The convergence of biology, technology, and medicine has revolutionised healthcare, with microbial biotechnology at the forefront. While many microbes are often considered solely for their infectious properties, many are major producers of natural products, including antimicrobials. Now, not only sources of clinically relevant drugs, they are also being directly engineered for advanced applications such as targeted drug delivery, immune modulation, and precision therapeutics. Microorganisms are key sources of novel antimicrobials, immunomodulatory, and anticancer agents, which synthetic biology and genomics mining can exploit. Bioengineering and exploration of underused microbial taxa offer promising solutions to the problem of rising antimicrobial resistance. Microbes also play crucial roles in modern vaccine development, from live attenuated to recombinant antigen production. The human microbiome has emerged as an interesting player in health, driving innovations in diagnostics and therapies that include next-generation probiotics and microbiota transplants. Furthermore, synthetic biology further empowers the design of 'smart' microbes for in situ therapeutic functions like imaging, biosensing, and targeted treatment. While transformative, these innovations also raise critical ethical and regulatory concerns, including biosafety, ecological impact, data privacy, and equitable access. This chapter explores the multifaceted roles of microbes in medical biotechnology-spanning therapeutics, vaccines, microbiome-based interventions, and engineered systems-underscoring their importance in the evolution of sustainable, personalised healthcare.
Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.
Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.
The human microbiota represents a complex and dynamic ecosystem composed of microorganisms from various taxonomic groups, including bacteria, viruses, fungi, archaea, and protozoa. These microorganisms inhabit different anatomical regions of the human body, such as the genitourinary system, the gastrointestinal tract, the oral cavity, the skin, and the respiratory tract, exhibiting distinct densities, compositions, and functional characteristics, and interact reciprocally with the host organism. The term microbiota not only defines the diversity and abundance of microorganisms but also encompasses their functional influence on host physiology. At this point, the concept of the microbiome becomes relevant. The microbiome refers to the collective genomic content of all microorganisms comprising the microbiota, that is, their genetic material and the potential biological functions encoded by their genes. Therefore, microbiome analysis enables not only the assessment of microbial diversity, but also of metabolic capacity, signal transduction, immune regulation, and other host-microbe interactions. The microbiota and microbiome play important roles in preserving human health and homeostatic balance. A healthy microbial composition promotes immune system development, aids digestion and nutrient absorption, reduces pathogenic microorganism colonization, and contributes to the integrity of the mucosal barrier. In contrast, dysbiosis, or disruption of microbial equilibrium, has been linked to a variety of pathophysiological illnesses, including inflammatory diseases, metabolic disorders, neurodegenerative diseases, and some neoplasms. Today, microbiome research is not only essential for understanding health and disease mechanisms but also forms the foundation for innovative future medical applications.
Bacteria exhibit extraordinary evolutionary and ecological diversity. They range from dominant, well-characterized phyla to rare lineages that are known only through environmental sequencing. This chapter reviews four key bacterial phyla, including Pseudomonadota, Bacillota, Actinomycetota, and Bacteroidota. These phyla are widely distributed, metabolically versatile, and play a central role in ecosystem functioning and human health. We discuss unique phyla within the PVC superphylum (Planctomycetota, Verrucomicrobiota, Chlamydiota) for their unusual cell biology, compartmentalization, and host associations. We also highlight hyperthermophilic phyla, such as Thermotogota, Aquificota, and Thermodesulfobacteriota, that thrive in geothermal ecosystems and drive sulfur and carbon cycling. We consider less-cultivated lineages, including Deinococcota, Acidobacteriota, Nitrospirota, Fusobacteriota, Fibrobacterota, Synergistota, Deferribacterota, and Chrysiogenota, in terms of their ecological niches, metabolic specializations, and roles in biogeochemical cycles, symbiosis, and disease. Collectively, these examples demonstrate the remarkable metabolic flexibility and ecological impact of bacteria, ranging from host-associated commensals and pathogens to free-living autotrophs in extreme environments. Despite advances in genomics and cultivation-independent methods, vast portions of bacterial diversity remain uncultured and poorly understood. Continued exploration of both dominant phyla and rare lineages promises to refine bacterial taxonomy, expand our understanding of microbial evolution, and reveal novel metabolic pathways with implications for ecology, medicine, and biotechnology.
