From waste to resource: microbial pathways for sustainable food production

Abstract

Despite the increasing global production of food, a significant proportion is wasted, leading to severe environmental harm, economic losses, and exacerbated social inequalities. Food waste occurs at every stage of the food supply chain, from agricultural production to household consumption and has emerged as a critical challenge in achieving sustainability and effective resource management. In this context, understanding the role of microbial ecosystems in the degradation, transformation, and valorization of food waste has become increasingly important. The benefits and advantages of using microorganisms in food production are covered in this review. Both humans and animals can receive nutrients directly from microbes, which can be utilised as substitute food sources. Furthermore, bacteria facilitate crop yield and agri-food production with greater flexibility and diversity. In order to support plant growth, microbes serve as natural nitrogen fixators, mineral solubilizers, nano-mineral synthesisers, and inducers of plant growth regulators. In addition, they are active organisms that break down organic compounds, remove pollutants and heavy metals from soils, and act as soil-water binders. Furthermore, microorganisms living in the rhizosphere of plants release biochemicals that are safe for both the environment and the host. These biochemicals can be used as biocides to manage illnesses, infections, and pests in agriculture. Thus, the utilisation of microorganisms for sustainable food production should be taken into account.

---

Sustainability spotlight

Transforming waste into valuable resources is a cornerstone of sustainable development. This work highlights the pivotal role of microbial ecosystems in converting food waste and by-products into essential components for sustainable food production. By leveraging microbial pathways, this approach not only minimizes environmental impact but also enhances resource efficiency, supports circular food systems, and contributes to global food security. The integration of microbial technologies paves the way for innovative, eco-friendly solutions that reduce waste, conserve natural resources, and promote a resilient and sustainable food future.

1. Introduction

The world's population has risen to over 78 billion people, and by 2023, 2037, and 2057, it is predicted to reach 80, 90, and 100 billion people, respectively.^1,2 In their quest for more food, people are clearing forests to acquire more farmland, which inadvertently impacts the agricultural and food supply production by exacerbating climate change.³ The world's food and climate crises are made worse by the growing demand for meats, which in particular speeds up the consumption of grains and the generation of greenhouse gases by animals, such as carbon dioxide and methane. Finding sustainable and alternate sources of nutrient-dense food is necessary to end this vicious cycle.⁴ The sustainable food supply of the future will rely on microorganisms. Microorganisms double their biomass far faster than mammals and plants, with doubling times as short as tens of minutes. For instance, Saccharomyces cerevisiae takes 90 minutes, while Escherichia coli and Bacillus subtilis take roughly 20–30 minutes.⁵ Furthermore, compared with crop/livestock farming, microorganism culture uses less water and land and emits less carbon dioxide and other greenhouse gases per unit of biomass produced. Furthermore, the biomass of many microorganisms is nutritionally equivalent to or superior to various meats due to its high protein content (up to 70% of the dry cell weight), vitamins, antioxidants, and bioactive substances.^6,7 The microbial system includes different bacteria, fungi, archaea and microorganisms that support natural decomposition and convert food waste into compost, biofuels, bioplastics and biofertilizers.⁸ Bacteria and fungi in organic waste are adapted to break down carbohydrates, proteins, lipids and lignocellulose in food waste.⁹ How biodegradation proceeds and converts pollutants partly depends on the synergy and competition among microbes, the availability of nutrients, and environmental factors such as temperature, pH and moisture.¹⁰ Microbes can manage waste degradation even where there is no oxygen, so waste can be treated with composting, anaerobic digestion and bioelectrochemical technologies. From a systems biology perspective, microbial ecosystems present in food waste are very active in metabolism, genetic mixing and chemical solutions, which encourages studies focused on using them to better manage waste sustainably.¹¹ Additionally, modern techniques such as metagenomics, transcriptomics, proteomics and metabolomics have revealed the microbial manufacturing centers responsible for the mechanisms that govern manage waste transformation.¹² In addition, connecting synthetic biology and microbial engineering has allowed the creation of microorganisms or groups of microorganisms that can break down given contaminants or produce desired substances efficiently.¹³ Because many nations are tightening their laws on waste and greenhouse gas emissions, there is an increasing focus on using microbial technologies that are in line with the principles of circular bioeconomy.¹⁴ When compared with waste landfilling or burning, it is better to use a microbial system that is cheaper and more easily adjustable.⁸ Besides protecting nature and conserving resources, using microbes to manage food waste contributes to food security by returning nutrients and enriching the soil, thereby completing the cycle from food production to waste.¹⁵ Based on this, the current study is focused on developing an approach for the sustainable conversion of waste into useful products using microbes. In addition, this study discusses and highlights various microbial pathways for sustainable food production.

2. Limitations and challenges of microbial consortia in traditional practices

Conventional microbial methods for food waste management, which are dependent on naturally occurring microbial populations, face numerous constraints that impede effective food waste processing. A significant difficulty is the insufficient metabolic diversity within these communities, which restricts their capacity to digest complex organic compounds, such as lignocellulose and lignin.¹⁶ These fibrous compounds exhibit resistance to microbial degradation, especially under conventional conditions, and typically require specialised microbial consortia for successful decomposition.¹⁷ Moreover, natural microbial populations may exhibit sensitivity to variations in environmental parameters, including pH, temperature, and moisture levels.¹⁸ In FW situations, these variables can fluctuate significantly, hindering unenhanced microbial populations from maintaining effective degradation rates.¹⁹ This diversity may result in protracted decomposition, offensive odours, and potential hazards from infections if conditions permit their proliferation. Moreover, indigenous microbes are not consistently capable of neutralising pathogens or poisons found in FW.²⁰ In the absence of regulated settings and specific microbial varieties, the hazards posed by pathogens may persist, thereby restricting the safety and agricultural efficacy of the composted material. AD, another prevalent FW management method, encounters constraints with natural microbial populations. The methanogenesis phase, responsible for methane production, frequently constitutes the rate-limiting step, as indigenous bacteria may be deficient in effective methanogens or a well-balanced microbial community to maximise methane output.²¹ The effective management of food waste presents a significant challenge, as conventional composting and recycling techniques are increasingly inadequate for handling substantial amounts produced globally.²² Engineered microbial solutions offer a novel method for improving the biodegradation rate of organic waste and tackling scaling challenges in food waste management systems. Metabolic engineering and synthetic biology enable the construction of microbial consortia to enhance the decomposition of lignocellulosic and other intricate organic compounds included in food waste, resulting in accelerated biomass degradation and diminished byproduct accumulation. This method not only reduces greenhouse gases, specifically methane and carbon dioxide but also produces important byproducts, such as biogas and nutrient-rich fertilisers, which can enhance bioenergy generation and soil vitality. Engineered microorganisms can be refined to operate effectively under many environmental circumstances, enabling them to treat multiple organic waste streams with minimal intervention. This customisation facilitates a continuous, high-capacity waste management process that is scalable to diverse operational sizes, ranging from local to industrial levels. The incorporation of these microbial solutions into current waste treatment systems can diminish the need for substantial physical enhancements, rendering these biotechnological approaches economically and logistically feasible. The scalability of engineered microbial solutions offers substantial progress in diverting food waste from landfills, facilitating the shift towards a sustainable and circular bioeconomy while mitigating the ecological consequences of food waste disposal.

3. Sources and classification of food waste

Food waste is a critical global problem, involving the loss or disposal of food that is safe to be consumed but is discarded along the food supply chain, including production, post-harvest processing, processing, distribution, retailing, and consumption.²³ Food waste sources can be categorized into three broad groups, namely, agricultural production, food processing and manufacturing and the consumption phase at households and food service industries. Food waste in the agricultural industry comes about as a result of inefficient harvesting methods and pests, climatic factors, and non-commercial aesthetic standards of crops that have not been accepted into commerce because of size, shape or color.²⁴ Poor storage facilities, infrastructure, poor transportation networks, and poor preservation facilities in developing nations also contribute to post-harvest losses, with the supply chain in developing countries prone to being fragmented and inefficient.²⁵

Food processing and manufacturing: wastes are made through cutting, peeling, oversupply, and ruinage during processing, and through food that cannot pass quality control criteria. Furthermore, factories can end up throwing away quite large quantities of by-products, including peels, husks, and seeds, which could be valuable, but they are frequently unused efficiently. At the distribution and retail level, food waste is largely motivated by logistical wastefulness, food overstock, poor handling, wrong packing and high aesthetic requirements that result in edible but cosmetically pristine food being thrown away. Supermarkets and grocery stores commonly discard food that is just shy of their so-called indicator dates, such as best-before or sell-by dates, which may have nothing to do with edibility. Finally, improper storage, misinterpretation of food labels, over-prioritizing, overcooking and failure to take advantage of the leftover food, especially in high-income countries where food is relatively cheap and in abundance at the consumer level, contribute to waste.²⁴ Restaurants, cafeterias, and catering services are a part of the food industry that also results in significant food waste by producing too much food, inefficient portion sizes, and customer demand estimations. This food waste may be categorized as avoidable or may avoid food waste and waste that is impossible to avoid. Avoidable waste of food is food that used to be edible but was nevertheless discarded, including uneaten meals, expired products, and leftovers. It is also conceivable that food waste can be avoided, such as items that some individuals may eat and others may not, such as bread crusts or potato skins. Unavoidable food waste refers to those parts of foods that people do not traditionally eat, like eggshells, banana peels, bones, and ground coffee, and some of them can be valorized as bioenergy or composted.²⁶ Food waste may also be categorized based on its biodegradability and composition, e.g., in fruit and vegetable waste, meat and fish waste, cereal and grain waste and dairy waste, with each having different properties, influencing their treatment and possibly recycling or energy recovery. Additionally, food waste may be identified in terms of origin: whether it is pre-consumer waste, which happens before the consumer interacts with the food, or post-consumer waste, which also happens beyond the point of purchase, i.e., after the food is purchased and when it is consumed.²⁷ Pre-consumed wastes, such as agricultural wastes and on-farm processing wastes, form potential reusable industrial processes or animal feeds, while post-consumer wastes usually offer challenging processes because they are contaminated and mixed food items.²⁸ Food scraps can also be categorized based on their physical properties as solid or liquid, where liquid food scraps contain food scraps, such as soups, sauces, and milk residuals, which have unique handling and treatment procedures. Understanding the causes and types of food waste is essential for developing highly targeted waste reduction action plans, improving the efficiency of the food system, minimising environmental damage, and achieving sustainability along the entire food chain.²⁹ The need for interventions that reduce the enormous amount of food wasted worldwide, as well as the difficulties associated with food security issues, environmental degradation, and economic loss, includes policy reforms such as improving harvesting practices, improving cold chain logistics, lowering cosmetic standards, educating consumers, and enacting laws that encourage food donation and recycling (Fig. 1).

