Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum

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

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.

Integrated Genomics and Phenotypic Analysis of Pediococcus pentosaceus BGI-N8 and Pediococcus acidilactici BGI-N9: Partial Evidence Suggesting In Vitro Probiotic Properties to Glycolipid Metabolism Regulation Potential

Dietary interventions using probiotics actively regulate metabolism in obesity and type 2 diabetes. This study aimed to characterize two novel co-isolated strains, P. pentosaceus BGI-N8 and P. acidilactici BGI-N9, using an integrated genome–phenotype approach. Whole-genome sequencing established their preliminary safety and functional genotypes, followed by in vitro assays measuring gastrointestinal tolerance, adhesion, and metabolic enzyme activity. Genomic analysis revealed that both strains achieved genome-based safety levels, and no high-confidence transferable AMR determinants and canonical virulence factors were identified. Functional annotation showed that BGI-N8 and BGI-N9 contain essential genes for gastrointestinal adaptation, including F0F1-ATPase, the dltA-D operon, and the opp transport system. Phenotypically, BGI-N9 exhibited superior acid resistance (79.3% survival at pH 2.0), while both strains showed robust auto-aggregation (>70%) and high adhesion to HT-29 cells (ranged from 5.4 to 5.9 adherent bacteria per cell). Furthermore, the strains displayed inhibitory activity against selected indicator pathogens (88.6–97.6% inhibition). Notably, BGI-N8 and BGI-N9 showed comparable α-glucosidase inhibitory activities, with inhibition rates of 44.53% and 39.94%, respectively, Both strains also exhibited comparable cholesterol-removal capacities under the tested conditions, with removal rates of 68.76% and 74.49%. Overall, these genomic and phenotypic results supported the potentials of BGI-N8 and BGI-N9 as candidate probiotic strains with distinct complementary strengths in glycolipid regulation, providing a theoretical basis for their synergistic application. Further mechanistic, safety, and in vivo studies are required to validate their metabolic-health-related relevance.

Evolutionary history and microbial cross-feeding shape lifestyle-stratified dominance of Bifidobacterium longum subspecies in infants

SAR11 Genome Atlas: a genome and gene catalog for functional profiling of the most abundant bacterial clade in the ocean

The SAR11 clade, also known as the order Candidatus Pelagibacterales, is among the most abundant bacterial lineages in the ocean and plays central roles in marine biogeochemical cycles. However, many SAR11 genes remain functionally uncharacterized, highlighting the need for a comprehensive, integrated catalog that supports genomic, functional, and ecological analyses across the clade. Here, we present the SAR11 Genome Atlas, an interactive ortholog group (OG)-centered web resource that integrates 542 SAR11 genomes, including all 132 cultured strain genomes, with functional annotations, synteny, phylogenetic distribution, metatranscriptomic expression, and predicted protein structure information. To demonstrate its utility, we used environmental expression profiles to identify OGs associated with high-latitude environments, recovering OGs known to be involved in cold adaptation and proposing a hypothesis for the function of uncharacterized protein. We further analyzed phylogenetic distribution patterns to identify mutually exclusive functional modules, including candidate alternative systems for Mn/Zn homeostasis and phosphate acquisition, and to associate these modules with distinct oceanographic environments. Together, these case studies demonstrate that the SAR11 Genome Atlas supports complementary analyses that connect environmental signals to genes of interest and use phylogenetic or functional distributions to generate hypotheses about ecological specialization. Through a user-friendly web interface, the SAR11 Genome Atlas enables researchers to explore genomic, environmental, and structural information without specialized computational expertise. All data and analysis outputs are freely accessible online at [https://stsnsn.github.io/SAR11_Atlas/]. The SAR11 Genome Atlas thus provides a scalable framework for generating and testing hypotheses that connect SAR11 genomic variation to protein function and oceanographic context, supporting advances in marine microbial ecology and biogeochemistry.

A pan-genome perspective uncovers the core genetic basis and evolutionary adaptation of lipid synthesis and vesicular transport in Nannochloropsis.

A pan-genome of 17 Nannochloropsis species comprising 14,851 gene families is constructed and a distinct genetic architecture for lipid metabolism is defined: Gene families associated with vesicular transport formed a conserved core functional module, whereas the genetic collection for lipid metabolism showed greater plasticity and was primarily classified as part of the soft-core genome.

Genome mining and comparative genome analysis of Pseudomonas fluorescens revealed diverse biosynthetic and metabolic potential

Understanding of the metabolic capabilities and genomic landscape of the P. fluorescens species is enhanced, providing a foundation for natural product discovery using bioinformatic approaches.