1 Introduction

1.1 Background on microorganisms’ contribution to sustainable develpoment

Microbial technology plays a pivotal role in driving sustainable development across diverse industries and applications [1]. Green microbiology focuses on harnessing the power of microorganisms to provide eco-friendly solutions, contribute to environmental sustainability, Furthermore, it aims to reduce industries’ environmental footprint by incorporating microbial technologies. This includes their applications in food production, energy generation, waste management, and bioremediation [2]. The objective is to promote sustainable practices by leveraging microorganisms in industry and offering eco-friendly solutions for different sectors.

Utilizing microbial cell factories offers a promising strategy for producing valuable products from renewable resources [3]. The industrialization of high-value chemicals through microbial cell factories has significantly increased in the bio-based production market [4]. Nevertheless, there exist critical challenges to tackle in the design and construction of microbial cell factories, such as understanding biosynthetic pathways, identifying bottleneck pathways, enhancing strain tolerance to stresses, and alleviating metabolic burden through synthetic microbial consortia [5].

In the bio-based production of chemicals and materials, microorganisms employed under mild conditions without the use of toxic solvents or metal catalysts [6]. The global market size of bio-based chemicals is expected to experience significant growth, highlighting the importance of developing microbial strains for efficient production [7].

Microorganisms can play a vital role in advancing the Sustainable Development Goals established by the United Nations, encompassing environmental, social, and economic growth [8]. By integrating microbial technology to achieve SDGs, it is possible to address significant global challenges related to resource depletion and environmental sustainability such as food security, healthcare provision, well-being improvement, and green energy development [9]. Educating people about the positive contributions of microbes in society can lead to intelligent utilization of microorganisms for sustainable development [10].

In conclusion, microorganisms have a substantial impact on sustainable development across various sectors and offer great potential for addressing global challenges related to resource depletion and environmental sustainability.

1.2 Overview of synthetic biology and systems biology

Synthetic biology and systems biology are pivotal disciplines in the development of microbial cell factories, a key component of sustainable development. Synthetic biotechnology has created new possibilities for building vitamin cell factories, resulting in high-yield strains and utilizing advanced engineering technology to enhance the production of vitamins [11]. The advancement of synthetic biotechnology offers new pathways for mining and genetically modifying chassis cells, utilizing high-throughput screening, CRISPR/Cas9 genome editing technology, along with automatic gene assembly technology [12]. In addition, systems biology plays a vital role in optimizing engineered strains to enhance product yield for constructing microbial cell factories. This entails identifying bottleneck pathways, improving strain tolerance, and designing synthetic microbial consortia to achieve greater product yields [13, 14].

The utilization of synthetic biology in agriculture is also significant for sustainable development. It has opened up new opportunities for crop breeding, enhancing plant photosynthesis, nitrogen fixation, and leveraging microorganisms in agriculture [15]. Utilizing microorganisms as biofertilizers can efficiently diminish the pollution stemming from chemical fertilizers and promote the environmentally friendly and sustainable advancement of contemporary agricultural practices [16].

Moreover, synthetic biology has shown promise in modifying genetic circuits, metabolic pathways, and plant structures to enhance crops is a key aspect of synthetic biology in agriculture. The application of synthetic biology in microorganisms is crucial for promoting sustainable agriculture through biofertilization, bio stimulation, and biocontrol [17].

Overall, synthetic biology and systems biology have paved the way for innovative approaches to using microorganisms for sustainable development across various sectors such as food production (Table 1), pharmaceuticals, chemical production, and agriculture [18]. The continuous advancement of these fields is expected to lead to broader, safer, and more sustainable manufacturing processes aligned aligning with the objectives outlined in the United Nations Sustainable Development Goals.

Table 1 The historical evolution of synthetic biology within the agricultural sector [14]
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2 Importance of microorganisms in sustainable develpoment

2.1 Impact on the economy and global societal development

Microorganisms play a pivotal role in sustainable development, exerting a significant influence on the global economy and societal progress. They contribute to the generation of renewable energy through processes such as the production of biofuels and electricity, facilitated by microbial fuel cells (MFCs) and the creation of bioethanol and biodiesel [20, 21]. This not only reduces pollutants and toxins in the environment but also has the potential to partially replace global fossil diesel needs by converting glucose into energy or deriving energy from biomass [22, 23].