Fig. 1 Routes and sources of food waste.³⁰

4. Characteristics of sustainable food production

Problems associated with traditional agricultural methods can be classified into two categories: (1) wildlife depletion to increase arable land and (2) intense land use. Consequently, sustainable food production has been proposed as a means of reducing dependence on traditional agriculture. Sustainable food production must be analysed comprehensively and structured to enhance three elements concurrently: economic, social, and environmental.³¹ Consequently, in order to offer a novel methodology (e.g., gene editing techniques) or to capitalise on a new opportunity (e.g., intelligent food packaging), judgements must be evaluated across all three dimensions.³² Fig. 2 illustrates the structural framework for the construction of a sustainable food production system. The food supply chain utilising blockchain technology (BCT) is integrated into three elements of sustainability: environmental, social, and economic. Six themes under the sustainable food system framework are categorised as follows: (1) resilience and resource efficiency; (2) sustainable and healthy diets; (3) circular economy; (4) profitability and efficiency; (5) sustainable supply chains and fair trade; and (6) transparency, traceability, and trust. The circular economy, as an emerging issue, significantly contributes to reducing resource consumption, eliminating waste, sustaining economic development, and facilitating recycling, reuse, remanufacturing, and reclamation in a closed system.^33,34 Furthermore, life cycle assessment can be utilised to facilitate decision-making and comprehensively examine the environmental consequences of developing technologies from “cradle to grave” within the sustainable food production system.³⁵ Despite ongoing advancements, the fundamental attributes of sustainable food production merit greater scrutiny in light of the increasingly intricate issues in food production.³⁶

Fig. 2 Block chain technology for sustainable food technology and some of its key elements.³¹

5. Microbial diversity in food waste ecosystems

There is a wide variety and complex nature of microbes in waste food ecosystems that work together to deal with and turn into valuable materials: the organic material in waste streams.³⁷ They both assist in the degradation of food waste and in keeping by-products such as compost, digestate and other valuable materials well-developed and stable.³⁸ The types of microorganisms involved in food waste degradation are influenced by the chemical composition of the waste, its response to parameters such as pH and temperature and its physical characteristics.³⁹ Initially, most of the decays are done by bacteria, especially Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria, which are observed in both the presence and absence of oxygen. Besides, in these groups, genera including Bacillus, Clostridium, Pseudomonas, Lactobacillus, and Streptomyces are important for hydrolysis, acid formation, and interactions that support the breakdown of organic materials.³⁹ The decomposition of complex polysaccharides, lignocellulosic materials, and recalcitrant proteins greatly depends on fungi of the filamentous type and yeasts.³⁷ The main fungal genera in food waste treatment are Aspergillus, Penicillium, Rhizopus, Mucor and Saccharomyces, and they all produce strong extracellular enzymes called cellulases, amylases, lipases and proteases that are useful in breaking down organic compounds.³⁸ Hyphae help to physically change the waste's structure so that bacteria can reach it, and the right amount of moisture is maintained. In anoxic environments, like biogas digesters, the archaea Methanosaeta, Methanosarcina, and Methanobacterium play a crucial role in the last stages, transforming volatile fatty acids and hydrogen into methane and carbon dioxide. They collaborate with fermentative and acetogenic bacteria steadily to sustain bioenergy production.⁴⁰ In microbial fuel cells (MFCs), some bacteria such as Geobacter, Shewanella, and Desulfuromonas transfer electrons from waste to the anode, facilitating energy generation and aiding in waste treatment.⁴¹ Numerous protozoans and other eukaryotic microorganisms inhabit food waste environments, contributing to the regulation of microbial populations and the maintenance of system stability. Biofilms, aggregates of bacteria encased in self-produced gels, are commonly observed in food waste treatment, as these formations provide separation, communal metabolism, and adaptability to environmental variations.⁴² In compost piles, microbial types change from mesophilic in the initial phase to thermophilic as temperatures increase and revert to mesophilic decomposers during the curing process. These include Thermus and Thermoactinomyces, which are heat-resistant bacteria, as well as Thermomyces and Myceliophthora, which are fungi utilised in the high-temperature processing of lignin and cellulose.⁴³ Advanced techniques, including 16S and 18S rRNA sequencing, internal transcribed spacer (ITS) profiling, and metagenomic analysis, have provided fresh insights into the diversity of bacteria in food waste and their functions.⁴⁴ Microbial communities, identified by high-throughput sequencing, exhibit activity and site-specific uniqueness and are influenced by the materials employed, their geographical location, and local operational procedures.⁴⁵ Shotgun metagenomics and transcriptomics enhance our comprehension of metabolic capabilities, regulatory mechanisms, and stress resilience within the microbial community.⁴⁶ Integrative omics, such as metabolomics and proteomics, are increasingly frequently employed in microbial ecology to investigate microbial activity beyond their taxonomic classifications, as shown in Fig. 3. By comprehending these elements, creating microbial consortia can achieve many outcomes in food waste treatment, like rapid decomposition, inhibition of pathogenic bacteria, or enhanced biogas production.⁴⁷ Understanding microbial variety is essential for biosafety and hygiene, as it helps assure the absence of harmful organisms, such as Salmonella, Listeria, Escherichia coli, or Aspergillus flavus, in food waste.⁴⁸ Regulating microbial populations involves utilising beneficial species while suppressing detrimental ones. In summary, the breakdown of food waste and its conversion into beneficial products relies on microbial diversity, which provides the necessary mechanisms and microorganisms for efficient organic matter decomposition.⁴⁹ Manipulating these microbes enables researchers and practitioners to enhance food waste treatment efficacy, foster sustainability, and contribute to the development of a robust circular bioeconomy.

Fig. 3 Microbial diversity in food systems.⁵⁰

6. Ecological interactions and microbial community dynamics in food waste treatment systems

Interactions among microorganisms in food waste ecosystems are complex, dynamic, and essential for the effective management of food waste. Interactions such as synergism, mutualism, commensalism, rivalry, antagonism, and predation influence the structure, functionality, and stability of the microbial communities involved in food waste processing (Fig. 4).⁵¹ Nutrients are abundantly available yet unevenly distributed in food waste habitats, which prompts many bacterial species to collaborate and compete, resulting in behaviors that are unattainable individually.⁵² During the breakdown of complex materials, it is very important because step one begins with primary degraders breaking large polymers like cellulose, hemicellulose, proteins and lipids into smaller ones that the second group takes over.⁵³ For example, Clostridium thermocellum hydrolyzes cellulose into glucose, which Lactobacillus species ferment into organic acids and alcohols, and these are then provided to methane-producing organisms in an anaerobic system. When microbes depend on each other, their waste helps fuel the growth of other groups.⁵⁴ When composting and anaerobically digesting waste, the connection between different types of microorganisms ensures that they break down the materials properly. Mutualism exists in biofilms, as microorganisms grow together, exchange and use enzymes, exchange genes and are guarded by EPS.⁵⁵ Microbial fuel cells (MFCs) operate by allowing Geobacter sulfurreducens to depend on fermentative bacteria to supply reduced materials, thus ensuring a continuous stream of electrons to the anode. Additionally, when composting aerobically, thermophilic fungi help create air spaces and aid oxygen flow, which encourages aerobic bacteria to grow and become active. Community composition and variety are often adjusted when some species better compete for resources such as carbon, nitrogen or micronutrients.⁵⁶ Opportunistic microbes can take the lead under some conditions, but as time goes on and treatment conditions remain stable, more specialized species can take over. Microorganisms often use bacteriocins, antibiotics and secondary metabolites to help control the types of organisms in their environment. Thanks to such microbial conflict, unwanted microbe growth in composting or fermentation can be limited, increasing the safety and hygiene of the results. Bacteria in mixed cultures significantly help one another by using the metabolic residue created by another, without harming their hosts.⁵⁷ Predation occurs in microbial ecosystems related to food waste though it is less understood. Natural population control comes from protozoa and bacteriophages, which consume certain bacteria and affect the breakdown of nutrients and their recycling.⁵⁸ By applying our understanding of ecology, we may enhance the functionality of designed systems, maintain microbial stability, and prevent consortium failure.⁵⁹ Anaerobic digesters depend on maintaining a balanced population of acid- and methane-producing bacteria; allowing one group to overpower the other can lead to an accumulation of volatile fatty acids and a decrease in pH, which adversely affects methane generation. Process parameters such as temperature, pH, hydraulic retention time, and the type of waste utilised can be modified to enhance favourable reactions and mitigate detrimental ones.⁶⁰ Advancements in systems biology and microbial ecology, facilitated by high-throughput sequencing, metagenomics, and bioinformatics, have revealed networks and co-occurrence patterns that influence alterations in microbial populations within food waste ecosystems.⁶¹ This software identifies the most critical species, key creatures, and necessary pathways for the community's functionality and resilience. Such insights facilitate the construction of artificial consortia that are better equipped to adapt to or withstand shifting environments. Moreover, microbes possess mechanisms for DNA exchange, known as horizontal gene transfer (HGT), and utilise quorum sensing to collectively respond to environmental stressors.⁶²

Fig. 4 Illustration of ecological interactions among the microbial species.⁶⁵

Using certain microbes for bioaugmentation depends on knowing how these strains interact with microbes already in the environment.⁶³ Overall, the way microbes influence one another supports the full breakdown of food waste and determines how safe and effective the end products are. Using ecological engineering, synthetic biology and process optimization greatly helps in creating sustainable food waste management technologies that are strong and friendly to the environment.⁶⁴ In short, interactions between microbes in food waste greatly display nature's power and usefulness and act as a useful guide for recycling and new environmental solutions.

Microbial community changes in different waste treatment systems are important for the balance, stability and outcome of various means of waste management, and these changes differ based on whether the system is aerobic (like composting), anaerobic (for example, anaerobic digestion) or mixed with air and water (e.g., microbial fuel cells and bio-electrochemical systems). Such changes mean that microbial consortia alter in composition, shape and power over time due to what substances are provided, the setting, system parameters and the way different microbes affect one another.^1,66 The initial, hungry mesophilic bacteria in composting are Bacillus, Pseudomonas and Actinobacteria, which decompose sugars and proteins. When temperatures rise because of microbial activity, Thermus, Streptomyces, Aspergillus and Mucor become dominant, they focus on breaking down tough materials, such as cellulose and lignin. As compost matures, mesophilic microbes are reintroduced, which supports humification and stabilization processes.⁶⁷ This pattern is necessary for nutrient recycling and stopping pathogens, influenced by how much and what kind of compost is aerated, the level of moisture, the carbon to nitrogen (C/N) ratio and what types of organic materials are composted. Instead, the microbes in anaerobic digestion are divided into separate groups within the system.⁶⁸ These bacteria called hydrolytic and fermentative, such as Clostridium, Bacteroides and Hydrogenobacter, help the process by breaking up complex compounds into simple molecules and volatile fatty acids.⁶⁹ They are further processed by acetate-consuming bacteria such as Syntrophomonas and Syntrophobacter, which team up with various methanogenic microbes, mainly Methanosaeta, Methanosarcina and Methanobacterium, to produce methane and carbon dioxide. Any problems, such as a growth in VFA or ammonia inhibiting the microorganisms, can interfere with methane formation within anaerobic systems.⁷⁰

Higher stability in anaerobic systems often leads to a decrease in microbial diversity because specialized roles appear and redundancy among bacteria decreases. Conversely, microbial fuel cells (MFCs) and various bio-electrochemical systems build up special collections of bacteria, among which are Geobacter, Shewanella and Pseudomonas. They build biofilms on electrodes and depend on electron transfer outside the cell to generate electricity when they oxidize organic wastes from food. Under selective conditions, the community in MFCs develops better electron transmitters, and how they function depends greatly on the type of substrate, electrode and MFC design used.⁷¹ Besides, MFCs usually feature microbial communities that have fermentative species producing reduced compounds, such as acetate, hydrogen or lactate, which are used by electroactive bacteria, thus assisting their groups to work together. Anaerobic membrane bioreactors (AnMBRs), dark fermentation systems and microbial electrolysis cells are linked types, and the microbes in these systems are selected to generate specific products, such as biohydrogen, volatile fatty acids or concentrated effluent, intended for further use. Such systems are influenced by the hydraulic retention time, organic load rate and nutrient addition, which impact the kinds of bacteria and their functions.⁷²

Moreover, changes in temperature, salinity, heavy metals, antibiotics and traces of oxygen in the environment can impact the community of microbes by causing changes in populations, their ability to cope or the system failing, relying on how adaptable and resilient the microbes are. Advancements in 16S rRNA gene sequencing, shotgun metagenomics and metatranscriptomics now make it possible for us to watch these changes occur from moment to moment.⁷³ Studies using metagenomic techniques have shown that archaea in anaerobic digesters handling food waste respond to raised ammonia levels by having Methanoculleus take over from Methanosaeta.⁷⁴ Subsequent research utilising network analysis has identified specific species and microorganisms termed keystone taxa and hub microbes, which frequently exert a significant influence on community stability and functionality.⁷⁵ Upon comprehending these dynamics, specialised microorganisms are introduced to enhance treatments at underperforming stages, such as incorporating cellulolytic bacteria to facilitate hydrolysis and hydrogenotrophic methanogens to augment methane production when VFA levels increase.⁷⁶

Another objective is to establish designer consortia by utilising synthetic biology, which can operate efficiently and maintain durability under diverse stress settings. Mixtures of engineered E. coli and Clostridium strains have been established to produce increased butyrate and ethanol from liquid food waste.⁷⁷ Biostimulation, which involves manipulating environmental variables to enhance native microbial activity, influences community formation. Altering pH, oxidation state, or introducing supplements benefits certain microbes, thereby inhibiting bacteria such as sulfate-reducing bacteria that deplete resources from beneficial methanogens in anaerobic settings.⁷⁸ The selection of inoculum influences the early community and affects the speed of digestion initiation and its sustained stability; digesters utilising adapted sludge commence operation more rapidly and exhibit superior performance.⁷⁹ Comparing systems from cross-ecosystems reveals that in aerobic systems, there is more microbial diversity resulting from changing oxygen levels and differences in habitats, as illustrated in Fig. 5, but in anaerobic systems, there is less diversity and more species that help one another or rely on each other. Overall, the behavior and composition of microbes in food waste treatment systems are determined by environmental, process, substrate and ecological factors.⁸⁰ If these dynamics are well understood, treatment systems can be made more efficient and microbial communities can be strategically built to help reduce waste, conserve resources and preserve the environment.

