Jeong, Haeyoung
(Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB))
,
Choi, Sanghaeng
(AtoGen Co., Ltd.)
,
Park, Gun-Seok
(AtoGen Co., Ltd.)
,
Ji, Yosep
(Advanced Green Energy and Environment, Handong Global University)
,
Park, Soyoung
(Advanced Green Energy and Environment, Handong Global University)
,
Holzapfel, Wilhelm Heinrich
(Advanced Green Energy and Environment, Handong Global University)
,
Mathara, Julius Maina
(Dept of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology)
,
Kang, Jihee
(AtoGen Co., Ltd.)
Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome ...
Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.
Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.
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제안 방법
rhamnosus BFE5264 [13]. In this study, we compared the genome sequence of L. rhamnosus BFE5264 which has a cholesterol-lowering effect through changes in intestinal microorganisms and performed a comparative genome analysis with other strains of the same species. Through this comparative analysis, we aimed to determine the specific genes expressed by this strain and utilize them as efficient industrial materials.
대상 데이터
At the time this article was prepared (April 2018), there were 112 available L. rhamnosus genomes from the RefSeq database, including type strain DSM 20021. Among them, there are two almost identical records from the same strain L.
이론/모형
To identify shared gene clusters among genomes and perform codon-based multiple sequence alignment, Roary was performed with a BLASTP percent sequence identity cutoff of 90% [21]. An approximate maximumlikelihood phylogenetic tree was constructed using FastTree 2 [22] with the generalized time-reversible model. Hierarchical clustering and visualization of ANI and BLAST score matrices, the latter being calculated using the LS-BSR [23], were carried out in R.
An approximate maximumlikelihood phylogenetic tree was constructed using FastTree 2 [22] with the generalized time-reversible model. Hierarchical clustering and visualization of ANI and BLAST score matrices, the latter being calculated using the LS-BSR [23], were carried out in R. Tree files with associated data matrices were visualized using iTOL [24].
성능/효과
Generic genome properties of 12 L. rhamnosus strains whose assembly levels were ‘Complete Genome’ or ‘Chromosome’ and the type strain DSM 20021T, being in scaffold level, were compared in Table 1, which shows that the genome sizes and GC values were very similar to each other.
Two consecutive CRISPR regions (1159 bp and 1092 bp), separated by an IS5-family transposase gene (AWJ15_06400) were found at around 1.38 Mb position. The IS in between two CRISPR regions might be active in the strain BFE5264 genome, because as many as 22 complete copies were found throughout the genome.
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