4.6 Article

Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches

Journal

GENES
Volume 12, Issue 10, Pages -

Publisher

MDPI
DOI: 10.3390/genes12101504

Keywords

Bifidobacterium bifidum; comparative genomics; diversity; genotype

Funding

  1. National Nature Science Foundation of China [31771953, 31820103010]
  2. Fundamental Research Funds for the Central Universities [JUSRP51903B]
  3. 111project [BP0719028]
  4. International Cooperation Fund Pool Project of Jiangsu Industrial Technology Research Institute
  5. collaborative innovation center of food safety and quality control in Jiangsu Province
  6. National First-class Discipline Program of Food Science and Technology [JUFSTR20180102]

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The research found that Bifidobacterium bifidum has an open pan-genome and a conserved core genome, with genetic diversity mainly reflected in carbohydrate metabolism and immune/competition-related factors. In addition, a novel CRISPR-Cas system was discovered in B. bifidum through this study.
The potential probiotic benefits of Bifidobacterium bifidum have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of B. bifidum isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of B. bifidum. The phylogenetic tree results indicated that the phylogeny of B. bifidum may be related to the geographical features of its isolation source. B. bifidum was found to have an open pan-genome and a conserved core genome. The genetic diversity of B. bifidum is mainly reflected in carbohydrate metabolism- and immune/competition-related factors, such as the glycoside hydrolase gene family, bacteriocin operons, antibiotic resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Additionally, the type III A CRISPR-Cas system was discovered in B. bifidum for the first time. B. bifidum strains exhibited niche-specific characteristics, and the results of this study provide an improved understanding of the genetics of this species.

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