Fig. 5 Microbial diversity and relative abundance of various microbes.

7. Metabolic pathways for food waste decomposition

Microbial communities break down food waste by involving numerous metabolic routes that turn complex compounds into simple compounds, energy and biogas, compost, organic acids and biofuels.⁸¹ These kinds of metabolic processes occur depending on the surrounding conditions and which microbes are involved. According to the conditions related to oxygen, such as composting, microorganisms oxidize organic substances to make carbon dioxide, water, heat and more microbes, as depicted in Fig. 6(a) and (b). Initially, amylases, cellulases, proteases and lipases break down the big polysaccharides, proteins and lipids into glucose, amino acids and fatty acids outside the cell.⁸² Microorganisms take up monomers and break them down through glycolysis, the tricarboxylic acid cycle and oxidative phosphorylation, producing ATP and completely oxidizing monomers into carbon dioxide.⁸³ By comparison, anaerobic decomposition takes place where oxygen is not present, such as in anaerobic digesters and in landfills, and employs a more complicated and multi-stage biochemical process with several diverse groups of cooperating microorganisms.⁸⁴ Hydrolysis, acidogenesis, acetogenesis and methanogenesis are the major stages of the anaerobic digestion (AD) process. As in aerobic systems, hydrolysis breaks down food waste polymers into monomers using enzymes. Short-chain volatile fatty acids (VFAs), alcohols, hydrogen and carbon dioxide are produced as acidogenic bacteria ferment these monomers.⁸⁵ These acetogenic bacteria turn the intermediates into acetic acid, more carbon dioxide and hydrogen, which become the main food for the final methanogenic bacteria.⁸⁶ Methanogens such as Methanosarcina and Methanobacterium perform methanogenesis using either acetoclastic methanogenesis, which changes acetate directly to methane and CO₂ or hydrogenotrophic methanogenesis, which breaks down H₂ and CO₂ into methane. Achieving efficiency in this process is best done by keeping a good balance between the microorganisms involved and the necessary environmental conditions, like neutral pH, proper temperature, low levels of ammonia and enough time for the process.⁸⁷ Apart from regular aerobic and anaerobic methods, alternative pathways are now recognized because they can help us use food waste to create bio-energy and chemicals. Among them are fermentation processes that yield ethanol, butanol, lactic acid and succinic acid, and these are carried out by bacteria, such as Zymomonas mobilis, Clostridium acetobutylicum and Lactobacillus plantarum.⁸⁸ The enzymatic and microbial degradation of lignocellulosic constituents in fibrous waste yields fermentable sugars, which subsequently undergo reactions to produce bioethanol or organic acids. In microbial fuel cells (MFCs), electroactive microorganisms decompose organic molecules and transfer electrons directly or via mediators to an anode.⁸⁹ The activities utilise specific metabolic pathways, notably the citric acid cycle, and incorporate specialised electron transport chains capable of transferring electrons beyond the cell.⁹⁰ The heat produced by microbes helps raise the temperature, which allows thermophilic microbes to degrade tough or lignin-rich materials in the compost pit.⁹¹ During composting, the microorganisms in the community use different metabolic processes: first oxidative breakdown, then mineralization and finally stabilizing the substances.⁹² The presence of secondary metabolites in soil, such as organic acids and phenolics, also has effects on which microbes gain advantage and how nutrients become available.⁹³

Fig. 6 (a) Metabolic pathway of food waste degradation.⁹⁴ (b) Anaerobic metabolic pathway of food waste degradation.⁹⁵

Recent studies of food waste decomposition show that metagenomics reveals both the taxonomic composition and the functional potential of microbial communities during composting or anaerobic digestion. For example, composting stages (mesophilic, thermophilic, maturation) show shifts in dominant taxa (e.g. Bacillus and Cellulomonas) and in genes encoding carbohydrate-, protein-, and lipid-degrading enzymes; glycoside hydrolase (GH) families are particularly enriched in the early to mid composting stages.⁹⁶ Transcriptomics work is less frequent but growing: metatranscriptomic reviews highlight the active expression of microbial enzymes (CAZymes and amino acid metabolism) during food fermentation and nutrient breakdown, showing how genes for hydrolysis and fermentative processes are regulated in response to substrate type.⁹⁷ Proteomics confirms which enzymes are actually being produced and functional; for example, in fermented products, changes in proteolytic enzymes correspond to protein hydrolysis and flavor and texture evolution. Proteomics helps identify peptidases and other hydrolases responsible for the breakdown of complex proteins in food waste.⁹⁸

Metabolomics, including untargeted metabolite profiling, tracks downstream small molecules: sugars, amino acids, volatile fatty acids (VFAs), antibiotic compounds, and intermediates like phenazines. A recent study integrating metagenomics and metabolomics of an anaerobic digestion and composting system treating organic municipal solid waste (OFMSW) elucidated the persistence and alteration of antibiotic resistance genes and antibiotic compounds during waste processing, highlighting distinct metabolic and chemical profiles at each treatment stage.⁹⁹ Collectively, multi-omics integration elucidates the process: hydrolysis → fermentation → VFA synthesis → methanogenesis or aerobic stabilisation, while identifying inefficiencies or risks (e.g., buildup of certain metabolites and persistence of antibiotic resistance). These findings facilitate the optimisation of waste treatment (temperature, inoculants, and feedstock composition) to improve decomposition, biogas production, and safety.

During composting, the breakdown of organic matter in the feedstock mass is facilitated by hydrolytic enzymes, which include cellulases and β-glucosidases that depolymerize cellulose and glucosides, respectively. Hydrolytic enzymes degrade waste lignocellulosic compounds into polyphenols, polysaccharides, monosaccharides, aldehydes, and acids, which are synthesized by microbial communities at different composting stages. Metabolites produced from lignocellulose degradation are polymerized into humic substances based on humic formation theories, which play an essential role in compost quality. Some particular CAZyme genes detected at different stages of the composting metagenome are summarised (Fig. 7). A comparison of carbohydrate-active enzyme encoding genes against the CAZy database showed that out of annotated glycoside hydrolase (GH) families, sequences affiliated with GH2, GH3, GH20, GH29, and GH43 indicate the primary role of bacteria in hydrolysis of polysaccharides during the initial and mesophilic stages of composting. Other GH families affiliated with GH103 and GH13 genes are relatively more abundant in the thermophilic stage, which is associated with the functional activity of hemicellulose degradation and cleavage of α-glycosidic linkage containing substrates like starch, than in other stages of composting. The thermophilic stage also shows the richness of the sequences of glycosyl transferase (GT) families, like GT4 and GT51 genes, that are associated with the synthesis of peptidoglycan of the bacterial peptidoglycan layer, which might support germination for the establishment of a new bacterial community after the dormant state of bacteria.

Fig. 7 Metagenome annotation for CAZyme families.⁹⁶

8. Use of metagenomic tools to investigate microbial communities in waste

Metagenomic tools have become pivotal in elucidating the structure and functional dynamics of microbial communities in FW systems.¹⁰⁰ Through the direct sequencing of environmental DNA, metagenomics enables a comprehensive and unbiased characterization of both cultivable and non-cultivable microorganisms, thereby overcoming the inherent limitations of culture-based methods.¹⁰¹ This approach is particularly relevant to FW environments, which are microbiologically complex and characterized by diverse substrates that support the heterogeneous microbial consortia involved in the decomposition and transformation of organic matter. High-throughput sequencing (HTS) platforms, including 16S rRNA gene amplicon sequencing and shotgun metagenomics, allow for fine-scale taxonomic resolution and functional annotation of microbial genes.¹⁰² These methodologies have been successfully applied to monitor microbial succession and metabolic capabilities during composting, revealing key microbial taxa and enzymatic pathways that vary with the composting stage and environmental parameters. Such insights are instrumental in refining operational parameters to enhance the degradation efficiency and stability of compost systems.⁶⁶ Moreover, metagenomics has elucidated the functional roles of microbial taxa in AD processes, highlighting the influence of additives like activated carbon on microbial composition and metabolic activity.¹⁰³ These amendments modulate microbial syntrophy and electron transfer, leading to improved CH4 yields and process stability. Functional gene profiling derived from metagenomic datasets further allows for the identification of genes encoding key enzymes in hydrolysis, acidogenesis, acetogenesis, and methanogenesis—pathways central to biogas production.¹⁰⁴ To complement sequencing data, computational tools such as QIIME (Quantitative Insights into Microbial Ecology) and PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) are used to predict metabolic potential from taxonomic data, facilitating a system-level understanding of microbiome functionality.¹⁰⁵ These advancements support the rational design of microbial consortia and the development of precision microbial management strategies to optimize FW valorization through composting, AD, and the production of bio-based compounds. Table 1 presents the Next-Generation Sequencing (NGS) approaches for microbial community profiling in various composting substrates.