In addition to energy production, microorganisms are harnessed in pharmaceutical manufacturing for the sustainable production of drugs, healthcare products, food additives, pharmaceutical intermediates, and natural products. By utilizing microbial cell factories, these processes minimize waste, reduce environmental pollution, and conserve natural resources while meeting consumer demand [21,22,23,24].

Microorganisms also play a vital role in sustainable chemical production by utilizing renewable resources as raw materials [25]. Advancing microbial cell factories through synthetic biology has enabled the production of various compounds such as fuels, bulk chemicals, enzymes, and natural products [24]. Through metabolic engineering techniques (Fig. 1), these cell factories optimize cellular performance to produce higher yields of bioproducts, contributing to sustainable chemical production [24, 26].

Fig. 1
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The utilization of synthetic biology in agricultural practices [14]

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Furthermore, microorganisms support responsible consumption and production by providing sustainable alternatives for producing a variety of chemicals and materials from renewable non-food biomass sources through microbial cell factories enhanced by synthetic biology [27, 28]. For example, biodegradable polymers like polyhydroxyalkanoates and polylactic acid can be efficiently produced through microbial fermentation processes engineered with systems metabolic engineering [29].

In conclusion, microorganisms are indispensable in driving sustainable development across diverse industries by facilitating renewable energy generation, pharmaceutical manufacturing, chemical production from renewable resources, and promoting responsible consumption and production practices [29, 30] (Fig. 2).

Below are outlined some exemplary achievements of systems metabolic engineering and their contributions to Sustainable Development Goals: considering the specified abbreviations:

  1. 1.

    Production of 2,3-Butanediol (2,3-BDO): SysME advancements have boosted microbial production of 2,3-BDO, a versatile platform chemical, aligning with SDG 9 by fostering sustainable and innovative bioprocessing technologies (Fig. 2).

  2. 2.

    Enhanced Biosynthesis of Inosine Monophosphate and Guanosine Monophosphate: SysME interventions have improved microbial production of IMP and GMP, essential for nucleotide synthesis, thus supporting SDG 3 (Good Health and Well-being) by advancing pharmaceutical and healthcare applications (Fig. 2).

  3. 3.

    Optimized Amino Acid Production: SysME approaches have optimized microbial production of essential amino acids, addressing SDG 2 (Zero Hunger) by enhancing efficiency in amino acid production for food and feed applications (Fig. 2).

  4. 4.

    Biopolymer Production (Poly (3-Hydroxybutyric Acid) PHB): SysME has enabled sustainable production of PHB, a biodegradable polymer, contributing to SDG 12 (Responsible Consumption and Production) by promoting eco-friendly materials (Fig. 2).

  5. 5.

    Engineering Microbes for Sustainable Plastics: SysME has contributed to the development of microbial platforms for producing sustainable plastics like PS, PLGA, PLA, and PET, supporting SDG 14 (Life Below Water) and SDG 15 (Life on Land) by mitigating the environmental impact of plastic waste (Fig. 2).

  6. 6.

    Biofuel Production (Fatty Acid Methyl Esters FAMEs, Fatty Acid Ethyl Esters FAEEs): SysME strategies have advanced microbial systems for biofuel production, in line with SDG 7 (Affordable and Clean Energy) by promoting sustainable alternatives to traditional fossil fuels (Fig. 2).

Fig. 2
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The role of probiotics in nutritional enhancement and food processing [1, 31, 32]

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These achievements highlight the diverse applications of SysME in addressing various Sustainable Development Goals, emphasizing its role in promoting environmentally friendly and economically viable solutions in biotechnology and industry [33,34,35]

2.2 Employment opportunities created by microorganisms

The increasing demand for sustainable practices and renewable resources has brought greater attention to the role of microorganisms in job creation [36]. Microorganisms are pivotal across a broad spectrum of industries, encompassing energy production, food processing, pharmaceuticals, and chemical production. Their utilization not only contributes to sustainable development but also opens up new employment opportunities [36].

