Fermentation

Fermentation is the enzyme-catalysed breakdown of organic substrates—most often carbohydrates—by microorganisms under oxygen-limited or anaerobic conditions. In its simplest form, fermentative pathways convert sugars into acids, alcohols and gases, liberating energy for cellular growth in the absence of respiration. Processes range from traditional food and beverage manufacture—yoghurt, cheese, sourdough, beer and wine—to large-scale production of bio-based chemicals, fuels and pharmaceuticals. Key parameters include pH, temperature, substrate composition and microbial community structure, all of which determine pathway fluxes and product profiles. Two principal formats prevail: submerged fermentation, in which cells grow in a free-flowing liquid medium, and solid-state fermentation, in which microbes colonise moist solid substrates. Advances in metabolic and microbial engineering, bioreactor design and downstream processing have substantially increased titres, yields and specific productivities, enabling a transition from bespoke artisanal products to integrated biorefineries that valorise waste streams and support circular-economy objectives.

Research from Nature Portfolio

Recent global sequencing of full-scale anaerobic digesters has expanded reference databases for bacteria and archaea, achieving species-level resolution across 285 reactors. This work revealed core consortia conserved despite diverse feedstocks and operating conditions, and identified environmental drivers—such as temperature and substrate type—that govern community structure. Such insights underpin the predictive design of digesters for stable biogas yield and enhanced waste treatment.

Multi-omics investigations of a traditional Indonesian fermented food uncovered a distinct subpopulation of Neurospora intermedia adapted to soymilk by-products. Transcriptome and metabolome analyses demonstrated efficient pectin and cellulose degradation, enabling upcycling of fruit and vegetable pomaces into a nutritious, mycotoxin-free matrix. This case study illustrates how molecular characterisation of non-conventional fermentative fungi can guide scalable waste-to-food conversions.

Pathway reconfiguration in an acid-tolerant yeast chassis has enabled high-level biosynthesis of succinic acid at low pH, reducing downstream purification costs. By coupling oxidative and reductive loops of the tricarboxylic acid cycle and employing adaptive evolution, engineered Issatchenkia orientalis attained over 100 g L⁻¹ succinate in pilot-scale fed-batch fermentations, with techno-economic analyses projecting 34–90 % lower greenhouse-gas emissions than petrochemical routes.

Research from all publishers

Pilot-scale trials converting source-separated municipal food waste to bioethanol compared separate hydrolysis and fermentation with simultaneous saccharification and fermentation. At high solids loadings, SSF increased ethanol yields by 77 % and reduced production cost to approximately €1.57 per kg, demonstrating the economic and environmental benefits of process integration for heterogeneous feedstocks.

A study evaluating organic fractions of municipal solid waste as a feedstock for succinic acid production showed that tailored enzymatic hydrolysates supported continuous fermentation by Actinobacillus succinogenes at productivities of 1.27 g L⁻¹ h⁻¹. Downstream purification delivered over 99 % succinate purity, and preliminary techno-economic modelling indicated a potential minimum selling price of USD 2.5 per kg, underscoring the viability of waste-derived platform chemicals.

Fermentation publication trend

The graph below shows the total number of articles in fermentation across all publications each year (not limited to Nature Index journals).

Technical terms

Submerged fermentation: Cultivation of microorganisms in a liquid medium, allowing precise control of parameters and easy downstream processing.

Solid-state fermentation: Microbial growth on moist solid substrates with minimal free water, often used for fungi on agro-residues.

Anaerobic digestion: Sequential hydrolysis, acidogenesis and methanogenesis by consortia of bacteria and archaea, yielding biogas.

Metabolic engineering: Rational modification of cellular pathways to redirect fluxes toward desired products.

Core microbiota: A conserved set of microbial taxa that consistently occurs across similar ecosystems or reactor types.

Techno-economic analysis: Integrated assessment of process design, costs and environmental impacts to gauge commercial feasibility.

References

1. Microorganisms in Fermentation.
2. MiDAS 5: Global diversity of bacteria and archaea in anaerobic digesters. Nature Communications (2024).
3. Neurospora intermedia from a traditional fermented food enables waste-to-food conversion. Nature Microbiology (2024).
4. An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis. Nature Communications (2023).
5. Valorisation of source-separated food waste to bioethanol: pilot-scale demonstration. Biomass Conversion and Biorefinery (2022).
6. Evaluation of organic fractions of municipal solid waste as renewable feedstock for succinic acid production. Biotechnology for Biofuels and Bioproducts (2020).