Aspergillus oryzae (koji mold) is a key microorganism in traditional food fermentations including soy sauce, sake, and miso and is important in novel culinary applications and modern biotechnology, such as sustainable meat alternatives and enzyme production. Despite its industrial importance, until recently, the most recent genome-scale metabolic model (GEM) for A. oryzae dated back to 2008 and was limited to a single strain (RIB40). Here, we present pAo, a pan-GEM for A. oryzae, integrating genomic data from 187 strains to capture species-wide metabolic diversity. Our model comprises 2,025 reactions, representing a 52% increase in metabolic coverage over the RIB40-based model and includes previously overlooked pathways, such as cytochrome P450-mediated xenobiotic metabolism and extended amino acid metabolism. Using this pan-GEM, we derived strain-specific GEMs and validated 8 of them through high-throughput phenotypic screening on 285 substrates. Growth experiments on 4 industrially relevant carbon sources revealed substantial interstrain metabolic diversity, although flux balance analysis indicated that this variability originates at the regulatory rather than network-structural level. This resource provides a foundation for informed strain selection for biotechnological applications and future metabolic engineering in A. oryzae.
An integrated omics study provides foundational insights into the endophytic potential and genomic distinctiveness of AwOcstreb1, isolated from halophytic rice, and opens new avenues for exploring A. welwitschiae for sustainable agriculture and fungal biology.
Nishat Tamanna, Md Nafis Ul Alam, Arifa Akhter Airin et al.· Microbial Genomics· 0 citations
Rec reconstructed genome-scale metabolic models of 44 Pseudomonas strains from various environments and investigated their capabilities to metabolize different carbon sources and metabolic intermediaries, demonstrating how GEM-predicted capabilities can differentiate between strains and that high metabolic versatility is associated with the predicted ability of the strains to remove toxic compounds while maintaining core functionalities.
C. Fócil-Espinosa, Christopher Dalldorf, Diego Martinez et al.· Computational and Structural...· 0 citations
A high-quality genome assembly and an in-depth genome analysis of V. victoriae strain D19 are presented, establishing a valuable foundation for future functional studies and providing keys for developing a new chassis for potential industrial applications.
Bartosz Wąsik, Patryk Kupaj, Paweł Moroz et al.· BMC Genomics· 0 citations
Aspergillus species are ecologically diverse and deeply entangled with human health and industry. A. fumigatus and A. flavus are the two principal species of invasive aspergillosis [1]. A. niger and A. oryzae, on the other hand, are responsible for global enzyme production, organic acid production [2], and koji-based fermentation industries [3]. The question of whether these similar phenotypes share the same genomic mechanisms across the genus is not yet understood. To address this, we constructed per-species pangenomes for the four Aspergillus species (929 initial genomes filtered to 210 ANI-verified, high-quality assemblies for a total of 88 A. fumigatus, 70 A. flavus, 33 A. oryzae, and 19 A. niger assemblies) alongside a genus-level pangenome of 15,163 orthogroups, and conducted phenotype-labeled pan-genome-wide association studies (pan-GWAS) with kinship correction across all species. Pan-GWAS identified up to 117 significant orthogroup presence/absence associations per species-phenotype comparison. However, convergence analysis showed that among the 92 and 62 distinct gene families significant for human pathogenicity in A. fumigatus and A. flavus respectively, the two species seldom agreed on whether the pathogenicity was associated with the enrichment or the depletion of a specific gene family. Convergence analysis of the functional annotations also yielded zero significant results at FDR < 0.05. A literature-curated gene panel analysis also showed that a species labeled pathogenic and another labeled GRAS carried the same aflatoxin and virulence genes, suggesting that gene presence alone cannot readily explain their phenotypic differences. Instead, we propose that niche adaptation operates through the use of the pangenomic rare genome. Reclassifying rare genes by homology identified truly rare subsets (156 to 391 orthogroups per species) distinct from paralogs and gene fragments. Human-pathogenic strains showed significant rare genome expansion of 2.44-fold for both A. fumigatus and A. flavus (kinship corrected, p = 6.6 × 10⁻⁸). Conversely, industrial strains showed rare genome contraction where both A. niger and A. oryzae industrial strains carried 0.57-fold (kinship corrected, p = 0.015) fewer rare genes than their non-industrial counterparts. Hence, we claim that Aspergillus niche evolution proceeds through directional rare genome changes, where there is expansion under pathogenic selection, and contraction under industrial domestication. The rare genome, often discarded as noise, may represent the primary evolutionary source for clinical and biotechnological adaptation in this genus.
Minji Kim, Omid Ardalani, E. Kerkhoven et al.· bioRxiv· 0 citations