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

Abstract

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. 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. 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.