402.02002

Received: February 8, 2024; Accepted: April 3, 2024

Complete Genome Sequence of Bifidobacterium longum subsp. longum DS0950 Isolated from Infant Feces with Obesity-Ameliorating Effects

Hana Jo1, Yong-Sik Kim2, and Doo-Sang Park1,3*

1Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
2Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
3Korea University of Science and Technology, Daejeon 34113, Republic of Korea

Correspondence to :
Doo- Sang Park,        dspark@kribb.re.kr

Abstract

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Bifidobacterium longum subsp. longum DS0950 (B. longum DS0950) was isolated from infant feces and has been reported to be effective in preventing obesity. The whole-genome sequence of B. longum DS0950 was obtained using the PacBio RS II platform, and it was consists of a single chromosome of 2,433,092 bp. The B. longum DS0950 contains genes associated with the synthesis of bacteriocins and a series of genes capable of producing xylitol from ribulose-5-phosphate.

Keywords: Probiotics, Bifidobacterium longum subsp. longum, anti-obesity, whole-genome sequencing

Body

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Bifidobacterium longum subsp. longum is a representative colonizer of the early intestinal microbiota of newborn and is commonly found in the human gastrointestinal tract [1]. Bifidobacterium longum subsp. longum DS0950 (B. longum DS0950) was isolated from infant feces and has been demonstrated as a potential probiotic that can alleviate obesity through mechanisms involving weight loss and reduced fat accumulation [2].

The bacterial genomic DNA was extracted using bead beating and phenol-chloroform method [3]. Subsequently, the purity of DNA was accessed using the NanoDrop Spectrophotometer (Thermo Fisher Scientific, USA). Genomic DNA library construction and sequencing on the PacBio RSII platform were carried out by Macrogen Inc. (Republic of Korea). De novo assembly was performed with HGAP (v3.0) [4] and annotated using Prokka (v1.12b) [5].

To assess the genetic safety of B. longum DS0950 and identify acquired antibiotic resistance genes, ResFinder v4.1 and VirulenceFinder v2.0 [6] were employed for the detection of antibiotic resistance and toxicity genes. Resistance genes were identified using the Comprehensive Antibiotic Resistance Database (CARD) and Resistance Gene Identifier (RGI) web server v5.2.0 [7]. Mobile genetic elements of the bacterial strains were determined using Mobile Genetic Elements (MGE) version 1.0.3 (database version 1.0.2) [8]. Bacteriocin production was investigated using BAGEL4 [9]. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to identify functional metabolic genes in B. longum DS0950.

The total genome length of B. longum DS0950 was 2,433,092 bp consisting of a single contig. The overall G+C content was 60.14%. The genome comprises 2,002 coding sequences, 12 rRNA genes, and 57 tRNA genes (Table 1). According to the results of the KEGG pathway analysis, key genes related to metabolism were identified: 165 genes involved in carbohydrate metabolism, 145 genes related to amino acid metabolism, 57 genes related to energy metabolism, 54 genes related to nucleotide metabolism, and 26 genes related to lipid metabolism (Fig. 1). Genes associated with carbohydrate metabolism, particularly those involved in glycolysis and the pentose phosphate pathway, facilitate the production of ribulose-5-phosphate. This strain was predicted to produce xylitol through genes encoding ribulose phosphate 3-epimerase (EC:5.1.3.1), D-xylulokinase (EC:2.7.1.17), and D-xylulose reductase (EC:1.1.1.9). These characteristics differ from typical features of B. longum, which produces only xylose by encoding xylose isomerase. Additionally, BAGEL4 genome mining detected one bacteriocin operon in B. longum DS0950 that exhibited homology with BLD 1648 of Bifidobacterium longum subsp. longum DJO10A (Fig. 2).

Table 1 . General genomic features of the B. longum DS0950.

StrainB. longum DS0950
Genome size (bp)2,433,093
G+C content (%)60.14
Total number of genes2,055
Total coding genes (CDS)2,002
tRNA57
rRNA12
ncRNAs3


Figure 1.Functional annotation by KEGG metabolic pathway of Bifidobacterium longum subsp. longum DS0950.

Figure 2.Illustrations of the BGC mining results for B. longum DS0950. (A) Bacteriocin biosynthetic gene cluster. (B) multiple sequence alignment results of putative lantibiotic peptide with BLD 1648 in Bifidobacterium longum subsp. longum DJO10A.

ResFinder, VirulenceFinder, and the CARD database were utilized to screen strains for antibiotic resistance and toxicity genes and evaluate their safety. The results indicated the absence of antibiotic resistance and toxicity genes in the B. longum DS0950 genome. However, a mutation (rpoB) was identified in chromosomal DNA.

Furthermore, no transposable or mobile elements that could facilitate the transfer of antibiotic resistance or toxicity genes were found, as there was an absence of mobility genes associated with horizontal gene transfer. Therefore, it has been deemed suitable for probiotic use. The genome sequence of B. longum DS0950, recognized for its efficacy in preventing obesity, offers valuable insights into the health-promoting characteristics of this strain and the mechanisms involved in its interaction with the host.

요약

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Bifidobacterium longum subsp. longum DS0950 (B. longum DS0950)은 신생아 분변에서 분리되었으며 비만 개선효능이 보고되었다. B. longum DS0950 전장유전체 서열은PacBio RS II platforms을 이용하여 확보하였으며, 유전체의 크기는 2,433,092 bp의 단일 contig로 분석이 되었다. B. longum DS0950 균주는 박테리오신의 합성에 관련된 유전자와, ribulose-5-phosphate로부터 xylitol 생산할 수 있는 일련의 유전자를 보유하고 있다.

Nucleotide Sequence Accession Number

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The genome sequences are available at GenBank under the accession number CP069278.

Acknowledgments

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This work was carried out with the support of a Korea Innovation Foundation (INNPOLIS) grant (2021-DD-UP-0380-01) funded by the Korean government (the Ministry of Science and ICT) and a grant from the National Research Foundation of Korea (2022M3H9A1084279) funded by the Ministry of Science and ICT.

Conflict of Interest

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The authors have no financial conflicts of interest to declare.

References

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