In the energy production sector, microorganisms are employed in utilizing microbial fuel cells (MFCs) for electricity generation through biochemical reactions [37]. Additionally, they are involved in producing biofuels such as bioethanol and biodiesel from biomass. Microorganisms like Clostridium species have shown effectiveness in converting glucose into energy and producing gaseous biofuels as alternatives to fossil fuels [38]. These advancements in microbial energy production offer promising job prospects in the renewable energy industry [39].

In food processing, microorganisms are used in fermenting plant biomass to produce nutritious animal feeds [40]. They also help preserve and enhance food products by reducing pressure on natural food sources [2, 41]. The use of microorganisms in food production creates employment opportunities in sustainable agriculture and food technology [42].

The pharmaceutical industry benefits from employing microorganisms in drug development and healthcare research. Microbial technologies play a vital role in producing biodegradable alternatives to major pollutants such as plastics, leading to job opportunities in sustainable product development and healthcare innovation [43].

Microorganisms also contribute significantly to chemical production through microbial cell factories [44]. Using these factories for chemical production brings innovations in renewable resource utilization and the creation of biodegradable alternatives to traditional chemical products [45]. This opens up employment opportunities in green chemistry and sustainable manufacturing [46].

Overall, integrating microorganisms into various industries for sustainable development not only promotes environmental conservation but also creates new job prospects across different sectors. As advancements continue to be made in synthetic and systems biology, there holds the potential for further growth and expansion of employment opportunities driven by microorganism-based technologies [45,46,47,48].

3 Microorganisms in food production

3.1 Role of microorganisms in food processing

Microorganisms are essential in food processing and production, particularly in the creation of mycelium-based food products, which are seen as environmentally friendly substitutes for conventional food sources [47, 48]. Startups like Leep Foods, Kernel MycoFood, and Meati are pioneering the production of oyster mushrooms and mycelium-derived food components using Submerged Fermentation techniques [42, 49]. Established companies like Quorn Foods also produce mycelium-based products worldwide. Microorganisms are also used in fermenting tempeh, with companies like Contemporary and Tempty Foods creating Nordic Tempeh using Solid State Fermentation techniques on various grains and legumes [2, 50]. Additionally, microorganisms are employed in repurposing nutrients from side streams generated by food industries, with companies like Mush labs utilizing fungi to minimize waste and extract value from by-products [42, 51]. Overall, microorganisms play a crucial role in developing sustainable food alternatives and addressing environmental challenges related to waste management, showcasing their potential contribution to sustainable development within the food industry.

3.2 Benefits of using microorganisms in food production

Microorganisms are a key player in food production in (Table 2), offering a multitude of advantages that contribute to sustainable development [42]. One major benefit is their role in enhancing soil fertility and stimulating plant growth [51]. Microorganisms living in the rhizosphere area of the soil facilitate the exchange of nutrients, reducing the reliance on chemical fertilizers and promoting sustainable farming practices [42]. This not only improves crop yields but also helps maintain the overall health of the agricultural ecosystem [54].

Table 2 Provides instances of emerging mycofood companies. The information is sourced from the reference [52, 53]
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In addition to their impact on soil fertility, microorganisms are utilized in the production of food ingredients and additives through precision fermentation [55]. This approach involves using engineered microbes to maximize the synthesis of molecules of interest, such as water-soluble vitamins, fat-soluble vitamins, nutraceuticals, sweeteners, flavor enhancers, and aroma compounds [56]. By bio-manufacturing these ingredients, microorganisms provide a sustainable alternative to conventional chemical synthesis or plant extraction methods [57].

Moreover, microalgae have emerged as a potential superfood that could revolutionize sustainable food production. Algae offer high protein content and Omega-3 fatty acids, making them an appealing option for replacing traditional meat and dairy sources of protein. Their ability to thrive with fewer natural resources further adds to their potential as a sustainable food source [58].

Additionally, microorganisms like yeast are extensively used in fermenting foods like beer and bread, extending their shelf life while preserving their flavor. This not only reduces food waste but also promotes environmental sustainability by enhancing resource efficiency [59, 60].

In summary, microorganisms provide various benefits in food production that align with the principles of sustainable development. From promoting soil fertility and enhancing crop growth to enabling precision fermentation and offering nutrient-rich superfoods, microorganisms play a crucial role in advancing sustainable agriculture and food systems [2, 50, 51].

