High-Quality Genome Assembly, Metabolome, Pangenome, and Metabolic Models of Megasphaera hexanoica KCCM 43214ᵀ

This dataset provides a complete multi-omics and systems biology resource for Megasphaera hexanoica KCCM 43214ᵀ (MH). It integrates genome functional annotation, comparative pangenomics, metabolomics, and genome-scale metabolic modeling (GSMM), offering a comprehensive view of its physiology, metabolism, and evolutionary context. 1. Functional Annotations RAST and Prokka outputs: Whole-genome functional annotation and subsystem classification. DRAM annotation: Metabolic pathway reconstruction including energy, carbon, nitrogen, and fermentation subsystems. HMMER domain searches: Detection of functional protein families and conserved domains. BioElements profiles: Gene-level mapping of elemental metabolism (C, N, S, P cycles). 2. Metabolomic Data Experimental metabolome measurements from culture assays, documenting end-products and intermediates under controlled growth conditions. 3. Genome-Scale Metabolic Models (GSMMs) Draft model reconstructed using CarveME. Two media specific gapfilling were done to prove their hexanoate production prediction with the curated model. This helps to strength the technical validation part. One gap-filled model under AuzoMedia (glucose-rich medium) enabling simulation of carbohydrate-driven fermentation dynamics. All models are provided in SBML format and the respective FBA results are deposited for reproducibility, validation, and downstream simulations. 4. Comparative Pangenomics Pangenome constructed with MH and 8 additional Megasphaera strains. Identification of orthologs, core, non-core, and singleton gene sets. Functional annotation of all categories using SEED, COG, Pfam, and related domain databases. 5. Orthology and Gene Feature Sets Complete matrices of orthologous groups and gene presence/absence across strains. Functional roles of core, accessory, and strain-specific gene families annotated with multiple databases.