Metagenomic sequencing of a two-stage anaerobic co-fermentation system converting food waste and goat manure into medium-chain fatty acids

This project provides comprehensive metagenomic sequencing data from a novel two-stage anaerobic co-fermentation process that converts food waste (FW) and goat manure (GM) into medium-chain fatty acids (MCFAs) without external electron donors. The system employs glucoamylase pretreatment and yeast inoculation in Stage I (pH 5.0, 28 deg C) to promote hydrolysis and self-produced ethanol accumulation, followed by Stage II (pH 7.0, 37 deg C) for acidogenesis and chain elongation (CE). Three substrate conditions were compared: FW alone, GM alone, and a 1:1 mixture (M group). The M group achieved the highest MCFAs yields (caproate up to 12.6 g COD/L; heptanoate up to 0.27 g COD/L).Metagenomic shotgun sequencing (Illumina NovaSeq PE150) was performed on end-point fermentation samples (Day 32) from all three groups. Raw reads were filtered with FASTP, assembled using MEGAHIT, and gene prediction was conducted via MetaGeneMark. A non-redundant gene catalogue was constructed using CD-HIT (>=95% identity, 90% coverage). Functional annotation was systematically carried out against eleven complementary databases to provide a multi-dimensional view of the microbial functional potential:- Species classification: taxonomic profiling based on marker genes or whole-genome alignment.- KEGG: metabolic pathways and key enzymes (e.g., hydrolysis, glycolysis, reverse beta-oxidation, fatty acid biosynthesis).- eggNOG: orthologous groups and evolutionary functional categories.- CAZy: carbohydrate-active enzymes (GHs, GTs, CBMs, CEs, PLs, AAs).- CARD: comprehensive antibiotic resistance gene (ARG) profiles and resistance mechanisms.- PHI: pathogen-host interaction genes relevant to virulence.- QS: quorum sensing system components involved in microbial communication.- MCycDB, NCycDB, SCycDB, PCycDB: element-specific functional gene databases for methane, nitrogen, sulfur, and phosphorus cycling, respectively.This dataset enables in-depth exploration of:- Microbial community functional differentiation under co-fermentation vs. mono-substrates;- Key enzyme genes driving substrate hydrolysis, acidogenesis, and chain elongation;- Carbohydrate degradation potential and its microbial hosts;- Antibiotic resistome fate and horizontal gene transfer risks;- Biogeochemical cycling potential associated with the fermentation digestate.All sequence data, assembled contigs, gene catalogues, and annotation results are linked to this BioProject [accession to be assigned]. This resource supports comparative studies on anaerobic fermentation, chain elongation, organic waste valorization, and functional metagenomics of engineered microbiomes.