Metagenome-Assembled Genome Reconstruction of Novel Antibiotic-Producing Microorganisms from Soil Ecosystems in the Niger Delta, South South Nigeria

The biodiversity-rich soils of the Niger Delta represent an underexplored reservoir of novel antibiotic-producing microorganisms whose secondary metabolite biosynthetic gene clusters may yield new pharmacological leads against multidrug-resistant pathogens. This research applies a culture-independent metagenomics approach to reconstruct metagenome-assembled genomes of novel antibiotic-producing microorganisms from mangrove, forest, and agricultural soils in Rivers State, South South Nigeria. Composite soil samples will be collected from 30 geographically distinct sites with contrasting land use patterns. Total environmental DNA will be extracted and subjected to short-read Illumina and long-read Oxford Nanopore Technologies co-sequencing. Metagenome assembly, binning, and quality assessment will be performed using MetaSPAdes, MetaBAT2, and CheckM. Antibiotic biosynthetic gene cluster annotation will employ antiSMASH, and putative novel clusters will be identified by sequence divergence thresholds from known databases. Representative MAGs carrying novel BGCs will be phylogenomically placed within microbial diversity frameworks. Culture-guided recovery of candidate producers will be attempted using selective and dilute nutrient media. Bioactivity screening against ESKAPE pathogens and priority WHO critical pathogens will be conducted on soil extract libraries. Original contributions include a comprehensive metagenome-resolved catalogue of Niger Delta soil biosynthetic potential, taxonomic novelty assessments, and identification of structurally novel antibiotic scaffold candidates. Findings provide a scientific foundation for bioprospecting programmes targeting antimicrobial drug discovery from Nigerian soil ecosystems. Keywords: metagenomics, biosynthetic gene clusters, Niger Delta soil, antibiotic discovery, MAG