Neurospora intermedia: the Indonesian oncom fungus that turns plant residues into nutritious food

AUTHORS

Vayu Maini Rekdal1,2,3, José Manuel Villalobos-Escobedo4,5,6,Nabila Rodriguez-Valeron7,8, Mikel Olaizola Garcia7, Diego Prado Vásquez7, Alexander Rosales3,9, Pia M. Sörensen10, Edward E. K. Baidoo3,11, Ana Calheiros de Carvalho12, Robert Riley13, Anna Lipzen13, Guifen He13, Mi Yan13, Sajeet Haridas13, Christopher Daum13, Yuko Yoshinaga13, Vivian Ng13, Igor V. Grigoriev4,5,13, Rasmus Munk7, Christofora Hanny Wijaya14, Lilis Nuraida14, Isty Damayanti14, Pablo Cruz-Morales12 & Jay. D. Keasling 1,3,9,11,12,15

1 Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA.
2 Miller Institute for Basic Research in Science, University of California Berkeley, Berkeley, CA, USA.
3 Joint BioEnergy Institute, Emeryville, CA, USA.
4 Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.
5 Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
6 Tecnológico de Monterrey, Institute for Obesity Research, Monterrey, Nuevo León, Mexico.
7 ALCHEMIST Explore, Research and Development, Alchemist Aps, Copenhagen, Denmark.
8 Basque Culinary Center, Mondragon Universitatea, Donostia, Gipuzkoa, Spain.
9 Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA, USA.
10 Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
11 Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
12 Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
13 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
14 Department of Food Science and Technology, Faculty of Agricultural Engineering, IPB University (Bogor Agricultural University), Dramaga, Indonesia.
15 California Institute of Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.

e-mail: keasling@berkeley.edu

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Neurospora
intermedia

In the markets of Java, Indonesia, reddish blocks of oncom sit stacked beside piles of tofu and tempeh.

At first glance, they look like another traditional ferment, but behind their orange hue and nutty aroma lies a microorganism with enormous biotechnological potential: the fungus Neurospora intermedia.

For centuries, Javanese families have prepared oncom from soybean residue —known as okara— allowing this fungus to colonize and transform it into a protein-rich food.

This fungus not only efficiently breaks down pectins and celluloses —key components of plant waste— but also converts agricultural residues into edible and nutritious biomass.

Through a multi-omics approach —integrating metagenomics, transcriptomics, metabolomics, and phylogenomics— we showed that the N. intermedia strains used in oncom fermentation form a genetically distinct population adapted to grow on human-derived by-products such as sugarcane bagasse and corn residues.

  • During fermentation, the fungus increased the protein and lipid content of okara, produced antioxidant compounds such as ergothioneine, and eliminated molecules associated with bitter flavors.
  • Its genome lacks genes linked to mycotoxin synthesis and shows few secondary biosynthetic pathways, reinforcing its safety for human consumption.
  • Transcriptomic analyses revealed high expression of CAZyme enzymes involved in the degradation of complex plant polysaccharides.
  • In sensory tests conducted in Denmark, foods fermented with N. intermedia received high scores for flavor, texture, and appearance.
  • Participants with no prior experience of oncom described it with notes of “nutty,” “miso,” and “earthy,” an aromatic profile that combines rusticity with natural sophistication.

Unlike other industrial fungi, N. intermedia does not produce mycotoxins or toxic secondary compounds and can grow on a wide range of plant residues without requiring complex equipment.

This makes it an ideal model for sustainable solid-state fermentation, capable of transforming agricultural by-products into high-nutritional-value foods.

The study demonstrates that an ancestral ferment can be scaled into a modern biotechnological platform.
Neurospora intermedia stands at the crossroads of culture, science, and sustainability —a striking example of how traditional knowledge can inspire global solutions to reduce waste and improve food security.

Figures
  • Fig. 1 ext_Neurospora intermedia
    Fig. 1 ext: Fotografías de muestras de oncom negro y rojo recolectadas de diferentes productores en Java, Indonesia.
  • Fig 1_Neurospora intermedia
    Fig. 1: Estudio metagenómico de oncom negro y rojo recolectado en Java, Indonesia.
  • Fig. 2 ext_Neurospora intermedia
    Fig. 2 ext: Mapeo de los datos del metagenoma de escopeta al genoma de N. intermedia
  • Fig. 2_Neurospora intermedia
    Fig. 2: La transcriptómica identifica la degradación de celulosa y pectina durante la descomposición de okara por N. intermedia.
  • Fig. 3 ext_Neurospora intermedia
    Fig. 3 ext: Perfil de nutrientes de la okara cruda y fermentada
  • Fig. 3_Neurospora intermedia
    Fig. 3: Las cepas de N. intermedia utilizadas para oncom pertenecen a una subpoblación genéticamente distinta asociada con subproductos de la actividad humana.
  • Fig. 4 ext_Neurospora intermedia
    Fig. 4 ext: Niveles de ergotioneína en okara cruda y fermentada.
  • Fig. 4_Neurospora intermedia
    Fig. 4: N. intermedia crece en diversos subproductos industriales del procesamiento de alimentos y productos agrícolas.
  • Fig. 5 ext_Neurospora intermedia
    Fig. 5 ext: El análisis de coexpresión global revela un módulo transcripcional compartido entre okara y avicel, así como genes expresados ​​de forma única en okara.
  • Fig. 5_Neurospora intermedia
    Fig. 5: N. intermedia tiene un bajo potencial de producción de metabolitos secundarios y es percibida positivamente por los consumidores fuera de Indonesia.
  • Fig. 6 ext_Neurospora intermedia
    Fig. 6 ext: Perfil de arabinosa y galactosa durante el crecimiento de N. intermedia en okara como única fuente de carbono en cultivos líquidos.
  • Fig. 7 ext_Neurospora intermedia
    Fig. 7 ext: Los representantes de los dos clados de Neurospora intermedia han informado previamente diferencias en la pigmentación de los conidios
  • Fig. 8 ext_Neurospora intermedia
    Fig. 8 ext: Expresión de la celulasa prevista perteneciente a la familia de la glicosil hidrolasa 7 en distintas fuentes de carbono
  • Fig. 9 ext_Neurospora intermedia
    Fig. 9 ext: Rendimiento de biomasa de cepas asociadas a subproductos y asociadas a la quema en okara

Data and code availability
  • Genome and annotation of Neurospora intermedia FGSC #2613 are available on MycoCosm (JGI) and GenBank under BioProject PRJNA982925.
  • Transcriptomic data of N. intermedia FGSC #2613 (carbon source experiments) have been deposited in the Sequence Read Archive (SRA); specific accession numbers are listed in Supplementary Table 11.
  • Genomes and sequencing reads for strains N. intermedia #1791, #2557, #2559, #2685, #5342, #5642, and #5644 are available in GenBank under BioProject PRJNA996151; sequencing details are provided in Supplementary Table 12.
  • 16S, ITS (amplicon) and metagenomic datasets are deposited in GenBank under BioProject PRJNA996151.
  • Scripts used for phylogenetic and SNP analyses of N. intermedia are available on GitHub and archived in Zenodo (Refs. 94 and 95).

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