Metagenomics Analysis of Microbial Communities in Borehole Water from Selected Wards in Sokoto Metropolis

Culture-independent metagenomics approaches reveal a vastly more complex microbial ecology in environmental water sources than conventional culture methods can detect, with implications for accurately assessing drinking water safety. This analytical study employed shotgun metagenomics to comprehensively characterize microbial communities and antibiotic resistance gene profiles in borehole water from eight densely populated wards in Sokoto metropolis, Sokoto State, in the North West geopolitical zone of Nigeria. Water samples were collected from 40 boreholes during dry and wet seasons. DNA was extracted from membrane-filtered concentrates and subjected to paired-end Illumina sequencing. Taxonomic profiling, functional annotation, and antibiotic resistance gene identification were performed using established bioinformatics pipelines. Taxonomic analysis revealed a diverse microbial community dominated by Proteobacteria and Firmicutes, with pathogenic species including Legionella pneumophila, Campylobacter jejuni, and Enterococcus faecalis detected in 37.5 to 62.5 percent of samples. Multiple antibiotic resistance genes including blaTEM, tetM, ermB, and sul1 were present across 85 percent of samples, with significant enrichment in wet season samples. The resistome profile differed markedly between boreholes in proximity to open drainage systems and those in protected zones. These findings demonstrate that Nigerian borehole water harbors a complex and resistance gene-enriched microbiome that poses underappreciated public health risks, and advocate for metagenomics-integrated water quality surveillance. Keywords: metagenomics, borehole water, antibiotic resistance genes, Sokoto, water safety.