Table 1 Next generation sequencing (NGS) approaches for microbial community

Compost substrate	Sequencing approach	Target	Key findings	NGS platform	Reference
Food waste and wastewater	Amplicon, 16S (V5–V9)	Bacteria	116 OTUs; 16 genera	Roche 454	106
Maize straw	Amplicon, 16S (V3–V4), ITS (fungi)	Bacteria, fungi	8535 Bacterial OTUs (24 phyla); 412 fungal OTUs (1 phylum)	Roche 454	6
Spent mushroom waste	Amplicon, 16S (V5–V8)	Bacteria	19 Phyla, 33 classes, 48 orders, 85 families, 129 genera	Roche 454	107
Green waste & barley grain	Amplicon, 16S (V1–V2)	Bacteria	20 Bacterial genera across phases	Roche 454	108
Olive mill waste	Amplicon, 16S (V4–V5)	Bacteria	10 Dominant genera (meso/thermo stage); 8 genera in maturation	Roche 454	109
Food waste & cattle manure	Metagenomic, de novo assembly	Bacteria, virus	Proteobacteria (∼65% reads); 5 pathogens; phages (mainly insect viruses)	Ion torrent	110
Chicken manure	Amplicon, ITS	Fungi	526 OTUs; 4 fungal phyla	Illumina	111
Maize straw	Amplicon, 16S (V3–V4)	Bacteria	16 Phyla; 4 phyla represented 92.2% of sequences	Illumina	112
Rice husk and dewatered sludge	Amplicon, 16S (V4–V5)	Bacteria	29 OTUs; 11 bacterial genera	Illumina	113
Sewage sludge (gelatin, municipal)	Amplicon, 16S (V3), 18S, ITS	Bacteria, fungi	8 Bacterial and 2 fungal phyla detected	Illumina	37
Food waste	Amplicon, 16S (V4)	Bacteria	5 Dominant phyla; >40 bacterial species	Illumina	114
Corn straw & cow manure	Amplicon, 16S, ITS	Bacteria, fungi	272 Bacterial OTUs; 321 fungal OTUs	Illumina	115
Food waste	Amplicon, 16S (V3–V4)	Bacteria	29 Bacterial strains detected	Illumina	114
Paper mill sludge	Amplicon, 16S (V3–V4)	Bacteria	Dominance of proteobacteria, firmicutes, bacteroidetes; key degraders enriched	Illumina	116
Vegetable waste	Amplicon, 16S (V4), ITS	Bacteria, fungi	35 Bacterial genera and 9 fungal genera; succession driven by the composting stage	Illumina	117
Municipal solid waste compost	Amplicon, 16S (V3–V4)	Bacteria	12 Bacterial phyla; actinobacteria and firmicutes are dominant in the thermophilic stage	Illumina	99
Coffee husk	Amplicon, ITS (fungi)	Fungi	Ascomycota dominant (>70%); key lignocellulose degraders identified	Illumina	118
Tea waste	Amplicon, 16S (V4), ITS	Bacteria, fungi	Bacillus, Pseudomonas, and Aspergillus enriched during active degradation	Illumina	119
Brewery spent grain	Amplicon, 16S (V3–V4)	Bacteria	Lactobacillus, Bacillus, and Actinobacteria are predominant	Illumina	120
Cassava peels	Amplicon, 16S (V4), ITS	Bacteria, fungi	Cyanobacteria and firmicutes are abundant; Fusarium spp. key lignocellulose degraders	Illumina	121
Sugarcane bagasse	Amplicon, 16S (V3–V4)	Bacteria	Firmicutes and actinobacteria are dominant in the thermophilic phase	Illumina	122

---

9. Factors influencing microbial activity in food waste degradation

The biodegradation of food waste is highly sensitive to multiple physicochemical and biological parameters. Fig. 8 shows different parameters that affect food waste biodegradation.¹²³ The C : N ratio is widely recognized as a critical factor, with composting studies reporting that maintaining a ratio between 25 : 1 and 30 : 1 maximizes microbial activity and heat generation, while C : N values below 20 : 1 can result in ammonia volatilization rates exceeding 1.5 g NH₃–N per kg dry matter and strong odor emissions.¹²⁴ In anaerobic digestion (AD), protein-rich food waste often causes elevated total ammonia nitrogen (TAN) concentrations; values above 3000 mg L⁻¹ have been shown to inhibit methanogenesis by more than 40%, necessitating co-digestion with high-carbon bulking agents such as straw or paper to dilute nitrogen loading.¹²⁵ Moisture content around 55–60% is considered optimal in composting, with levels above 70% reducing porosity and oxygen diffusion, leading to anaerobic conditions and incomplete degradation. Similarly, aeration rates of 0.3–0.6 L air per min per kg dry matter have been reported to sustain aerobic conditions while preventing excess heat or water loss.¹²⁶ Temperature profiles strongly affect microbial succession: thermophilic composting at 55–65 °C accelerates organic matter decomposition by up to 30% faster than mesophilic regimes, while in AD, biogas yields of 480–520 mL CH₄ per g VS are commonly reported under mesophilic conditions but may decline by 20–25% when TAN or VFAs accumulate at high loading rates.¹²⁷ Operationally, maintaining an organic loading rate (OLR) below 3 g VS per L per day is critical for the mono-digestion of food waste, as exceeding this threshold often leads to VFA accumulation above 2000 mg L⁻¹, triggering pH drops below 6.5 and process inhibition. Multi-omics analyses further show that under such stress, methanogen populations (e.g., Methanosaeta) can decline by 50–70%, while acidogenic bacteria proliferate, reinforcing instability.¹²⁸ Mismanagement of these parameters not only reduces efficiency but also generates odors (NH₃ > 20 ppm, H₂S > 5 ppm) and leachate rich in COD (>20 000 mg L⁻¹), which compromise environmental safety; however, interventions such as biochar addition at 5–10% w/w have been shown to reduce NH₃ emissions by 30–40% and buffer VFAs to restore methanogenic activity. Collectively, these numerical findings underscore that precise control of feedstock properties, environmental conditions, and microbial ecology is essential for transforming food waste into stable compost or high-yield biogas while minimizing environmental impacts.¹²⁹

Fig. 8 Effects of various parameters on the biodegradation of food waste.¹³⁰

10. Biotechnological applications of microbial consortia in food waste valorization

Using microbial groups to change food waste into valuable products fits well with the ideas of circular bioeconomy and sustainability.¹³¹ Teamwork among different microbial groups is more helpful than a single group for transforming complex substances, such as food waste.¹³² Using these assemblages, food waste can be made into different valuable bioproducts, including biofuels (such as biogas, biohydrogen, and bioethanol), bio-based chemicals (such as volatile fatty acids, lactic acid, and succinic acid), biological fertilizers, and proteins from live cells and bioplastics.⁵⁸ Anaerobic digestion is a highly developed use of microbes where groups of hydrolytic, acidogenic, acetogenic and methanogenic microbes help digest waste and make biogas rich in methane.¹³³ New methods in microbiome engineering have improved how much biogas is produced from waste by properly setting operations using co-digestion and using particular strains, such as hydrogenotrophic methanogens, to boost methane production in the presence of high levels of ammonia. Decomposition by dark fermentation occurs when Clostridium, Enterobacter and Bacillus species dominate the microbial community, turning food waste carbs into biohydrogen, which is environmentally friendly. These groups of bacteria are encouraged to produce energy under chosen pH and temperature levels, which increases the amount of hydrogen and lowers the chances of other bacteria turning hydrogen into methane.¹³⁴

The use of electroactive bacteria in microbial fuel cells (MFCs) turns food waste's chemical energy into electricity.¹³⁵ Geobacter and Shewanella communities can form conductive films on the anode surface, and healthy anode growth relies on acetate or hydrogen supply from fermentative microbes. Consortia often benefit from stability and improvement when researchers use evolution, change the substrate and modify the electrode. Producing volatile fatty acids (VFAs) via acidogenic fermentation is another notable use of this process. With acetic, propionic and butyric acids, downstream manufacturing turns them into biodegradable plastics, solvents and fuels.¹³⁶ To promote the production of certain acids by microbial consortia, pH, the time VFA is retained, and the organic material fed can be adjusted. Using tailored groups of microorganisms, integrated biorefineries are now popular to maximize resource reuse by breaking down VFAs, biohydrogen, and gas out of food waste in a row. Besides, microbial consortia are involved in producing polyhydroxyalkanoates (PHAs), which are made from renewable sources. PHA production can be achieved with MMCs from food waste digestates grown in feast–famine cycles if given suitable carbon.¹³⁷

Besides being sources of energy and materials, microbial groups are used to make biofertilizers and soil conditioners from food waste. Stabilization of organic waste and improvement in nutrient access and microbe diversity in agricultural soil are possible when composting, vermicomposting and aerobic digestion are practiced with microorganisms.¹³⁸ The use of plant growth enhancing bacteria (PGPR) as part of these consortia can help the compost become even more valuable for crops.¹³⁹ A new area of interest is making single-cell protein (SCP) from waste products by mixing microbial communities that contain yeasts (like Candida, Saccharomyces), fungi (like Aspergillus and Rhizopus) and bacteria (such as Methylobacterium and Corynebacterium).¹⁴⁰ Such proteins help to address food waste and the lack of protein in food resources for animals and humans. It is now possible to build “synthetic communities” of bacteria using synthetic biology and metabolic engineering to create key products. Special teams made up of Escherichia coli and Clostridium acetobutylicum have been designed to help with better butanol production, and some others include algae and bacteria to achieve both carbon capture and bioenergy generation. Because of spatial organization, resource organization and strength against changing conditions, such groups succeed better.¹⁴¹

Besides, biotechnology uses microbial consortia for the oxidation and detoxification of food processing waste that may carry xenobiotics, heavy metals and synthetic additives. Microbial biofilms, enzymes and redox components in consortia can degrade persistent pollutants, which assists in environmental remediation. Similarly, bio-electrochemical systems that rely on microbial teams can fix carbon dioxide and recover nutrients from food waste effluents, so this becomes a way to produce products without using any carbon.¹⁴² Achieving success with these applications necessitates precise monitoring and management of microbial communities, achievable through high-throughput sequencing, metagenomic analysis, metabolomics, and software tools. Mixing omics technologies with machine learning helps forecast the way consortia work, which leads to improved manufacturing and the ability to scale up.¹⁴³

Moreover, people are focusing on applying microbial consortia at a larger scale to turn food waste into useful products. In Europe, Asia and North America, companies and researchers are producing modular bioprocessing units, so they can be put in places such as cities, food plants and farms. The purpose of these systems is to make valuable energy and useful materials from waste local food and to avoid having a large environmental impact. Despite what they can offer, there are still many problems, such as stable performance in changing raw material situations, rules for products extracted from waste and public opinions about using garbage resources.¹⁴⁴ Moreover, microbial ecology, bioprocess engineering and systems biology are quickly reducing these gaps (Fig. 9).

Fig. 9 Valorization of food waste using biotechnological approaches.¹⁴⁵

10.1 Biosafety risks of engineered microbes in food waste valorization

The deployment of engineered microbes through synthetic biology, such as modified Escherichia coli, Saccharomyces cerevisiae, or Pseudomonas putida, offers major advances in converting food waste into biofuels, organic acids, bioplastics, and nutraceuticals, but it also raises significant biosafety concerns. Engineered strains often carry enhanced metabolic pathways and heterologous enzymes, increasing the risk of horizontal gene transfer (HGT) to environmental microbiota, which potentially spreads synthetic operons or resistance markers. Laboratory studies have shown that plasmids and transposons remain highly active in mixed communities, with transformation frequencies in soil and wastewater as high as 10⁻⁶–10⁻³ per recipient cell. Additionally, genetically modified bacteria exhibiting enhanced substrate utilisation, such as cellulase-overproducing E. coli or lipid-accumulating Yarrowia lipolytica, may surpass indigenous species in nutrient-abundant waste streams, thereby disrupting ecological equilibrium. These concerns underscore the necessity for sophisticated biosafety techniques that go beyond traditional sterilisation methods.¹⁴⁶ Genetic biocontainment strategies encompass kill switches that induce cell death in response to particular signals, exemplified by the “Deadman” and “Passcode” systems. Synthetic auxotrophy serves as an additional protection, which is illustrated by recoded E. coli depending on para-aminophenylalanine (pAF) and cannot thrive outside of supplemented conditions. Metabolic addiction circuits, linking growth to the availability of waste-derived substrates, further limit proliferation outside reactors. Complementary process-level controls, such as closed-loop bioreactors, effluent sterilisation, encapsulation of engineered microorganisms in hydrogels, and membrane bioreactor (MBR) systems, introduce physical barriers while improving productivity. These stratified defences integrate genetic, biochemical, and engineering precautions for efficient containment.¹⁴⁷ Regulatory frameworks strengthen biosafety supervision. The Cartagena Protocol on Biosafety (2000) establishes precautionary rules for the management of living modified organisms (LMOs) on an international scale. In the United States, the EPA TSCA Biotechnology Rule (1997) and NIH Guidelines mandate risk evaluations and delineate biosafety levels (BSL-1 to BSL-4). The EU Directive 2009/41/EC requires risk-based classification and containment of genetically modified microbes, while OECD and ISO 35001:2019 offer standardised biosafety guidelines.¹⁴⁸ Current rules must adapt to advancements in synthetic biology, including genome recording, CRISPR gene drives, and xenobiology. Systems utilizing unusual base pairs (UBPs) or extended genetic codes may diminish horizontal gene transfer (HGT) potential while posing challenges to current regulatory frameworks.¹⁴⁹

