In Silico Comparative Genomic and Pan-Genomic Characterization of Bacteroides uniformis JCM5828 reveals Genome Plasticity, Biosynthetic Potential, and Functional Diversity

Background Bacteroides uniformis is a common human gut commensal associated with carbohydrate metabolism and host–microbe interactions. However, its genomic diversity, genome plasticity, and biosynthetic potential remain incompletely characterized. This study aimed to comparatively characterize the genome and pan-genome of B. uniformis, to assess genomic islands, functional diversity, and putative biosynthetic features using publicly available genomic data. Methods An in-silico comparative genomic and pan-genomic analysis was performed using the genome of B. uniformis JCM5828 (RefSeq GCF_044361425.1; BioProject PRJNA224116). Genome annotation was performed using PGAP v6.9, Prokka v1.14.6, and RAST v2.0, followed by average nucleotide identity (ANI) analysis. A 14-strain pan-genome was analyzed using PanExplorer, while genomic islands and biosynthetic features were predicted using IslandViewer 4, antiSMASH, and BAGEL4. Results The JCM5828 genome was approximately 4.7 Mb with a GC content of 46.5% and contained 3,675–4,007 predicted coding sequences depending on the annotation pipeline. ANI analysis confirmed high genomic similarity with closely related B. uniformis genomes. The pan-genome comprised 23.5% core, 34.7% dispensable, and 41.8% strain-specific genes, indicating substantial genomic variability among the analyzed strains. Genomic island predicted regions potentially contributing to genome plasticity. antiSMASH predicted putative lincosamide-like, phosphonate, terpene, and RiPP-associated biosynthetic gene clusters , while BAGEL4 identified a putative sactipeptide-associated locus. Conclusions The comparative analysis highlights genomic variation and predicted biosynthetic capacity in B. uniformis JCM5828 and related strains. However, these findings are strictly computational predictions and should not be interpreted as evidence of experimentally confirmed antimicrobial activity, biosynthetic production, or ecological function. The major limitations of this study are its in-silico design and the relatively small 14-genome dataset , which may limit the generalizability of pan-genomic patterns. Experimental validation approaches such as transcriptomic analysis, RT-qPCR, metabolomic/LC-MS/MS profiling, and functional antimicrobial assays will be required to confirm the predicted functions. Database registration The genome analyzed is available under RefSeq GCF_044361425.1 and BioProject PRJNA224116 .