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Microbiology and Biotechnology Letters

Genome Report(Note)

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Genome Report  |  Genome Report

Microbiol. Biotechnol. Lett. 2023; 51(4): 566-568

https://doi.org/10.48022/mbl.2311.11016

Received: November 27, 2023; Revised: December 22, 2023; Accepted: December 26, 2023

Complete Genome Sequence of Bifidobacterium bifidum DS0908, Isolated from Human Fecal Sample

Haneol Yang1,2, Yong-Sik Kim3, and Doo-Sang Park1*

1Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup 56212, Republic of Korea
2Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
3Department of Microbiology, College of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea

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

In this report, we present the whole-genome sequence of Bifidobacterium bifidum DS0908 isolated from the human fecal sample. The genome composed of a single circular chromosome is 2,223,317 bp long and the DNA G+C content is 62.65%. No virulence genes were detected in the genomic sequences of B. bifidum DS0908.

Keywords: Bifidobacterium bifidum, whole genome sequencing, fecal sample

Bifidobacterium, an anaerobic gram-positive bacterium, is one of the commonly studied genera that receive attention as probiotics, along with Lactobacillus [1]. Previous research has demonstrated the anti-obesity effects of Bifidobacterium bifidum DS0908, confirming its potential as a probiotic that can assist in obesity treatment by improving glucose metabolism, insulin sensitivity, and plasma lipid profiles [2]. In this report, genomic analysis was conducted on B. bifidum strain DS0908 and analysis of virulence factor-related genes was performed because it is one of the factors used to assess the safety of probiotics [3].

B. bifidum strain DS0908 was isolated from human fecal microbiota screening using De Man, Rogosa and Sharpe (MRS) agar. The genomic DNA of B. bifidum strain DS0908 was extracted using phenol: chloroform: isoamyl alcohol method [4]. Whole-genome sequencing was carried out using a PacBio RS II (Macrogen, Seoul, South Korea). The total number of subreads was 1,000,097, with a total of 951,472,998 subread bases, and HGAP3 was used to assemble the long-reads. The entire assembled genome was visualized using Proksee [5]. Genome annotation was performed using Prokka (v1.14.6) [6]. In addition, the investigation of virulence genes was conducted using the VirulenceFinder 2.0 Server provided by the Center for Genomic Epidemiology (CGE) (http://www.genomicepidemiology.org/), analyzing genes belonging to 16 different classes. The percentage of identity was established with a 5% threshold [7].

One circular contig formed as result of assembly comprised a single chromosome (Fig. 1). The length of the contig was 2,223,317 bp; the N50 value was also 2,223,317 bp, and the DNA G+C content was 62.65%. A total of 1,793 protein-coding genes, 53 transfer RNA genes, and 9 ribosomal RNA genes were identified through genome annotation (Table 1). In the analysis of virulence factor-related genes, it was confirmed that B. bifidum strain DS0908 lacks any virulence genes as summarized in Table 2, indicating its safety with regard to toxicity.

Table 1 . Genome features of Bifidobacterium bifidum DS0908.

Genome featuresValue
Number of contigs1
Chromosome size (bp)2,223,317
GC contents (%)62.65
Coding genes (CDSs)1,793
Transfer RNAs (tRNAs)53
Ribosomal RNAs (rRNAs)9


Table 2 . Analysis for the existence of potential genes associated with virulence factors in the genome of Bifidobacterium bifidum DS0908.

ClassGeneBifidobacterium bifidum DS0908
Contig1
Enterotoxinselk, selq, set
LeucotoxinlukD
CytolysincylA
Cytotoxin KcytK
Hemolysinhbl
GelatinasegelE
Amino acid decarboxylasehdc1, hdc2
tdc
odc
ldc
Hyaluronidasehyl
Endocarditis antigenefaA
Enterococcal surface proteinesp
Aggregation substanceasa1
Adhesion of collagenace
CereulidecesA
Serine proteasesprE
Sex pheromonesccf, cob, cpd
Transposon-related genesint, intTN

−: not detected



Figure 1.Genome map of Bifidobacterium bifidum DS0908, generated using the Proksee tool.

The complete genome sequence data of B. bifidum strain DS0908 was submitted to the GenBank database with the accession number CP069279.1. The BioProject accession number is PRJNA698755 and the Bio-Sample accession number is SAMN17735950.

This work was carried out with the support of a Korea Innovation Foundation (INNPOLIS) grant (2021-DD-UP-0380-03-203) funded by the Korean government (the Ministry of Science and ICT) and a grant from the National Research Foundation of Korea (2022M3H9A108427912) funded by the Ministry of Science and ICT.

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