Lactic acid bacteria mechanism of protein degradation in anaerobic co-fermentation of cabbage waste with wheat bran

Chemical Engineering Journal, Journal Year: 2025, Volume and Issue: unknown, P. 160738 - 160738

Published: Feb. 1, 2025

Language: Английский

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GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 5, 2025

ABSTRACT Genome foundation models hold transformative potential for precision medicine, drug discovery, and understanding complex biological systems. However, existing are often inefficient, constrained by suboptimal tokenization architectural design, biased toward reference genomes, limiting their representation of low-abundance, uncultured microbes in the rare biosphere. To address these challenges, we developed GenomeOcean , a 4-billion-parameter generative genome model trained on over 600 Gbp high-quality contigs derived from 220 TB metagenomic datasets collected diverse habitats across Earth’s ecosystems. A key innovation is training directly large-scale co-assemblies samples, enabling enhanced microbial species improving generalizability beyond genome-centric approaches. We implemented byte-pair encoding (BPE) strategy sequence generation, alongside optimizations, achieving up to 150× faster generation while maintaining high fidelity. excels representing generating protein-coding genes evolutionary principles. Additionally, its fine-tuned demonstrates ability discover novel biosynthetic gene clusters (BGCs) natural genomes perform zero-shot synthesis biochemically plausible, complete BGCs. sets new benchmark research, product synthetic biology, offering robust advancing fields.

Language: Английский

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A genetically tractable branch of environmental Pedobacter from the phylum Bacteroidota represents a hotspot for natural product discovery

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 14, 2025

Emerging global challenges, such as antimicrobial resistance, have shifted the focus of natural product discovery from well-characterized microbial producers to underexplored taxonomic groups. Here, we computationally and experimentally characterize biosynthetic potential genus Pedobacter, a Bacteroidota taxon known for antibiotic production that harbors numerous uncharacterized secondary metabolite (SM)-encoding gene clusters (BGCs). Through phylogenomic analysis identify distinct clade enriched in lipopeptide-associated BGCs, most which lack chemical products. By developing de novo genetic tools integrating metabolomics, linked specific metabolites their corresponding BGCs. Using synthetic analytical chemistry proof concept, isolated structurally characterized twelve linear lipopeptides (cryopeptins A–N), containing rare dehydrovalines Pedobacter cryoconitis. We demonstrate all cryopeptins, despite structural heterogeneity, are biosynthesized by single multi-domain non-ribosomal peptide synthetase (NRPS) cluster. Mechanistically, propose this BGC drives diversity through combinatorial fatty acid incorporation iterative amino assembly, resulting variable chain lengths. This work highlights versatility Pedobacter outlines methods manipulation systematically access its cryptic repertoire.

Language: Английский

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Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research

Nature Biotechnology, Journal Year: 2025, Volume and Issue: unknown

Published: April 29, 2025

Language: Английский

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