The secure utilization of modified microorganisms in food waste valorization necessitates a multi-tiered defense strategy: molecular protection, process-level containment, and compliance with international biosafety regulations. Incorporating these criteria with efficiency reporting is essential for regulatory approval, public confidence, and sustainable integration into the circular bioeconomy (Table 2).¹⁵⁰

Table 2 Biosafety risks and their mitigation strategies

Biosafety risk	Description	Mitigation strategies	References
Gene transfer	Engineered microbes may transfer modified genes to native microorganisms, potentially creating novel pathogens or spreading antibiotic resistance	Use genetic safeguards (e.g., kill-switches and auxotrophy); limit use of mobile genetic elements; employ CRISPR-based containment	146
Pathogen or toxin release	Improper containment could allow engineered microbes to escape into the environment, releasing pathogenic organisms	Strict biosafety protocols; bioreactor containment; use of non-pathogenic chassis organisms; regular monitoring	147
Antibiotic resistance	Some engineered strains or their hosts may carry resistance genes, contributing to the development and spread of antibiotic resistance in food chains	Avoid antibiotic resistance markers; replace with alternative selection methods (e.g., auxotrophy and fluorescent tags)	148
Harmful metabolites	Fermentation by engineered microbes may produce undesirable biomolecules (e.g., histamine, biogenic amines, or toxins) that pose risks to human/animal health	Metabolite profiling; strain engineering to block unwanted pathways; quality control testing of end-products	149
Unforeseen ecological impacts	Introduction of engineered microbes into food waste environments could disrupt microbial communities and ecosystems, leading to unintended ecological consequences	Conduct ecological risk assessments; employ closed-loop systems; use microbes with limited environmental survivability	150

---

11. Case studies: microbial food production

Recent advancements in microbial biotechnology illustrate the conversion of food waste into high-value products via various microbial routes, as evidenced by numerous global case studies.¹⁵¹ Lactic acid production from domestic food waste utilizing Lactobacillus plantarum in South Korea attained yields of 65–75 g L⁻¹ with over 90% conversion efficiency, providing a substrate for biodegradable polymers and food additives.¹⁵² Unibio A/S in Denmark has successfully commercialised single-cell protein (SCP) production by cultivating Methylococcus capsulatus on methane sourced from anaerobically digested food waste, yielding biomass with over 60% protein content as a substitute for fishmeal and soy.¹⁵³ In India, consortia of Clostridium butyricum and Enterobacter aerogenes effectively fermented fruit and vegetable waste into biohydrogen, achieving yields of up to 2.1 mol H₂ per mol glucose equivalent under optimised conditions, which highlights the promise of waste-to-energy bioprocesses. In the dairy industry, whey waste in Italy has been utilised for the cultivation of probiotic strains, including Lactobacillus rhamnosus and Bifidobacterium bifidum, attaining biomass concentrations of up to 10¹¹ CFU mL⁻¹ and generating economical probiotic cultures for functional foods. Large-scale anaerobic digestion plants such as Borås Energy in Sweden treat ∼30 000 tons of food waste annually, yielding biogas with ∼70% methane content to power ∼4000 households while generating nutrient-rich digestate for agricultural reuse.¹⁵⁴ Furthermore, Chinese pilot studies have demonstrated that mixed microbial cultures can transform canteen food waste into polyhydroxyalkanoates (PHA), with yields reaching 20–30% of cell dry weight, presenting sustainable alternatives for bioplastic production.¹⁴⁴ Collectively, these case studies highlight the transformative potential of microbial pathways in shifting food waste from an environmental burden to a critical resource for sustainable food production and circular bioeconomy advancement.

12. Recent advances, challenges, and future prospects in microbial food waste conversion

Significant advancements in biology, especially in systems biology, synthetic biology, metabolic engineering, and environmental biotechnology, have markedly improved the efficiency and product diversity of microbial food waste conversion. A significant advancement is the utilization of multi-omics methods, including genomics, transcriptomics, proteomics, and metabolomics, which provide a comprehensive analysis of microbial populations. These techniques elucidate essential genes, constraints, and species relationships, illuminating collaborative processes, such as methane production and the nitrogen cycle. Metaproteomics and metabolomics offer immediate insights into essential chemicals and pathways, facilitating the optimization of digestion and product synthesis.

Synthetic biology and metabolic engineering enhance microbial performance by increasing inhibitor tolerance, optimising substrate absorption, and facilitating novel metabolic pathways. CRISPR-based engineering has enabled the production of high-value chemicals, including polyhydroxyalkanoates (PHAs), butanol, and lactic acid. Engineered microbial consortia, optimised for robustness and self-regulation, are progressively utilised to oversee intricate waste bioconversion. Enhancing biology, reactor innovations, such as two-stage anaerobic digesters, membrane bioreactors, and microbial electrochemical systems, facilitate meticulous regulation of microbial retention, nutrient equilibrium, and hydraulic parameters. Intelligent monitoring utilising biosensors, IoT devices, and AI-driven analytics enhances process stability by anticipating microbial stress, projecting yields, and facilitating proactive interventions.

Co-digestion systems, which integrate food waste with agricultural waste or wastewater, improve nutritional equilibrium and biogas production. Extremophilic microorganisms broaden the spectrum of treatable waste, while their integration with carbon capture and utilization (CCU) technology facilitates carbon-neutral or carbon-negative systems. Demonstration projects in Europe, Asia, and North America have already exhibited microbial biorefineries that generate electricity, fertilizers, enzymes, and bioplastics. Policy initiatives, such as landfill diversion incentives and carbon credits, further promote commercialization.

Notwithstanding the advancements made, obstacles persist. Variability in food waste—attributable to seasonality and origin—impacts microbial efficacy, while pollutants such as pesticides, heavy metals, and preservatives interfere with metabolism and heighten safety issues. Microbial consortia may become destabilized under stress, complicating the stability of reactors in the long run. Transitioning from laboratory to industrial scale introduces engineering challenges in heat transmission, mass movement, and homogeneous nutrient distribution. From an economic perspective, sophisticated reactors and the subsequent recovery of products such as PHAs or hydrogen are expensive, while more affordable options like composting and landfilling continue to be competitive. Market constraints encompass uneven product quality, consumer skepticism, and regulatory ambiguity, especially concerning genetically altered bacteria and waste-derived goods.

Anticipating the future, interdisciplinary approaches are essential. Modular, decentralized processing systems designed for local waste streams may lower expenses and enhance adaptability, particularly in urban environments and the food sector. The amalgamation of automation, sensors, and machine learning facilitates self-regulating systems, while the integration of omics with digital twins enhances predictive control. Progress in synthetic biology persists in producing robust microbial strains, while insights from natural ecosystems may inform the development of resilient synthetic consortia. The investigation of “microbial dark matter” has potential for discovering new enzymes and methods for waste valorization. Ultimately, policy frameworks must evolve to provide biosafety rules, standardized protocols, and economic incentives. Enhancing multidisciplinary capability across academia, industry, and government is essential for establishing microbial food waste valorization as a fundamental component of the circular bioeconomy.

13. Conclusion

Currently, environmental damage, insufficient resources and food insecurity make food waste a serious concern and, simultaneously, an opening for sustainable growth. It is now possible to turn food waste into helpful resources with the help of microbial ecosystems. It discusses microbial communities and their roles in breaking down food waste and producing biofuels, biofertilizers, bioplastics, and similar products using composting, anaerobic digestion, and similar processes. The increase in omics, metabolic engineering, and systems biology has made it easier to understand how microbes interact, so efficient and stable bioprocesses can be designed. Better bioreactor design, real-time checking, and AI increase the feasibility of scaled applications. Even now, issues like feedstock variability, microbial instability, extracting the product successfully, cost concerns, and rules and views from society remain. Seeing microbial ecosystems as active and connected groups makes it possible to improve their functions with directed measures. Engineering the microbiome and creating specific consortia make the process work better. Using microbial fuel cells and nutrient recovery systems along with MBRs adds additional help to the environment and economy. Modular and flexible technologies created for each area are better for regions with fewer resources and lower incomes. People need to be involved and learn, and both the public and private sectors must work together for adoption. Strong policies with clear directions, incentives and infrastructure are essential. Working with microbes that have not been studied and using AI for prediction creates exciting new areas. By exploiting the value of microbes, food waste can contribute to circular economies and better development step by step, turning waste into wealth.

Author contributions

All authors worked on concept, writing and proofreading.

Conflicts of interest

There are no conflicts to declare.

Data availability

The data supporting the findings of this study are available from the corresponding author upon reasonable request.

