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Background <p><i>Bifidobacteria</i> are the initial colonizers of the human gastrointestinal tract. Due to an obligate anaerobic character, the isolation and culture of <i>Bifidobacterium</i> spp. is challenging. This bottleneck has led to studies being focused on metagenomic analysis rather than genome sequencing of <i>Bifidobacterium</i> spp. from pure cultures. Our metadata analysis revealed paucity of <i>Bifidobacterium</i> genomes reported from the Indian subcontinent. In this report, we describe the selective isolation and whole genome sequencing (WGS) of <i>Bifidobacterium crudilactis</i> from a pure culture of dairy origin from India.</p> Results <p>The WGS by Oxford Nanopore long-read sequencing of genomic DNA of <i>B. crudilactis</i> isolate NASR_001 revealed a single circular chromosome of 2,347,652&#xa0;bp with a GC content of 57.5%. Genome annotation predicted 1923 coding sequences, 6 rRNAs, 46 tRNAs with no CRISPR arrays. Moreover, average nucleotide identity (ANI) analysis with <i>B. crudilactis</i> LMG 23 609 (RefSeq accession GCF_000738005.1) and <i>B. crudilactis</i> MAG UW_FK_BIF1_1 (RefSeq accession GCF_047836735.1) showed 98.8% and 97.3% similarity, respectively, revealing thereby a closest identity and functional similarity to <i>B. crudilactis.</i> The presence of genetic attributes for carbohydrate metabolism, stress response genes and absence of antimicrobial resistance (AMR) encoding genes, as well as paucity of virulence genes signify <i>B. crudilactis</i> NASR_001 to be a putative probiotic organism.</p> Conclusion <p>The genome sequence of <i>B. crudilactis</i> NASR_001 represents a high-quality genome, representative of the species. It offers valuable insights for further exploration of its promising probiotic potential and functional characteristics.</p>

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Comparative genomics of Bifidobacterium crudilactis NASR_001 – unveiling the tapestry of a putative probiotic

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月22日

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  • Sneha Kedia,
  • Pittu Sandhya Rani,
  • Mahanga Nyambero,
  • Viraj Bandsode,
  • Vidyullatha Peddireddy,
  • Niyaz Ahmed

摘要

Background

Bifidobacteria are the initial colonizers of the human gastrointestinal tract. Due to an obligate anaerobic character, the isolation and culture of Bifidobacterium spp. is challenging. This bottleneck has led to studies being focused on metagenomic analysis rather than genome sequencing of Bifidobacterium spp. from pure cultures. Our metadata analysis revealed paucity of Bifidobacterium genomes reported from the Indian subcontinent. In this report, we describe the selective isolation and whole genome sequencing (WGS) of Bifidobacterium crudilactis from a pure culture of dairy origin from India.

Results

The WGS by Oxford Nanopore long-read sequencing of genomic DNA of B. crudilactis isolate NASR_001 revealed a single circular chromosome of 2,347,652 bp with a GC content of 57.5%. Genome annotation predicted 1923 coding sequences, 6 rRNAs, 46 tRNAs with no CRISPR arrays. Moreover, average nucleotide identity (ANI) analysis with B. crudilactis LMG 23 609 (RefSeq accession GCF_000738005.1) and B. crudilactis MAG UW_FK_BIF1_1 (RefSeq accession GCF_047836735.1) showed 98.8% and 97.3% similarity, respectively, revealing thereby a closest identity and functional similarity to B. crudilactis. The presence of genetic attributes for carbohydrate metabolism, stress response genes and absence of antimicrobial resistance (AMR) encoding genes, as well as paucity of virulence genes signify B. crudilactis NASR_001 to be a putative probiotic organism.

Conclusion

The genome sequence of B. crudilactis NASR_001 represents a high-quality genome, representative of the species. It offers valuable insights for further exploration of its promising probiotic potential and functional characteristics.