4 Microorganisms in pharmaceutical industry

4.1 Utilization of microorganisms in drug development

Microorganisms have been instrumental in the pharmaceutical sector, particularly in drug production and dietary supplements [61]. The discovery of antibiotics, which fall into three categories of microorganisms and a class of synthetic antibiotics, has been hailed as one of the most significant medical breakthroughs of the twentieth century [11]. Microorganisms like actinomycetes, bacteria, and fungi have played a pivotal role in creating a wide variety of antibiotics that combat harmful bacteria in the body [2]. Furthermore, microorganisms serve as carriers in vaccines, stimulating an immune response within the body and priming the host to defend against potential infections in the future. Probiotics, such as Lactobacillus and Streptococcus bacteria, are also utilized for their beneficial effects on gut health and overall well-being., used in fermenting dairy and other fermented food products, have been shown to offer health benefits that cannot be obtained from other foods. Furthermore, pharmaceutical companies have employed microorganisms to produce dietary supplements derived from algae and fungi [62].

Throughout the Covid-19 pandemic, pharmaceutical firms, microbiologists, and pharmacists showcased the vital role of microorganisms in crafting vaccines that leverage viral and bacterial vector systems to confer immunity upon vaccine recipients [63]. This dependence on microbial technology for manufacturing supplements, vaccines, and medication is essential for human endurance but poses challenges related to environmental sustainability due to medical waste contamination [64]. Nevertheless, ongoing research is being conducted on using microorganisms for bioremediation to appropriately treat waste and remove toxins from contaminated land and waterways [64, 65].

In conclusion, microorganisms are at the forefront of drug development through their significant contributions to antibiotic production, vaccine development, and supplement manufacturing. Their contributions are vital for human survival but require sustainable approaches to address environmental concerns [66].

4.2 Contributions to healthcare through microbial research

Microorganisms have been pivotal in the healthcare and pharmaceutical sectors by making significant contributions to the production of drugs and dietary supplements (Fig. 3) [45, 69]. Antibiotics, celebrated as one of the most significant medical advancements of the twentieth century, are classified into three categories of microorganisms and one group of synthetic antibiotics [70]. Actinomycetes, bacteria, and fungi are utilized to combat harmful bacteria in the body. Moreover, microorganisms are indispensable in vaccine production as they serve as carriers to stimulate an immune response [71]. Examples of probiotics include Lactobacillus and Streptococcus bacteria provide health benefits that are unique compared to other food sources [72]. Pharmaceutical companies also utilize microorganisms to manufacture various dietary supplements like spirulina, a microalga with numerous health-boosting properties [73].

Fig. 3
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Illustrates the role of microorganisms in the health and drug industries [67, 68]

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In recent times, the critical role of microorganisms in vaccine development has been demonstrated by pharmaceutical companies, microbiologists, and pharmacists [63]. The urgency to develop a Covid-19 vaccine highlighted how microbial technology is essential for human survival. However, this reliance on microbial technology presents challenges for environmental sustainability through contamination from medical waste. Fortunately, microorganisms can be employed for bioremediation processes to effectively treat waste and remove toxins from polluted land and water bodies [74,75,76].

The potential applications of microorganisms extend beyond healthcare and pharmaceutical industries into food production. Yeast is extensively used for fermentation in beer and bread production, while lactic acid bacteria are utilized for dairy product fermentation and food preservation. Algae also play a role in enhancing nutrients in cereal-based food products [77, 78].

In conclusion, microorganisms greatly contribute to healthcare through their involvement in drug development and manufacturing, the production of dietary supplements like probiotics, as well as vaccine development. Their use extends beyond health industries into bioremediation processes for treating contamination from medical waste.

5 Microorganisms in chemical production

5.1 Benefits of utilizing microbial cell factories for chemical production

Microbial cell factories play a pivotal role in the sustainable production of chemicals, facilitating the transition from fossil fuels to renewable resources [79]. By harnessing the metabolic capabilities of microorganisms, these factories offer numerous benefits for chemical production. One significant advantage is their ability to transform abundant and renewable resources, such as CO2, into valuable chemicals and materials [23]. This aligns with the objective of developing environmentally friendly and sustainable bioprocesses that lessen dependence on nonrenewable resources. Moreover, microbial cell factories enable the creation of high-value products from low-value substrates, demonstrating their potential in achieving a circular economy [80, 81].