Microbial biotechnology has historically relied heavily on bacteria, both in fundamental science and applied research. Their rapid growth capacity, ease of genetic manipulation, and extraordinary metabolic diversity enable them to offer a wide range of applications across all areas of modern biotechnology. Today, model bacteria such as Escherichia coli, Bacillus subtilis, and Pseudomonas species are at the center of multidimensional research ranging from recombinant protein production to biofuel synthesis, bioremediation, and probiotic therapies. The biotechnological potential of bacteria extends beyond industrial product development to enable the creation of sustainable solutions for global health, food safety, and environmental issues. In the medical field, bacteria serve as cellular factories for the large-scale production of recombinant proteins, including insulin, growth hormones, and monoclonal antibodies. Additionally, bacterial vectors are utilized as platforms in vaccine development and gene therapy applications. Probiotic bacteria are used to regulate the gut microbiota, strengthen the immune system, and prevent infections. In the agricultural sector, bacteria are utilized as biofertilizers, nitrogen-fixing agents (Rhizobium, Azotobacter), and biocontrol agents. They also contribute to reducing chemical fertilizer use by increasing productivity through the production of phytohormones that promote plant growth and by enhancing the availability of nutrients to plants. Bacteria have gained an important place in industrial applications by being used in the production of valuable metabolites such as antibiotics, vitamins, amino acids, and organic acids. With advances in metabolic engineering and synthetic biology, they are also involved in the production of biofuels, biodegradable plastics, and enzymes used in the food and textile industries. In environmental biotechnology, bacteria have a wide range of applications in bioremediation processes. Natural or genetically modified bacteria make important contributions to the degradation or detoxification of petroleum derivatives, heavy metals, and industrial waste. They also play critical roles in wastewater treatment and sustainable environmental management. In conclusion, bacteria serve as biological tools that offer innovative solutions in various areas of biotechnology. Advances in genomics, CRISPR-based gene editing, and systems biology are expanding the biotechnological applications of bacteria, increasing their importance by offering sustainable solutions to global issues such as health, food safety, and environmental protection.
Archaea are prokaryotes that represent a unique evolutionary lineage distinct from bacteria and eukaryotes. Once thought to exist only in extreme environments, archaea inhabit a wide range of habitats, including soil, marine environments, and the digestive systems of living organisms. This section highlights the systematic diversity of archaea, particularly the superphyla Euryarchaeota, TACK, DPANN, and Asgard, along with their respective phyla. Additionally, the ecological distribution of archaea, their morphological and structural differences, their extensive metabolic properties, and their adaptation mechanisms in extreme conditions are discussed to highlight their biological importance and contribute to our understanding of life on our planet.
Microbial metabolism encompasses the biochemical networks that enable cells to convert nutrients into the energy and biosynthetic precursors necessary for cellular function. Understanding microbial metabolism is crucial for ecology, microbiology, and applications in biotechnology, agriculture, and medicine, as it underpins the biological processes that sustain life in various environments. Microbial metabolic products can be broadly classified as primary or secondary metabolites. Primary metabolites, such as amino acids, carbohydrates, organic acids, and alcohols, are essential for energy generation, biosynthesis, and cellular maintenance, typically accumulating during the exponential growth phase. In contrast, secondary metabolites, including compounds such as antibiotics, toxins, and alkaloids, are predominantly synthesised during the stationary growth phase and are not essential for basic cellular functions. However, they are often involved in ecological interactions and may provide adaptive advantages to the organisms. This distinction emphasises the dual function of microbial metabolism in supporting life and influencing ecological processes. The regulation of microbial metabolite biosynthesis is influenced by nutrient availability, environmental stresses, and intricate genetic networks. Advances in metabolic engineering, synthetic biology, and CRISPR-based technologies have enabled the redirection of central carbon fluxes to enhance the yield of both primary and secondary metabolites. Multi-omics approaches and computational modeling now provide deeper insights into metabolic regulation, pathway optimization, and the discovery of novel bioactive molecules. In conclusion, microbial metabolites are an invaluable resource for biotechnological innovation. While primary metabolites are essential for metabolic physiology, secondary metabolites offer unique bioactivities that have transformed pharmaceutical development, sustainable agriculture and industrial microbiology. Research focusing on uncovering new microbial diversity and optimising biosynthetic pathways is expected to continue providing insights that could deliver sustainable strategies and innovative solutions to urgent global challenges such as food security, healthcare, and environmental restoration.