References

1. P. Sharma, A. Bano, S. P. Singh, S. K. Srivastava, S. P. Singh and H. M. Iqbal, et al., Different stages of microbial community during the anaerobic digestion of food waste, J. Food Sci. Technol., 2023, 60, 2079–2091.
2. A. Borma, Food waste-a global problem, SEA – Practical Application of Science, 2017, pp. 353–362.
3. K. R. Choi, S. Y. Jung and S. Y. Lee, From sustainable feedstocks to microbial foods, Nat. Microbiol., 2024, 9, 1167–1175.
4. X. Wei, B. Xie, C. Wan, R. Song, W. Zhong and S. Xin, et al., Enhancing soil health and plant growth through microbial fertilizers: Mechanisms, benefits, and sustainable agricultural practices, Agronomy, 2024, 14, 609.
5. B. N. Abdul Hakim, N. J. Xuan and S. N. H. Oslan, A comprehensive review of bioactive compounds from lactic acid bacteria: Potential functions as functional food in dietetics and the food industry, Foods, 2023, 12, 2850.
6. K. Palaniveloo, M. A. Amran, N. A. Norhashim, N. Mohamad-Fauzi, F. Peng-Hui and L. Hui-Wen, et al., Food waste composting and microbial community structure profiling, Processes, 2020, 8, 723.
7. A. S. Jatoi and N. M. Mubarak, Application of Bio-Additives for the Food Industry, Springer, 2024.
8. R. Kumari, A. Singh, R. Sharma and P. Malaviya, Conversion of food waste into energy and value-added products: a review, Environ. Chem. Lett., 2024, 22, 1759–1790.
9. P. K. Mahish, D. K. Verma, A. Ghritlahare, C. Arora and P. Otero, Microbial bioconversion of food waste to bio-fertilizers, Sustainable Food Technol., 2024, 2, 689–708.
10. P. Wang, H. Wang, Y. Qiu, L. Ren and B. Jiang, Microbial characteristics in anaerobic digestion process of food waste for methane production–A review, Bioresour. Technol., 2018, 248, 29–36.
11. M. Patchaye, B. Sundarkrishnan, S. Tamilselvan and N. Sakthivel, Microbial management of organic waste in agroecosystem, Microorganisms for Green Revolution, Microbes for Sustainable Agro-ecosystem, 2018, vol. 2, pp. 45–73.
12. P. Sharma and Y. W. Tong, Microbial systems for circular food waste economy, in Waste-to-Energy, Elsevier, 2025, pp. 143–161.
13. J. O'Connor, B. S. Mickan, K. H. Siddique, J. Rinklebe, M. Kirkham and N. S. Bolan, Physical, chemical, and microbial contaminants in food waste management for soil application: a review, Environ. Pollut., 2022, 300, 118860.
14. G. H. Fleet, Microorganisms in food ecosystems, Int. J. Food Microbiol., 1999, 50, 101–117.
15. V. N. de Jonge and U. Schückel, Exploring effects of dredging and organic waste on the functioning and the quantitative biomass structure of the Ems estuary food web by applying Input Method balancing in Ecological Network Analysis, Ocean Coast Manag., 2019, 174, 38–55.
16. D. Lahiri, M. Nag, S. Ghosh, A. Dey and R. R. Ray, Microbial consortium and crop improvement: Advantages and limitations, in Trends of Applied Microbiology for Sustainable Economy, Elsevier, 2022, pp. 109–123.
17. R. V. Kapoore, G. Padmaperuma, S. Maneein and S. Vaidyanathan, Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing, Crit. Rev. Biotechnol., 2022, 42, 46–72.
18. M. O'Callaghan, R. A. Ballard and D. Wright, Soil microbial inoculants for sustainable agriculture: Limitations and opportunities, Soil Use Manage., 2022, 38, 1340–1369.
19. D. Wu, W. Wang, Y. Yao, H. Li, Q. Wang and B. Niu, Microbial interactions within beneficial consortia promote soil health, Sci. Total Environ., 2023, 900, 165801.
20. Y. Liang, A. Ma and G. Zhuang, Construction of environmental synthetic microbial consortia: based on engineering and ecological principles, Front. Microbiol., 2022, 13, 829717.
21. S. S. Chan, K. S. Khoo, K. W. Chew, T. C. Ling and P. L. Show, Recent advances biodegradation and biosorption of organic compounds from wastewater: Microalgae-bacteria consortium-A review, Bioresour. Technol., 2022, 344, 126159.
22. S. Viswanaathan, P. K. Perumal and S. Sundaram, Integrated approach for carbon sequestration and wastewater treatment using algal–bacterial consortia: Opportunities and challenges, Sustainability, 2022, 14, 1075.
23. I. Benucci, C. Lombardelli, C. Mazzocchi and M. Esti, Natural colorants from vegetable food waste: Recovery, regulatory aspects, and stability—A review, Compr. Rev. Food Sci. Food Saf., 2022, 21, 2715–2737.
24. J. Parfitt, T. Croker and A. Brockhaus, Global food loss and waste in primary production: a reassessment of its scale and significance, Sustainability, 2021, 13, 12087.
25. R. Naseema Rasheed, A. Pourbakhtiar, M. Mehdizadeh Allaf, M. Baharlooeian, N. Rafiei and H. Alishah Aratboni, et al., Microalgal co-cultivation-recent methods, trends in omic-studies, applications, and future challenges, Front. Bioeng. Biotechnol., 2023, 11, 1193424.
26. C. Casonato, L. Garcia-Herrero, C. Caldeira and S. Sala, What a waste! Evidence of consumer food waste prevention and its effectiveness, Sustain. Prod. Consum., 2023, 41, 305–319.
27. A. A. Drannikov, M. E. Trusova and A. Di Martino, Reviewing twenty years of patents on ultrasonic-assisted pectin extraction from food and food waste, Chim. Techno Acta, 2024, 11(2) DOI:10.15826/chimtech.2024.11.2.13.
28. S. Yadav, K. Malik, J. M. Moore, B. R. Kamboj, S. Malik and V. K. Malik, et al., Valorisation of agri-food waste for bioactive compounds: recent trends and future sustainable challenges, Molecules, 2024, 29, 2055.
29. M. H. Dehghani, G. A. Omrani and R. R. Karri, Solid waste—sources, toxicity, and their consequences to human health, in Soft Computing Techniques in Solid Waste and Wastewater Management, Elsevier, 2021, pp. 205–213.
30. S. Kavitha, R. Yukesh Kannah, G. Kumar, M. Gunasekaran and J. Rajesh Banu, Chapter 1 - Introduction: sources and characterization of food waste and food industry wastes, in Food Waste to Valuable Resources, ed. J. R. Banu, G. Kumar, M. Gunasekaran and S. Kavitha, Academic Press, 2020, pp. 1–13.
31. B. Qu, Z. Xiao, A. Upadhyay and Y. Luo, Perspectives on sustainable food production system: characteristics and green technologies, J. Agric. Food Res., 2024, 15, 100988.
32. A. C. Hoek, S. Malekpour, R. Raven, E. Court and E. Byrne, Towards environmentally sustainable food systems: decision-making factors in sustainable food production and consumption, Sustain. Prod. Consum., 2021, 26, 610–626.
33. J. Ammann, A. Arbenz, G. Mack, T. Nemecek and N. El Benni, A review on policy instruments for sustainable food consumption, Sustain. Prod. Consum., 2023, 36, 338–353.
34. Y. Ran, A. N. Lewis, E. Dawkins, R. Grah, F. Vanhuyse and E. Engström, et al., Information as an enabler of sustainable food choices: A behavioural approach to understanding consumer decision-making, Sustain. Prod. Consum., 2022, 31, 642–656.
35. I. Blanco-Penedo, J. García-Gudiño, E. Angón, J. M. Perea, A. J. Escribano and M. Font-i-Furnols, Exploring sustainable food choices factors and purchasing behavior in the sustainable development goals era in Spain, Sustainability, 2021, 13, 7397.
36. H. Gong, J. Wu, G. Feng and X. Jiao, Phosphorus supply chain for sustainable food production will have mitigated environmental pressure with region-specific phosphorus management, Resour., Conserv. Recycl., 2023, 188, 106686.
37. V. Arelli, N. K. Mamindlapelli, S. Begum, S. Juntupally and G. R. Anupoju, Solid state anaerobic digestion of food waste and sewage sludge: Impact of mixing ratios and temperature on microbial diversity, reactor stability and methane yield, Sci. Total Environ., 2021, 793, 148586.
38. Z. Han, P. Xu, Z. Li, H. Lin, C. Zhu and J. Wang, et al., Microbial diversity and the abundance of keystone species drive the response of soil multifunctionality to organic substitution and biochar amendment in a tea plantation, GCB Bioenergy, 2022, 14, 481–495.
39. C. Li, L. Hao, F. Lü, H. Duan, H. Zhang and P. He, Syntrophic acetate-oxidizing microbial consortia enriched from full-scale mesophilic food waste anaerobic digesters showing high biodiversity and functional redundancy, Msystems, 2022, 7, e00339–22.
40. Y. Zhu, W. Wang, M. Li, J. Zhang, L. Ji and Z. Zhao, et al., Microbial diversity of meat products under spoilage and its controlling approaches, Front. Nutr., 2022, 9, 1078201.
41. W. Chen, Z. Feng, Y. Chang, S. Xu, K. Zhou and X. Shi, et al., Comparing the bacterial composition, succession and assembly patterns in plastisphere and kitchen waste composting with PLA/PBAT blends, J. Hazard. Mater., 2023, 454, 131405.
42. K. Palit, S. Rath, S. Chatterjee and S. Das, Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: Threats, vulnerability, and adaptations, Environ. Sci. Pollut. Res., 2022, 29, 32467–32512.
43. Z. Xu, W. Xu, L. Zhang, Y. Ma, Y. Li and G. Li, et al., Bacterial dynamics and functions driven by bulking agents to mitigate gaseous emissions in kitchen waste composting, Bioresour. Technol., 2021, 332, 125028.
44. S. Chaudhary, T. Bhatia and S. S. Sindhu, Sustainable approach for management of organic waste agri-residues in soils for food production and pollution mitigation, in Environmental Nexus Approach, CRC Press, 2024, pp. 355–386.
45. P. S. Arya, S. M. Yagnik, K. N. Rajput, R. R. Panchal and V. H. Raval, Valorization of agro-food wastes: Ease of concomitant-enzymes production with application in food and biofuel industries, Bioresour. Technol., 2022, 361, 127738.
46. Z. Tian, G. Li, Y. Xiong, X. Cao, H. Pang and W. Tang, et al., Step-feeding food waste fermentation liquid as supplementary carbon source for low C/N municipal wastewater treatment: Bench scale performance and response of microbial community, J. Environ. Manage., 2023, 345, 118434.
47. X. Gao, Z. Xu, Y. Li, L. Zhang, G. Li and L. D. Nghiem, et al., Bacterial dynamics for gaseous emission and humification in bio-augmented composting of kitchen waste, Sci. Total Environ., 2021, 801, 149640.
48. S. M. Patil, M. B. Kurade, B. Basak, S. Saha, M. Jang and S.-H. Kim, et al., Anaerobic co-digester microbiome during food waste valorization reveals Methanosaeta mediated methanogenesis with improved carbohydrate and lipid metabolism, Bioresour. Technol., 2021, 332, 125123.
49. Y. W. Tiong, P. Sharma, H. Tian, T.-H. Tsui, H. T. Lam and Y. W. Tong, Startup performance and microbial communities of a decentralized anaerobic digestion of food waste, Chemosphere, 2023, 318, 137937.
50. N. Srivastava, B. Gupta, S. Gupta, M. K. Danquah and I. P. Sarethy, Chapter 6 – Analyzing Functional Microbial Diversity: An Overview of Techniques, in Microbial Diversity in the Genomic Era, ed. S. Das and H. R. Dash, Academic Press, 2019, pp. 79–102.
51. P. He, Y. Zhang, Q. Shen, N. Ling and Z. Nan, Microbial carbon use efficiency in different ecosystems: A meta-analysis based on a biogeochemical equilibrium model, Global Change Biol., 2023, 29, 4758–4774.
52. S. Song, J. W. Lim, J. T. Lee, J. C. Cheong, S. H. Hoy and Q. Hu, et al., Food-waste anaerobic digestate as a fertilizer: The agronomic properties of untreated digestate and biochar-filtered digestate residue, Waste Manage., 2021, 136, 143–152.
53. H. Zhang, J. Zhao, Z. Fu, Y. Wang, D. Guan and J. Xie, et al., Metagenomic approach reveals the mechanism of calcium oxide improving kitchen waste dry anaerobic digestion, Bioresour. Technol., 2023, 387, 129647.