Additionally, these cell factories aid in addressing environmental challenges linked to conventional chemical production methods [82]. By utilizing renewable feedstocks and decreasing greenhouse gas emissions, they support endeavors to combat climate change and promote sustainable development. Utilizing microbial cell factories also facilitates the establishment of biocontainment systems to prevent uncontrolled proliferation of engineered organisms that could disrupt natural ecosystems [69].

To sum up, microbial cell factories offer unique advantages for chemical production within the framework of sustainable development [69]. They facilitate the use of renewable resources, diminish environmental impacts, and contribute to the shift towards a more sustainable bio-based industry [1].

5.2 Innovations in renewable resource utilization by microorganisms

In recent times, there has been a surge of advancements in the use of renewable resources by microorganisms, especially in the realm of sustainable development [32]. Microbes have been leveraged to generate renewable and biodegradable biofuels, providing a hopeful alternative to traditional fossil fuels. Efforts are currently underway to enhance the efficiency of using microbial strains such as Saccharomyces cerevisiae, Escherichia coli, and Zymomonas mobilis for bioethanol production from xylose and glucose, which is poised to transform the energy sector [1, 83]. Additionally, Researchers are investigating diverse methods to cultivate algae, a photosynthetic microorganism adept at harnessing sunlight for renewable energy through ethanol production. Algal systems offer a broad spectrum of benefits, producing biomass for clean energy generation, facilitating wastewater treatment, and offering an economical protein source. These endeavors leverage the principles of Green Microbiology to offer sustainable solutions aimed at mitigating or eradicating the adverse environmental effects associated with processes like energy production [58, 84, 85].

Moreover, microorganisms present alternatives to environmentally harmful products such as plastics and dairy items. As an illustration, probiotics offer an alternative to traditional fermented dairy items, whereas microalgae demonstrate promise as a substitute for beef, demanding notably less land and water resources for cultivation. Furthermore, ongoing investigations into microbial consortia seek to uncover novel combinations of microorganisms capable of supplanting conventional chemical products, thereby fostering sustainable development [85].

The utilization of cow dung as a bioresource is another promising avenue for sustainable development. Cow dung harbors various microorganisms with properties that can significantly contribute to sustainable agriculture and energy needs [86]. By understanding the mechanisms that enable cow dung microbes to degrade hydrocarbons, researchers can promote the bioremediation of environmental pollutants and develop microbial enzymes with broad applications in agriculture, chemistry, and biotechnology [87].

Overall, these innovations underscore the potential of microorganisms in utilizing renewable resources for sustainable development across various industries such as energy production, food processing, pharmaceuticals, and chemical manufacturing [88,89,90].

6 Role of synthetic biology in enhancing microbial cell factories

6.1 Understanding the concepts of synthetic biology

Synthetic biology has emerged as a crucial instrument in crafting and assembling microbial cell factories to foster sustainable development [11]. Synthetic biology has emerged as a crucial instrument in crafting and assembling microbial cell factories to foster sustainable development [12]. Synthetic biology serves as a linchpin in addressing environmental sustainability concerns by streamlining the creation of efficient microbial cell factories [13]. The amalgamation of traditional metabolic engineering with systems biology, synthetic biology, and evolutionary engineering expedites the production of a wide range of chemicals and materials, spanning biofuels, bulk and fine chemicals, polymers, amino acids, natural products, and pharmaceuticals [91].

The methodologies and tactics utilized in systems metabolic engineering play a pivotal role in optimizing microbial strains to yield desired products efficiently [12]. Developing microbial cell factories encompasses the utilization of various tools, including in silico genome-scale metabolic simulation, advanced enzyme engineering, modulation of optimal gene expression, in vivo biosensors, de novo pathway design, and genomic engineering [16]. The objective is to establish highly efficient cell factories capable of sustainably producing chemicals from renewable non-food biomass sources. Furthermore, synthetic biology tools facilitate the design and construction of enzymes and pathways for manufacturing a diverse array of chemicals and materials [17]. This process entails pinpointing potential bottleneck pathways for strain enhancement to amplify product yield. Integrating systems biology techniques such as transcriptomics, proteomics, metabolomics, and fluxomics supports strain optimization by characterizing new mutants and metabolic pathways [16, 92]. Elaborating detailed kinetic models that incorporate precise regulatory network parameters further aids in identifying enzymatic bottlenecks within metabolic pathways [93].

