In a recent article published in Nature Microbiology, researchers explored the potential of Neurospora intermedia (N. intermedia), a filamentous fungus, to convert food and agricultural by-products into a nutritious and sustainable food source. They focused on oncom, a traditional Indonesian fermented food, to identify specific strains, enzymes, and processes that could enable the conversion of by-products into valuable food products through solid-state fermentation (SSF).
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Background
Minimizing food waste is essential for a sustainable global food system. In industrialized countries, about one-third of all food produced is wasted, contributing to nearly half of the total greenhouse gas emissions from the food system. Upcycling, which involves converting waste into value-added products, can reduce the environmental impact of food production, improve food security, and provide financial benefits.
Filamentous fungi, such as molds and mushrooms, are suitable for microbial upcycling waste streams generated during food processing. For example, growing fungi on the by-products or waste in large-scale liquid fermentations can produce alternative protein sources, reducing the environmental impact of resource-intensive animal agriculture.
About the Research
In this paper, the authors used a multi-omics approach to investigate the potential of N. intermedia, commonly used in oncom, for waste-to-food upcycling. Oncom is traditionally made from soymilk by-products in Java, Indonesia. The researchers initially analyzed black and red oncom samples from small-scale producers in Western Java using metagenomics. They focused on red oncom due to the fungal dominance of N. intermedia and the unique cultivation of this fungus in the food.
To better understand the genetic and molecular traits that make N. intermedia effective for waste-to-food conversion, a high-quality reference genome for the oncom-derived N. intermedia strain FGSC #2613 was generated using long-read sequencing.
Transcriptomics analysis was then performed to examine the fungus's response to okara, a soy-based by-product, as the sole carbon source. This analysis demonstrated the upregulation of several enzymes in breaking down complex plant-based substrates, such as glycosyl hydrolases and pectinases.
Research Findings
The transcriptomics analysis showed that N. intermedia significantly upregulated several predicted carbohydrate-active enzymes (CAZymes) in response to okara, indicating active degradation of complex plant-based substrates. Biochemical validation confirmed the release and consumption of pectin-bound sugars like arabinose and galactose and the degradation of cellulose during fermentation.
Comparative genomics of N. intermedia strains from various environments, including those associated with by-products and those from burned habitats, revealed that strains associated with by-products had a larger pan-genome enriched in hydrolytic enzymes. This genetic difference was mainly driven by single nucleotide polymorphisms (SNPs) rather than gene content, suggesting the adaptive evolution of N. intermedia to diverse plant-based waste streams.
The study identified genes associated with cellulose degradation, including glycosyl hydrolases, critical for breaking down complex carbohydrates. It also showed that N. intermedia could effectively use okara as a growth and biomass production substrate. Further research on the genetic basis of N. intermedia’s ability to thrive on by-products revealed a larger pan-genome in strains associated with by-products enriched with genes related to hydrolase activity, suggesting an adaptation for utilizing diverse by-products.
Screening N. intermedia #2613 on 30 industrially relevant by-products demonstrated its ability to grow on various substrates, including plant-based milk, fruit and vegetable pomace, grain by-products, and oilseed presscakes. The researchers noted a consistent increase in protein content after SSF of these by-products, indicating the potential to upcycle diverse waste streams into more nutritious foods.
Applications
This research has significant implications for developing sustainable food systems. The use of N. intermedia in upcycling food waste into value-added products could help reduce the climate impact of food production and enhance food security. It also highlights the potential of traditional fermented foods as a source of novel microorganisms for food production. The upcycled product could have applications in animal feed, biofuels, and other industries. The findings could guide the development of new sustainable food products from diverse by-products, contributing to a more resilient food system.
Conclusion
The paper summarized that N. intermedia could be a valuable tool for upcycling food waste into nutritious, sustainable food sources and addressing food waste issues. It provided a comprehensive understanding of the fungus's genetic and molecular mechanisms, paving the way for further development and optimization of this technology. It also highlighted the importance of preserving traditional food practices, which can offer valuable insights into sustainable food production. Future work should focus on scaling up the process and evaluating this approach's economic and environmental feasibility.
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Source:
Maini Rekdal, V., Villalobos-Escobedo, J.M., Rodriguez-Valeron, N. et al. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nat Microbiol (2024). DOI: 10.1038/s41564-024-01799-3, https://www.nature.com/articles/s41564-024-01799-3