Neurospora intermedia from a traditional fermented food enables waste-to-food conversion
Fungal fermentation of food and agricultural by-products holds promise for improving food sustainability and security. However, the molecular basis of fungal waste-to-food upcycling remains poorly understood. Here we use a multi-omics approach to characterize oncom, a fermented food traditionally produced from soymilk by-products in Java, Indonesia. Metagenomic sequencing of samples from small-scale producers in Western Java indicated that the fungus Neurospora intermedia dominates oncom. Further transcriptomic, metabolomic and phylogenomic analysis revealed that oncom-derived N. intermedia utilizes pectin and cellulose degradation during fermentation and belongs to a genetically distinct subpopulation associated with human-generated by-products. Finally, we found that N. intermedia grew on diverse by-products such as fruit and vegetable pomace and plant-based milk waste, did not encode mycotoxins, and could create foods that were positively perceived by consumers outside Indonesia. These results showcase the traditional significance and future potential of fungal fermentation for creating delicious and nutritious foods from readily available by-products.
Authors
- Jay D. Keasling (ORCID: https://orcid.org/0000-0003-4170-6088)
- Vivian Ng (ORCID: https://orcid.org/0000-0001-8941-6931)
- Diego Prado Vásquez (ORCID: https://orcid.org/0000-0001-5261-7393)
- C. Hanny Wijaya (ORCID: https://orcid.org/0000-0002-2938-7662)
- Igor V. Grigoriev (ORCID: https://orcid.org/0000-0002-3136-8903)
- Ana Calheiros de Carvalho (ORCID: https://orcid.org/0000-0002-7326-6913)
- Rasmus Munk
- Vayu Maini Rekdal (ORCID: https://orcid.org/0000-0002-8699-8902)
- Guifen He (ORCID: https://orcid.org/0000-0003-0433-2822)
- Sajeet Haridas (ORCID: https://orcid.org/0000-0002-0229-0975)
- Anna Lipzen (ORCID: https://orcid.org/0000-0003-2293-9329)
- Pia M. Sörensen (ORCID: https://orcid.org/0000-0001-7433-0844)
- Edward E. K. Baidoo (ORCID: https://orcid.org/0000-0001-5787-1219)
- Robert Riley (ORCID: https://orcid.org/0000-0003-0224-0975)
- Yuko Yoshinaga (ORCID: https://orcid.org/0000-0002-4978-9394)
- Mikel Olaizola García
- Irma Putri Damayanti
- José Manuel Villalobos‐Escobedo (ORCID: https://orcid.org/0000-0002-8412-6748)
- Pablo Cruz‐Morales (ORCID: https://orcid.org/0000-0002-6751-8897)
- Lilis Nuraida
- Mi Yan (ORCID: https://orcid.org/0000-0002-2027-0249)
- Nabila Rodriguez-Valeron
- Alexander Rosales
- Christopher Daum (ORCID: https://orcid.org/0000-0003-3895-5892)
Institutions
- QB3 (US)
- Berkeley College (US)
- Harvard University (US)
- Lawrence Berkeley National Laboratory (US)
- Joint Genome Institute (US)
- IPB University (ID)
- Basque Culinary Center (ES)
- Novo Nordisk Foundation (DK)
- Miller College (US)
- Joint BioEnergy Institute (US)
- University of California, Berkeley (US)
- Technical University of Denmark (DK)
- Tecnológico de Monterrey (MX)
Publication Details
- Journal
- Nature Microbiology
- Published
- 2024-08-29
- DOI
- https://doi.org/10.1038/s41564-024-01799-3
- Citations
- 59
- Primary Topic
- Agriculture Sustainability and Environmental Impact
- Type
- article
- Field-Weighted Citation Impact
- 27.07
Funders
- U.S. Department of Energy
- Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley
- Joint Genome Institute
- Novo Nordisk
- Novo Nordisk Fonden
- Office of Science
- Biological and Environmental Research
- Lawrence Berkeley National Laboratory