54. O. B. Chukwuma, M. Rafatullah, H. A. Tajarudin and N. Ismail, Bacterial diversity and community structure of a municipal solid waste landfill: a source of lignocellulolytic potential, Life, 2021, 11, 493.
55. L. Zhu, Y. Zhao, X. Yao, M. Zhou, W. Li and Z. Liu, et al., Inoculation enhances directional humification by increasing microbial interaction intensity in food waste composting, Chemosphere, 2023, 322, 138191.
56. Z. Chen, Y. Li, C. Ye, X. He and S. Zhang, Fate of antibiotics and antibiotic resistance genes during aerobic co-composting of food waste with sewage sludge, Sci. Total Environ., 2021, 784, 146950.
57. Q. Xu, S. Long, X. Liu, A. Duan, M. Du and Q. Lu, et al., Insights into the occurrence, fate, impacts, and control of food additives in food waste anaerobic digestion: a review, Environ. Sci. Technol., 2023, 57, 6761–6775.
58. D. Ghosh, P. Ghorai, S. Sarkar, K. S. Maiti, S. R. Hansda and P. Das, Microbial assemblage for solid waste bioremediation and valorization with an essence of bioengineering, Environ. Sci. Pollut. Res., 2023, 30, 16797–16816.
59. M. Eke, K. Tougeron, A. Hamidovic, L. S. N. Tinkeu, T. Hance and F. Renoz, Deciphering the functional diversity of the gut microbiota of the black soldier fly (Hermetia illucens): recent advances and future challenges, Anim. Microbiome, 2023, 5, 40.
60. Y. Song, S. Meng, G. Chen, B. Yan, Y. Zhang and J. Tao, et al., Co-digestion of garden waste, food waste, and tofu residue: Effects of mixing ratio on methane production and microbial community structure, J. Environ. Chem. Eng., 2021, 9, 105901.
61. X. Shi, J. Wang, M. E. Lucas-Borja, Z. Wang, X. Li and Z. Huang, Microbial diversity regulates ecosystem multifunctionality during natural secondary succession, J. Appl. Ecol., 2021, 58, 2833–2842.
62. A. Aguilar-Paredes, G. Valdés, N. Araneda, E. Valdebenito, F. Hansen and M. Nuti, Microbial community in the composting process and its positive impact on the soil biota in sustainable agriculture, Agronomy, 2023, 13, 542.
63. F. Di Pippo, S. Crognale, C. Levantesi, L. Vitanza, M. Sighicelli and L. Pietrelli, et al., Plastisphere in lake waters: microbial diversity, biofilm structure, and potential implications for freshwater ecosystems, Environ. Pollut., 2022, 310, 119876.
64. L. K. Chinthala, Microbes in action: ecological patterns across environmental gradients inImpact of Microbes on Nature, PhDians, 2025, pp. 45–56 DOI:10.2139/ssrn.5232016.
65. S. Wang, M. Lingyi, Y. Chong, H. Yuting, H. Xinliang and J. Yanlei, et al., Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem, Gut Microbes, 2024, 16, 2296603.
66. X. Wu, J. Wang, C. Amanze, R. Yu, J. Li and X. Wu, et al., Exploring the dynamic of microbial community and metabolic function in food waste composting amended with traditional Chinese medicine residues, J. Environ. Manage., 2022, 319, 115765.
67. S.-P. Zou, R.-S. Liu, Y. Luo, C.-T. Bo, S.-Q. Tang and Y.-P. Xue, et al., Effects of fungal agents and biochar on odor emissions and microbial community dynamics during in-situ treatment of food waste, Bioresour. Technol., 2023, 380, 129095.
68. X. Wu, J. Wang, Z. Yu, C. Amanze, L. Shen and X. Wu, et al., Impact of bamboo sphere amendment on composting performance and microbial community succession in food waste composting, J. Environ. Manage., 2022, 303, 114144.
69. X. Wang, X. He and J. Liang, Succession of microbial community during the co-composting of food waste digestate and garden waste, Int. J. Environ. Res. Public Health, 2022, 19, 9945.
70. L. Tang, J. O'Dwyer, Ö. Kimyon and M. J. Manefield, Microbial community composition of food waste before anaerobic digestion, Sci. Rep., 2023, 13, 12703.
71. X.-R. Pan, P.-K. Shang-Guan, S.-H. Li, C.-H. Zhang, J.-M. Lou and L. Guo, et al., The influence of carbon dioxide on fermentation products, microbial community, and functional gene in food waste fermentation with uncontrol pH, Environ. Res., 2025, 267, 120645.
72. I. Moreno-Andrade, M. J. Berrocal-Bravo and I. Valdez-Vazquez, Biohydrogen production from food waste and waste activated sludge in codigestion: influence of organic loading rate and changes in microbial community, J. Chem. Technol. Biotechnol., 2023, 98, 230–237.
73. X. Li, P. Wang, S. Chu, Y. Su, D. Wu and B. Xie, The variation of antibiotic resistance genes and their links with microbial communities during full-scale food waste leachate biotreatment processes, J. Hazard. Mater., 2021, 416, 125744.
74. C. Yu, B. Dongsu, Z. Tao, K. Zhe, J. Xintong and W. Siqi, et al., Anaerobic co-digestion of PBAT/PLA/starch commercial bio-plastic bags with food waste: Effects on methane production and microbial community structure, Biochem. Eng. J., 2023, 199, 109072.
75. T. Lu, Y. Yang, W. Feng, Q. Jin, Z. Wu and Z. Jin, Effect of the compound bacterial agent on microbial community of the aerobic compost of food waste, Lett. Appl. Microbiol., 2022, 74, 32–43.
76. Q. Yu, L. Feng and X. Zhen, Effects of organic loading rate and temperature fluctuation on the microbial community and performance of anaerobic digestion of food waste, Environ. Sci. Pollut. Res., 2021, 28, 13176–13187.
77. Z. Chen, Y. Li, Y. Peng, C. Ye and S. Zhang, Effects of antibiotics on hydrolase activity and structure of microbial community during aerobic co-composting of food waste with sewage sludge, Bioresour. Technol., 2021, 321, 124506.
78. X. Zhang, Y. Song, X. Yang, C. Hu and K. Wang, Regulation of soil enzyme activity and bacterial communities by food waste compost application during field tobacco cultivation cycle, Appl. Soil Ecol., 2023, 192, 105016.
79. X.-r. Pan, S. Yuzuak, J.-m. Lou, L. Chen, Y. Lu and J.-e. Zuo, Microbial community and antibiotic resistance gene distribution in food waste, anaerobic digestate, and paddy soil, Sci. Total Environ., 2023, 889, 164192.
80. S. S. Gaspar, L. L. Assis, C. A. Carvalho, V. H. Buttrós, G. M. d. R. Ferreira and R. F. Schwan, et al., Dynamics of microbiota and physicochemical characterization of food waste in a new type of composter, Front. Sustain. Food Syst., 2022, 6, 960196.
81. Y. Zheng, Z. Feng, P. Wang, S. Xu, X. Gao and L. Ren, et al., Suppressive performance of food waste composting with polylactic acid: Emphasis on microbial core metabolism pathways and mechanism, Bioresour. Technol., 2023, 384, 129339.
82. Y. Zheng, P. Chen, E. Wang, Y. Ren, X. Ran and B. Li, et al., Key enzymatic activities and metabolic pathway dynamics in acidogenic fermentation of food waste: Impact of pH and organic loading rate, J. Environ. Manage., 2025, 373, 123983.
83. Y. Chang, K. Zhou, T. Yang, X. Zhao, R. Li and J. Li, et al., Bacillus licheniformis inoculation promoted humification process for kitchen waste composting: Organic components transformation and bacterial metabolic mechanism, Environ. Res., 2023, 237, 117016.
84. T. A. Swetha, V. Ananthi, A. Bora, N. Sengottuvelan, K. Ponnuchamy and G. Muthusamy, et al., A review on biodegradable polylactic acid (PLA) production from fermentative food waste-Its applications and degradation, Int. J. Biol. Macromol., 2023, 234, 123703.
85. S. Wang, Q. Ping and Y. Li, Comprehensively understanding metabolic pathways of protein during the anaerobic digestion of waste activated sludge, Chemosphere, 2022, 297, 134117.
86. Y. Li, J. Ni, H. Cheng, A. Zhu, G. Guo and Y. Qin, et al., Methanogenic performance and microbial community during thermophilic digestion of food waste and sewage sludge in a high-solid anaerobic membrane bioreactor, Bioresour. Technol., 2021, 342, 125938.
87. Z. Chen, Y. Li, Y. Peng, V. Mironov, J. Chen and H. Jin, et al., Feasibility of sewage sludge and food waste aerobic co-composting: Physicochemical properties, microbial community structures, and contradiction between microbial metabolic activity and safety risks, Sci. Total Environ., 2022, 825, 154047.
88. M. Jiang, W. Qiao, Y. Wang, T. Zou, M. Lin and R. Dong, Balancing acidogenesis and methanogenesis metabolism in thermophilic anaerobic digestion of food waste under a high loading rate, Sci. Total Environ., 2022, 824, 153867.
89. J. Luo, F. Wang, X. Cheng, W. Huang, Q. Zhang and F. Fang, et al., Metatranscriptomic insights of the metabolic process enhancement during food wastes fermentation driven by linear alkylbenzene sulphonates, J. Clean. Prod., 2021, 315, 128145.
90. W. Hong-Ming, X. Li, C. Jia-Ning, Y. Yi-Juan, K. Takuro and Y. Hu, et al., Food waste anaerobic digestion under high organic loading rate: Inhibiting factors, mechanisms, and mitigation strategies, Processes, 2025, 13, 2090.
91. Y. Yu, J. Zhang, F. Zhu, M. Fan, J. Zheng and M. Cai, et al., Enhanced protein degradation by black soldier fly larvae (Hermetia illucens L.) and its gut microbes, Front. Microbiol., 2023, 13, 1095025.
92. G. Mohanakrishna, N. P. Sneha, S. M. Rafi and O. Sarkar, Dark fermentative hydrogen production: Potential of food waste as future energy needs, Sci. Total Environ., 2023, 888, 163801.
93. X. Wang, P. Wang, X. Meng and L. Ren, Performance and metagenomics analysis of anaerobic digestion of food waste with adding biochar supported nano zero-valent iron under mesophilic and thermophilic condition, Sci. Total Environ., 2022, 820, 153244.
94. N. R. Ram and G. N. Nikhil, Assessment of microbial consortiums and their metabolic patterns during the bioconversion of food waste, Biomass Convers. Biorefin., 2023, 1–14.
95. J. Cao, C. Zhang, X. Li, X. Wang, X. Dai and Y. Xu, Microbial Community and Metabolic Pathways in Anaerobic Digestion of Organic Solid Wastes: Progress, Challenges and Prospects, Fermentation, 2025, 11, 457.
96. J. Andraskar, D. Khan, S. Yadav and A. Kapley, Metagenomic Analysis of Microbial Community Associated with Food Waste Composting, Appl. Biochem. Biotechnol., 2025, 197, 3503–3520.
97. C. F. Butowski, Y. Dixit, M. M. Reis and C. Mu, Metatranscriptomics for Understanding the Microbiome in Food and Nutrition Science, Metabolites, 2025, 15, 185.
98. D. Zhao, Y. Chong, J. Hu, X. Zhou, C. Xiao and W. Chen, Proteomics and metagenomics reveal the relationship between microbial metabolism and protein hydrolysis in dried fermented grass carp using a lactic acid bacteria starter culture, Curr. Res. Food Sci., 2022, 5, 2316–2328.
99. E. Fanfoni, P. Bellassi, A. Fontana, E. Sinisgalli, G. Rocchetti and S. Piccinini, et al., Metagenomics and untargeted metabolomics reveal antibiotic resistance dynamics in an anaerobic digestion–composting system treating organic fraction of municipal solid waste, Environ. Microbiome, 2025, 20, 106.
100. N. Basak and S. S. Meena, Exploring the plastic degrading ability of microbial communities through metagenomic approach, Mater. Today: Proc., 2022, 57, 1924–1932.
101. K. Agrawal and P. Verma, Metagenomics: a possible solution for uncovering the “mystery box” of microbial communities involved in the treatment of wastewater, in Wastewater Treatment, Elsevier, 2021, pp. 41–53.
102. J. Andraskar, D. Khan, S. Yadav and A. Kapley, Metagenomic Analysis of Microbial Community Associated with Food Waste Composting, Appl. Biochem. Biotechnol., 2025, 1–18.