In essence, synthetic biology emerges as a potent tool pivotal in propelling sustainable development forward through the establishment of efficient microbial cell factories. By integrating systems biology with metabolic engineering techniques, it enables the fine-tuning of microbial strains for heightened production efficiency while ensuring environmental sustainability [19, 94, 95].

6.2 Applications of synthetic biology in improving microbial functions

Synthetic biology is a game-changer in the enhancement of microbial functions for sustainable development [96]. Through harnessing the capabilities of synthetic biology, it becomes feasible to build, integrate, and refine novel metabolic pathways using resilient oleaginous yeast [96]. This pioneering method involves screening robust oleaginous yeast strains possessing specific tolerance traits essential for converting aromatic wastes into lipids, which serve as a substrate for biodiesel conversion [96]. Additionally, crafting an optimal metabolic pathway/network to optimize lipid transformation and accumulation rates from aromatic wastes requires employing various “omics” technologies or a synthetic biology methodology [96]. This entails scrutinizing genome characteristics, pioneering new base mutation gene editing technology, and comprehending the impact of inserting aromatic compounds and other biosynthetic pathways on expression levels and genome stability within the industrial chassis genome [97].

Furthermore, systems biology analysis can systematically explore the genetic and metabolic pathways in microbial consortia, contributing to a holistic understanding of the molecular mechanisms underlying interactions within microbial consortia [98, 99]. This comprehensive comprehension is vital for augmenting microbial functions and attaining optimal outcomes in sustainable development. In summary, synthetic biology holds immense potential in enhancing microbial functions for sustainable development by enabling the construction of cell factories capable of yielding high-yielding products through advanced biotechnological approaches [2].

7 Systems biology approaches for optimizing microorganism performance

7.1 Overview of systems biology techniques

Within the domain of sustainable development, there is a growing focus on establishing microbial cell factories to produce valuable goods, recognized for their environmentally friendly and sustainable attributes [100]. Systems biology, offering a comprehensive understanding of living cells, plays a crucial role in this process [75]. This approach facilitates the design and establishment of microbial cell factories from various angles, including the exploration of functional genes/enzymes, pinpointing bottleneck pathways, bolstering strain tolerance, and devising synthetic microbial consortia [13, 15].

Tools within systems biology enable the discovery of functional genes/enzymes involved in biosynthetic pathways [101]. The identified genes are then incorporated into suitable chassis strains to alter microorganisms capable of manufacturing valuable products [102]. Moreover, systems biology tools are utilized to pinpoint bottleneck pathways within engineered strains and to steer the design and formation of synthetic microbial consortia. This methodology leads to enhanced yields from engineered strains and the effective establishment of microbial cell factories [16, 103].

Additionally, systems biology integrates traditional metabolic engineering with synthetic biology and evolutionary engineering, culminating in systems metabolic engineering [103]. This integration encompasses processes ranging from raw material preparation to fermentation and recovery/purification [92]. Leveraging synthetic biology tools facilitates the design and construction of enzymes and pathways tailored for the production of a wide range of chemicals and materials [92, 104].

Additionally, omics technologies have been developed to analyze cellular changes that drive efficient microorganisms for biofuels production [105]. These technologies comprise genomics, transcriptomics, proteomics, metabolomics, and fluxomics—all contributing to the understanding of cellular behaviors in response to environmental or genetic perturbations [106].

In summary, systems biology occupies a central role in fine-tuning metabolic pathway fluxes to achieve efficient production of valuable products within microbial cell factories [107, 108].

7.2 Combining systems biology with metabolic engineering enhances output

The fusion of systems biology with metabolic engineering has driven the progress of efficient microbial cell factories for sustainable chemical production [97, 101]. By considering upstream, midstream, and downstream processes simultaneously, microbial strains can be engineered to efficiently produce a diverse range of chemicals and materials [109]. Utilizing tools and methodologies from systems biology, microbial cell factories are undergoing optimization to achieve heightened output. Techniques include in silico genome-scale metabolic simulation, advanced enzyme engineering, optimal modulation of gene expression, in vivo biosensors, de novo pathway design, and genomic engineering [31].

