Multi-Omics Characterisation of the Microbiome of Traditional Nigerian Fermented Beverages Under Controlled and Artisanal Conditions

Traditional fermented beverages including kunu zaki, ogi water, burukutu, and palm wine constitute a microbiome-rich landscape that is fundamental to their flavour, safety, and potential probiotic functionality. The microbial ecology of these beverages under Nigerian conditions has been characterised predominantly by culture-dependent methods, leaving a substantial portion of the unculturable microbiome unknown. This study applies multi-omics methods encompassing metagenomics, metatranscriptomics, and metabolomics to characterise the microbiomes of these four traditional beverages under both artisanal production conditions across four Nigerian geopolitical zones (South West, North West, North Central, and South South) and controlled laboratory fermentation conditions. The theoretical contribution is a meta-regulatory network model that integrates genomic potential, transcriptional activity, and metabolite production data to identify key microbial interactions governing fermentation outcomes. Metagenomic sequencing was conducted using Illumina HiSeq with taxonomic profiling by MetaPhlAn and functional annotation by HUMAnN. Metatranscriptomic data identified active metabolic pathways during active fermentation phases. Metabolomics profiling by liquid chromatography with high-resolution mass spectrometry identified 312 volatile and non-volatile compounds across all beverages. Multi-omics integration using multi-block partial least squares revealed microorganism-metabolite associations linking specific Lactobacillus and Saccharomyces taxa to key aroma-active compounds. The study contributes the first comprehensive multi-omics dataset for traditional Nigerian fermented beverages and a novel meta-regulatory network modelling approach. Findings enable rational design of defined starter cultures for standardised traditional beverage production. Keywords: metagenomics, multi-omics, traditional fermented beverages, microbiome, Nigeria