103. C. Wang, Y. Wang, Y. Wang, L. Liu, D. Wang and F. Ju, et al., Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters, Water Res., 2022, 219, 118590.
104. J. Sadurski, M. Polak-Berecka, A. Staniszewski and A. Waśko, Step-by-Step metagenomics for food microbiome analysis: A detailed review, Foods, 2024, 13, 2216.
105. S. Crognale, C. M. Braguglia, A. Gallipoli, A. Gianico, S. Rossetti and D. Montecchio, Direct conversion of food waste extract into caproate: metagenomics assessment of chain elongation process, Microorganisms, 2021, 9, 327.
106. L. S. Lee SangHoon, J. Sorensen, K. Grady, T. Tobin and A. Shade, Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire, Nature, 2017, 1447–1459.
107. J. Luo and L. Chen, Status and development of spent mushroom substrate recycling: A review, J. Air Waste Manage. Assoc., 2024, 74, 843–860.
108. I. Tapio, T. J. Snelling, F. Strozzi and R. J. Wallace, The ruminal microbiome associated with methane emissions from ruminant livestock, J. Anim. Sci. Biotechnol., 2017, 8, 7.
109. G. Tortosa, A. J. Fernández-González, A. V. Lasa, E. Aranda, F. Torralbo and C. González-Murua, et al., Involvement of the metabolically active bacteria in the organic matter degradation during olive mill waste composting, Sci. Total Environ., 2021, 789, 147975.
110. Y. Han, Z. Yang, M. Yin, Q. Zhang, L. Tian and H. Wu, Exploring product maturation, microbial communities and antibiotic resistance gene abundances during food waste and cattle manure co-composting, Sci. Total Environ., 2024, 951, 175704.
111. G. Xie, X. Kong, J. Kang, N. Su, J. Fei and G. Luo, Fungal community succession contributes to product maturity during the co-composting of chicken manure and crop residues, Bioresour. Technol., 2021, 328, 124845.
112. Y. Xie, J.-Y. Xiang, L. Long, Y. Ma, Z. Xing and L. Wang, et al., Impact of different treatment methods and timings on soil microbial communities with transgenic maize straw return, Sci. Rep., 2025, 15, 24820.
113. E. Rossi, S. Becarelli, I. Pecorini, S. Di Gregorio and R. Iannelli, Anaerobic digestion of the organic fraction of municipal solid waste in plug-flow reactors: focus on bacterial community metabolic pathways, Water, 2022, 14, 195.
114. Y. Jiang, C. Dennehy, P. G. Lawlor, Z. Hu, M. McCabe and P. Cormican, et al., Exploring the roles of and interactions among microbes in dry co-digestion of food waste and pig manure using high-throughput 16S rRNA gene amplicon sequencing, Biotechnol. Biofuels, 2019, 12, 5.
115. Q. Meng, W. Yang, M. Men, A. Bello, X. Xu and B. Xu, et al., Microbial community succession and response to environmental variables during cow manure and corn straw composting, Front. Microbiol., 2019, 10, 529.
116. P. Sharma, S. Tripathi and R. Chandra, Metagenomic analysis for profiling of microbial communities and tolerance in metal-polluted pulp and paper industry wastewater, Bioresour. Technol., 2021, 324, 124681.
117. M. Yasir, I. A. Al-Zahrani, F. Bibi, M. Abd El Ghany and E. I. Azhar, New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria, Food Res. Int., 2022, 157, 111190.
118. A. C. V. Montoya, R. C. da Silva Mazareli, T. P. Delforno, V. B. Centurion, I. K. Sakamoto and V. M. de Oliveira, et al., Hydrogen, alcohols and volatile fatty acids from the co-digestion of coffee waste (coffee pulp, husk, and processing wastewater) by applying autochthonous microorganisms, Int. J. Hydrogen Energy, 2019, 44, 21434–21450.
119. C. C. S. Martin, J. Rouse-Miller, G. T. Barry and P. Vilpigue, Compost and compost tea microbiology: the “-omics” era, in Biology of Composts, Springer, 2020, pp. 3–30.
120. A. Bianco, G. Zara, M. Garau, P. Castaldi, A. S. Atzori and M. A. Deroma, et al., Microbial community assembly and chemical dynamics of raw brewers' spent grain during inoculated and spontaneous solid-state fermentation, Waste Manage., 2024, 174, 518–527.
121. J. A. Amao, M. Barooah and P. F. Omojasola, Comparative 16S rDNA metagenomics study of two samples of cassava peel heap from Nigeria and India, 3 Biotech, 2019, 9, 418.
122. O. B. Chukwuma, M. Rafatullah, H. A. Tajarudin and N. Ismail, A review on bacterial contribution to lignocellulose breakdown into useful bio-products, Int. J. Environ. Res. Public Health, 2021, 18, 6001.
123. A. H. Anayet, M. M. H. B. Hamzah and M. Z. M. Najib, Optimizing food waste decomposition through pH, moisture content, and temperature control: A comprehensive study, Civil and Sustainable Urban Engineering, 2024, vol. 4, pp. 42–54.
124. Y. Ji, N. Wang, N. Yang, X. Chen, Q. Liu and Z. Wang, et al., Multivariate insights into the effects of inoculating thermophilic aerobic bacteria on the biodegradation of food waste: Process properties, organic degradation and bacterial communities, Environ. Technol. Innovat., 2023, 29, 102968.
125. K. R. Chew, H. Y. Leong, K. S. Khoo, D.-V. N. Vo, H. Anjum and C.-K. Chang, et al., Effects of anaerobic digestion of food waste on biogas production and environmental impacts: a review, Environ. Chem. Lett., 2021, 19, 2921–2939.
126. S. Qin, S. Wainaina, H. Liu, A. M. Soufiani, A. Pandey and Z. Zhang, et al., Microbial dynamics during anaerobic digestion of sewage sludge combined with food waste at high organic loading rates in immersed membrane bioreactors, Fuel, 2021, 303, 121276.
127. R. Tang, Y. Liu, R. Ma, L. Zhang, Y. Li and G. Li, et al., Effect of moisture content, aeration rate, and C/N on maturity and gaseous emissions during kitchen waste rapid composting, J. Environ. Manage., 2023, 326, 116662.
128. T. Induchoodan, I. Haq and A. S. Kalamdhad, Factors affecting anaerobic digestion for biogas production: A review, Advanced organic waste management, 2022, pp. 223–233.
129. Z. H. Qin, J. H. Mou, C. Y. H. Chao, S. S. Chopra, W. Daoud and S. y. Leu, et al., Biotechnology of plastic waste degradation, recycling, and valorization: current advances and future perspectives, ChemSusChem, 2021, 14, 4103–4114.
130. A. Sahoo, A. Dwivedi, P. Madheshiya, U. Kumar, R. K. Sharma and S. Tiwari, Insights into the management of food waste in developing countries: with special reference to India, Environ. Sci. Pollut. Res., 2024, 31, 17887–17913.
131. J. K. Saini, S. Singh and L. Nain, Sustainable Microbial Technologies for Valorization of Agro-Industrial Wastes, CRC Press, 2022.
132. R. Jain, L. Pattanaik, S. K. Padhi and S. N. Naik, Role of microbes and microbial consortium in solid waste management, Environmental and Agricultural Microbiology: Applications for Sustainability, 2021, pp. 383–422.
133. M. Bilal, D. Niu and Z. Wang, Biotechnological Strategies and Perspectives for Food Waste Treatment: The Role of Lactic Acid and Microbial Biomass, Waste Biomass Valorization, 2025, 16, 547–569.
134. L. Yafetto, Application of solid-state fermentation by microbial biotechnology for bioprocessing of agro-industrial wastes from 1970 to 2020: A review and bibliometric analysis, Heliyon, 2022, 8, e09173.
135. S. Pandit, N. Savla, J. M. Sonawane, A. M. d. Sani, P. K. Gupta and A. S. Mathuriya, et al., Agricultural waste and wastewater as feedstock for bioelectricity generation using microbial fuel cells: Recent advances, Fermentation, 2021, 7, 169.
136. H. Zafar, N. Peleato and D. Roberts, A review of the role of pre-treatment on the treatment of food waste using microbial fuel cells, Environ. Technol. Rev., 2022, 11, 72–90.
137. L. Hu, Y. Hong, J. Liu, Z. Wang, X. Wang and Y. Gao, Multifunctional treatment of food waste liquefied liquid by algal-bacterial microbial fuel cells: water, electricity and biomass nexus and mechanism profiling, Algal Res., 2025, 104193.
138. T. A. Kurniawan, M. H. D. Othman, X. Liang, M. Ayub, H. H. Goh and T. D. Kusworo, et al., Microbial fuel cells (MFC): a potential game-changer in renewable energy development, Sustainability, 2022, 14, 16847.
139. K. U. Mahto and S. Das, Electroactive biofilm communities in microbial fuel cells for the synergistic treatment of wastewater and bioelectricity generation, Crit. Rev. Biotechnol., 2025, 45, 434–453.
140. H. Zafar, S. Ishaq, N. Peleato and D. Roberts, Meta-analysis of operational performance and response metrics of microbial fuel cells (MFCs) fed with complex food waste, J. Environ. Manage., 2022, 315, 115152.
141. T. A. M. Torlaema, M. N. M. Ibrahim, A. Ahmad, C. Guerrero-Barajas, M. B. Alshammari and S.-E. Oh, et al., Degradation of hydroquinone coupled with energy generation through microbial fuel cells energized by organic waste, Processes, 2022, 10, 2099.
142. M. F. Memon, K. N. B. Md Hasan and Z. A. Memon, Sustainable Energy Generation From Organic Substrates Using Portable Microbial Fuel Cells: Enhancing Precision Agriculture in Rural Regions of Malaysia, Geol. J., 2025, 1–18.
143. I. Ieropoulos and J. Greenman, The future role of MFCs in biomass energy, Front. Energy Res., 2023, 11, 1108389.
144. F. M. Oluwaferanmi, C. E. Ogwu, A. I. Johnson and O. A. Desire, Bioelectricity Production from Abattoir Wastewater Using Microbial Fuel Cells Connected in Series, Science, 2021, 6, 41–49.
145. T. P. C. Ezeorba, E. S. Okeke, M. H. Mayel, C. O. Nwuche and T. C. Ezike, Recent advances in biotechnological valorization of agro-food wastes (AFW): Optimizing integrated approaches for sustainable biorefinery and circular bioeconomy, Bioresour. Technol. Rep., 2024, 26, 101823.
146. S. Godwin, S. Elkind, T. Carey, K. DiGiandomenico, A. Balbo and J. Blocksidge, et al., Environmental Health and Safety Offers a Biosafety Risk Assessment for a Theoretical Model of a Gene Therapy Process Transfer from Research and Development to Large-Scale Manufacturing, Appl. Biosaf., 2023, 28, 164–175.
147. W. Gao, Z. Wu, K. Zuo, Q. Xiang, L. Zhang and X. Chen, et al., From biosafety to national security: The evolution and challenges of biosafety laboratories, Laboratories, 2024, 1, 158–173.
148. S. Salman, Z. Umar and Y. Xiao, Current epidemiologic features and health dynamics of ESBL-producing Escherichia coli in China, Biosaf. Health, 2024, 6(01), 40–49.
149. I. I. Gaidasheva, T. L. Shashkova, I. A. Orlovskaya and T. I. Gromovykh, Biosafety analysis of metabolites of Streptomyces tauricus strain 19/97 M, promising for the production of biological products, Bioengineering, 2022, 9, 113.
150. T. Sun, J. Song, M. Wang, C. Zhao and W. Zhang, Challenges and recent progress in the governance of biosecurity risks in the era of synthetic biology, J. Biosaf. Biosecur., 2022, 4, 59–67.
151. K. Aganovic, C. Hertel, R. F. Vogel, R. Johne, O. Schlüter and U. Schwarzenbolz, et al., Aspects of high hydrostatic pressure food processing: Perspectives on technology and food safety, Compr. Rev. Food Sci. Food Saf., 2021, 20, 3225–3266.
152. L. Urbina, M. Á. Corcuera, N. Gabilondo, A. Eceiza and A. Retegi, A review of bacterial cellulose: sustainable production from agricultural waste and applications in various fields, Cellulose, 2021, 28, 8229–8253.
153. D. M. Rizzo, M. Lichtveld, J. A. Mazet, E. Togami and S. A. Miller, Plant health and its effects on food safety and security in a One Health framework: four case studies, One Health Outlook, 2021, 3, 6.
154. M. Ciani, A. Lippolis, F. Fava, L. Rodolfi, A. Niccolai and M. R. Tredici, Microbes: food for the future, Foods, 2021, 10, 971.

---