The origin of life on Earth is a profound biological question, with Bacteria and Archaea-the two principal prokaryotic lineages-central to the inquiry. Together, they represent microbial diversity and offer insights into Earth's earliest biosphere and evolutionary history. Microorganisms are of significant relevance to humanity, not only as disease agents for some infections but also due to their indispensable contributions to ecosystem functioning, primarily because of their involvement in biogeochemical cycling in various habitats. They influence soil fertility, plant growth, and the overall stability of biological communities across different habitats by mediating the turnover of energy and matter through processes such as decomposition, nutrient cycling, and regulating atmospheric gases. The fields of microbial evolution and systematics are mainly concerned with elucidating the origins, diversification, and classification of these two domains of life. These disciplines are fundamental for comprehending the extensive diversity of life on Earth and the evolutionary mechanisms that have shaped it. Notably, horizontal gene transfer, recombination, mutation, and selection are key evolutionary mechanisms driving genetic innovation and ecological differentiation in microbial populations, influencing phylogeny, function, and ecosystem dynamics. Advances in genomics and bioinformatics have transformed microbial systematics by enhancing polyphasic taxonomy through the integration of phenotypic and phylogenetic data, and have also provided valuable tools to gain deep insight into microbial evolution. This chapter examines the evolutionary history of microorganisms in the context of Bacteria and Archaea, the mechanisms underlying their evolution, the modern methodologies employed in microbial systematics, and the broader implications of these studies for science and society.
Archaea are the "silent and unseen majority of life" with an extraordinary capacity to live in some of the most unfavorable habitats in nature, and continue to exist in regions with extreme features that are inhospitable to most other living organisms. They are prokaryotic and frequently found in environments with high pH, salinity, and temperatures. Asgard, Euryarchaeota, TACK, and DPANN are the four main superphyla that make up the Archaea, one of the three domains of life on Earth. Extremophiles, the first Archaea found, are classified into four major physiological types. These are halophiles, thermophiles, alkaliphiles, and acidophiles. The Archaea domain is the subject of extensive research, particularly for potential biotechnological applications. Archaea play a crucial role in environmental sustainability and human health, particularly through their enzymes, metabolites, and biochemical processes. These are some core characteristics of Archaea enabling biotechnological usage. This chapter aims to provide an overview of the various roles that Archaea have in biotechnological usage, both current and potential. Their classification is based on the industry to which the application is targeted, which includes industrial enzyme and catalysis, energy production, and medical and pharmaceutical applications.
Polyanions as polymers carrying multiple negative charges have been extensively studied with regard to their potential antiviral activity. Most studies to date focused on organic polyanionic polymers, both natural and synthetic. The inorganic polymer, polyphosphate (polyP), despite the ubiquitous presence of this molecule from bacteria to man, has attracted much less attention. More recently, and accelerated by the search for potential antiviral agents in the fight against the pandemic caused by the coronavirus SARS-CoV-2, it turned out that polyP disrupts the first step of the viral replication cycle, the interaction of the proteins in the virus envelope and in the cell membrane that are involved in the docking process of the virus with the target host cell. Experiments on a molecular level using the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein and the cellular angiotensin converting enzyme 2 (ACE2) receptor revealed that polyP strongly inhibits the binding reaction through an electrostatic interaction between the negatively charged centers of the polyP molecule and a cationic groove, which is formed by positively charged amino acids on the RBD surface. In addition, it was found that polyP, due to its morphogenetic and energy delivering activities, enhances the antiviral host innate immunity defense of the respiratory epithelium. The underlying mechanisms and envisaged application of polyP in the therapy and prevention of COVID-19 are discussed.
Many pathological conditions are characterized by a deficiency of metabolic energy. A prominent example is nonhealing or difficult-to-heal chronic wounds. Because of their unique ability to serve as a source of metabolic energy, inorganic polyphosphates (polyP) offer the opportunity to develop novel strategies to treat such wounds. The basis is the generation of ATP from the polymer through the joint action of two extracellular or plasma membrane-bound enzymes alkaline phosphatase and adenylate kinase, which enable the transfer of energy-rich phosphate from polyP to AMP with the formation of ADP and finally ATP. Building on these findings, it was possible to develop novel regeneratively active materials for wound therapy, which have already been successfully evaluated in first studies on patients.