Employing synthetic biology tools enables the design and development of enzymes and pathways tailored to produce a diverse range of chemicals and materials [75]. This approach facilitates the advancement of microbial cell factories capable of producing biofuels, as well as bulk and fine chemicals, polymers, amino acids, natural products, and drugs. Evolutionary engineering further enhances the performance of these cell factories by rapidly evolving strains to exhibit desired cellular and metabolic phenotypes [110, 111].

Omics technologies play a pivotal role in guiding the optimization of microbial manufacturing processes [105]. Genomic and transcriptomic analyses aid in evaluating the contributions of genome engineering, while proteomics and metabolomics provide intracellular metabolic insights that reflect the function and phenotype of microorganisms [106]. These insights lead to multi-scale process optimization that takes into consideration molecular-cellular-microenvironment factors.

The identification of bottleneck pathways is crucial for enhancing cell production performance (Table 3) [52]. Metabolomics serves as a valuable tool for quantitatively analyzing intracellular metabolite concentrations to identify bottleneck pathways in engineered strains [112]. This process aids in improving product yield and efficiency by addressing limitations within metabolic pathways [113].

Table 3 Cases of optimizing microbial manufacturing processes guided by omics technologies [106]
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In conclusion, integrating systems biology with metabolic engineering is essential for progressing the construction and optimization of microbial cell factories. This approach facilitates the development of highly efficient cell factories capable of producing bio-based chemicals, fuels, and materials [114, 115].

8 Challenges and future directions in utilizing microorganisms for sustainable development

Microorganisms present numerous advantages for sustainable development, yet they also pose challenges such as the excessive use of pesticides, herbicides, and chemical fertilizers, along with the management of pharmaceutical waste and non-biodegradable plastics [22, 141]. Green Microbiology provides solutions by promoting cleaner production and sustainable waste management through the utilization of microbial technologies. Microbial-based technologies are biocompatible and can break down harmful waste without posing harm to humans or other forms of life [45, 68]. They also play a crucial role in restoring ecosystems and promoting renewable resources (Table 4).

Table 4 Contrast between green microbiology and environmental microbiology [146]
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Microbial cell factories are being engineered to produce chemicals from renewable carbon sources, but there are still challenges in sustainable production from non-edible biomass [142, 143]. Systems-guided metabolic engineering and synthetic biology play crucial roles in achieving sustainability objectives by creating bio-based substitutes for chemical processes. These include degradable plastics, biofuels, bulk chemicals, and mitigating emissions of harmful chemical waste [144]. Cross-sector collaboration is imperative to ensure the widespread adoption of current solutions and the development of novel microbial technologies that promote environmental sustainability [145].

9 Conclusion

In summary, the integration of microbial technology holds significant promise for advancing the Sustainable Development Goals set forth by the United Nations. Microorganisms are pivotal in sustainable development efforts, contributing to various aspects of the economy, creating job opportunities, enhancing food and pharmaceutical production, and advancing chemical manufacturing. The utilization of microorganisms in these sectors brings about various advantages, including the use of cleaner production methods, the utilization of renewable resources, and contributions to healthcare.

Despite the potential benefits, there are obstacles to overcome in applying microorganisms for environmental sustainability. These include the high cost of scaling processes, the time required for ecological restoration, and limitations in culturing specific microorganisms. Moreover, further research is required to improve existing microbial technologies and develop new solutions that promote environmental sustainability.

The key to unlocking the complete potential of microorganisms lies in understanding synthetic biology and systems biology approaches. By leveraging these state-of-the-art technologies, it is feasible to enhance microbial cell factories and optimize microorganism performance for sustainable development.

Moving forward, collaboration across diverse sectors is imperative to ensure the widespread adoption of existing and upcoming microbial solutions aimed at enhancing environmental sustainability. Furthermore, ongoing research into metabolic engineering and process design approaches will be crucial for enhancing bioproduction from PET-derived substrates and creating superior microbial biocatalysts for upcycling PET.

To conclude, despite the existence of challenges, the significance of microorganisms in sustainable development cannot be underestimated. With continuous innovation and collaboration across disciplines, there is great potential to harness the power of microorganisms for a cleaner environment paves the way for a more sustainable future.