Leukocytes are immune cells derived from hematopoietic stem cells of the bone marrow which play essential roles in inflammatory and immune responses. In contrast to anucleate platelets and erythrocytes, leukocytes are differentiated from other blood cells by the presence of a nucleus, and consist of monocytes, neutrophils, lymphocytes, basophils, and eosinophils. Factors released from platelets mediate immune responses in part by recruitment and regulation of leukocyte activity. Platelet dense granules contain the highly anionic polymer polyphosphate (polyP) with monomer chain lengths of approximately 60-100 phosphates long, which are released into the microenvironment upon platelet activation. Recent studies suggest that polyP released from platelets plays roles in leukocyte migration, recruitment, accumulation, differentiation, and activation. Furthermore, bacterial-derived polyphosphate, generally consisting of phosphate monomer lengths in the hundreds to thousands, appear to play a role in pathogenic evasion of the host immune response. This review will discuss the effects of host and pathogenic-derived polyphosphate on leukocyte function.
Inorganic polyphosphate is a polymer which plays multiple important roles in yeast and bacteria. In higher organisms the role of polyP has been intensively studied in last decades and involvements of this polymer in signal transduction, cell death mechanisms, energy production, and many other processes were demonstrated. In contrast to yeast and bacteria, where enzymes responsible for synthesis and hydrolysis of polyP were identified, in mammalian cells polyP clearly plays important role in physiology and pathology but enzymes responsible for synthesis of polyP or consumption of this polymer are still not identified. Here, we discuss the role of mitochondrial F0F1-ATP synthase in polyP synthesis with results, which confirm this proposal. We also discuss the role of other enzymes which may play important roles in polyP metabolism.
In this chapter, the current understanding of the potential roles played by polyphosphate in mitochondrial function with a specific focus on energy metabolism and mitochondrial pathologies caused by stress is summarized. Here we will discuss details of the possible ion transporting mechanisms of mitochondria that might involve polyP and their role in mitochondrial physiology and pathology are discussed.
With an aging population, the presence of aging-associated pathologies is expected to increase within the next decades. Regrettably, we still do not have any valid pharmacological or non-pharmacological tools to prevent, revert, or cure these pathologies. The absence of therapeutical approaches against aging-associated pathologies can be at least partially explained by the relatively lack of knowledge that we still have regarding the molecular mechanisms underlying them, as well as by the complexity of their etiopathology. In fact, a complex number of changes in the physiological function of the cell has been described in all these aging-associated pathologies, including neurodegenerative disorders. Based on multiple scientific manuscripts produced by us and others, it seems clear that mitochondria are dysfunctional in many of these aging-associated pathologies. For example, mitochondrial dysfunction is an early event in the etiopathology of all the main neurodegenerative disorders, and it could be a trigger of many of the other deleterious changes which are present at the cellular level in these pathologies. While mitochondria are complex organelles and their regulation is still not yet entirely understood, inorganic polyphosphate (polyP) could play a crucial role in the regulation of some mitochondrial processes, which are dysfunctional in neurodegeneration. PolyP is a well-preserved biopolymer; it has been identified in every organism that has been studied. It is constituted by a series of orthophosphates connected by highly energetic phosphoanhydride bonds, comparable to those found in ATP. The literature suggests that the role of polyP in maintaining mitochondrial physiology might be related, at least partially, to its effects as a key regulator of cellular bioenergetics. However, further research needs to be conducted to fully elucidate the molecular mechanisms underlying the effects of polyP in the regulation of mitochondrial physiology in aging-associated pathologies, including neurodegenerative disorders. With a significant lack of therapeutic options for the prevention and/or treatment of neurodegeneration, the search for new pharmacological tools against these conditions has been continuous in past decades, even though very few therapeutic approaches have shown potential in treating these pathologies. Therefore, increasing our knowledge about the molecular mechanisms underlying the effects of polyP in mitochondrial physiology as well as its metabolism could place this polymer as a promising and innovative pharmacological target not only in neurodegeneration, but also in a wide range of aging-associated pathologies and conditions where mitochondrial dysfunction has been described as a crucial component of its etiopathology, such as diabetes, musculoskeletal disorders, and cardiovascular disorders.
In recent years, inorganic polyphosphate (polyP) has attracted increasing attention as a biomedical polymer or biomaterial with a great potential for application in regenerative medicine, in particular in the fields of tissue engineering and repair. The interest in polyP is based on two properties of this physiological polymer that make polyP stand out from other polymers: polyP has morphogenetic activity by inducing cell differentiation through specific gene expression, and it functions as an energy store and donor of metabolic energy, especially in the extracellular matrix or in the extracellular space. No other biopolymer applicable in tissue regeneration/repair is known that is endowed with this combination of properties. In addition, polyP can be fabricated both in the form of a biologically active coacervate and as biomimetic amorphous polyP nano/microparticles, which are stable and are activated by transformation into the coacervate phase after contact with protein/body fluids. PolyP can be used in the form of various metal salts and in combination with various hydrogel-forming polymers, whereby (even printable) hybrid materials with defined porosities and mechanical and biological properties can be produced, which can even be loaded with cells for 3D cell printing or with drugs and support the growth and differentiation of (stem) cells as well as cell migration/microvascularization. Potential applications in therapy of bone, cartilage and eye disorders/injuries and wound healing are summarized and possible mechanisms are discussed.
The endoplasmic reticulum (ER) is a biosynthetic organelle in eukaryotic cells. Its capacity to produce proteins, lipids and oligosaccharides responds to physiologic and pathologic demand. The transcriptional and translational unfolded protein response (UPR) programs increase ER size and activity. In contrast, ER-phagy programs in all their flavors select ER subdomains for lysosomal clearance. These programs are activated by nutrient deprivation, accumulation of excess ER (recov-ER-phagy), production of misfolded proteins that cannot be degraded by ER-associated degradation and that are removed from cells by the so-called ER-to-lysosome-associated degradation (ERLAD). Selection of ER subdomains to be cleared from cells relies on ER-phagy receptors, a class of membrane-bound proteins displaying cytosolic domains that engage the cytosolic ubiquitin-like protein LC3. Mechanistically, ER clearance proceeds via macro-ER-phagy, micro-ER-phagy and LC3-regulated vesicular delivery.
The endoplasmic reticulum, as the site of synthesis for proteins in the secretory pathway has evolved select machineries to ensure the correct folding and modification of proteins. However, sometimes these quality control mechanisms fail and proteins are misfolded. Other factors, such as nutrient deprivation, hypoxia or an increased demand on protein synthesis can also cause the accumulation of unfolded or misfolded proteins in the endoplasmic reticulum. There are mechanisms that recognise and deal with this accumulation of protein through degradation and/or export. Many diseases are associated with aberrant quality control mechanisms, and among these, cancer has emerged as a group of diseases that rely on endoplasmic reticulum homeostasis to sustain development and growth. The knowledge of how protein quality control operates in cancer has identified opportunities for these pathways to be pharmacologically targeted, which could lead to newer or more effective treatments in the future.
Protein aggregation is now a common hallmark of numerous human diseases, most of which involve cytosolic aggregates including Aβ (AD) and ⍺-synuclein (PD) in Alzheimer's disease and Parkinson's disease. However, it is also evident that protein aggregation can also occur in the lumen of the endoplasmic reticulum (ER) that leads to specific diseases due to loss of protein function or detrimental effects on the host cell, the former is inherited in a recessive manner where the latter are dominantly inherited. However, the mechanisms of protein aggregation, disaggregation and degradation in the ER are not well understood. Here we provide an overview of factors that cause protein aggregation in the ER and how the ER handles aggregated proteins. Protein aggregation in the ER can result from intrinsic properties of the protein (hydrophobic residues in the ER), oxidative stress or nutrient depletion. The ER has quality control mechanisms [chaperone functions, ER-associated protein degradation (ERAD) and autophagy] to ensure only correctly folded proteins exit the ER and enter the cis-Golgi compartment. Perturbation of protein folding in the ER activates the unfolded protein response (UPR) that evolved to increase ER protein folding capacity and efficiency and degrade misfolded proteins. Accumulation of misfolded proteins in the ER to a level that exceeds the ER-chaperone folding capacity is a major factor that exacerbates protein aggregation. The most significant ER resident protein that prevents protein aggregation in the ER is the heat shock protein 70 (HSP70) homologue, BiP/GRP78, which is a peptide-dependent ATPase that binds unfolded/misfolded proteins and releases them upon ATP binding. Since exogenous factors can also reduce protein misfolding and aggregation in the ER, such as chemical chaperones and antioxidants, these treatments have potential therapeutic benefit for ER protein aggregation-associated diseases.
