1. INTRODUCTION
1.1. Metabolomics for metabolites identification and quantification
Metabolomics is one of the newest “omics” sciences, along with proteomics, genomics, and transcriptomics. These three sciences are closely related, with the study of DNA in the cell (genomics), RNA and differences in mRNA expression (transcriptomics), complemented by metabolomics with the study of the entire set of low molecular weight compounds in a cell at a given time (metabolome).
Metabolomics is a new branch of biology, medicine, and environmental sciences that focuses on the study of metabolites – small molecules in the cells, tissues, and biological fluids of organisms produced by metabolic processes in the body (Fig. 4.1). It focuses on analyzing the metabolic profile of a given organism to understand changes in the metabolic activity of cells, tissues, or the entire organism under different physiological conditions or diseases.
Figure 4.1. Example of a metabolic network model for Escherichia coli
Metabolites (small molecules) are amino acids, carbohydrates, lipids, nucleotides, and other end or intermediate products of metabolism that play a key role in cellular processes. They are the end products of the processes occurring in the cell, and therefore, the metabolome includes all metabolites in a biological cell, tissue, or organism. Metabolomes perform different functions, such as providing energy (glucose), maintaining cell structure, indicating catalytic activity or stimulating and inhibiting effects on enzymes, and protecting the organism.
Metabolomics is very important, considering the role of metabolites in the life and functions of cells. It provides information about the profile of the sample and the compounds in it at a defined time under specific environmental conditions. It is an important information about the physiological state of the organism. Metabolomics can determine the differences between the levels of thousands of molecules between a healthy and a diseased organism, between traditional and genetically modified cultures, etc.
Metabolomics studies the complete biochemical phenotype (or metabotype) of any biofluid, cell, tissue, or organism, both qualitatively and quantitatively. Genetic and environmental factors can influence the state of small molecules, chemical processes, and their interactions in a biological cell, tissue, or organism (metabolome). Metabolomics aims to discover metabolites by determining all metabolites in biological samples (e.g., blood, urine, tissue), assessing their concentrations in different conditions or diseases, and mapping metabolic pathways to understand how biochemical reactions in cells change.
The most widely used methods in metabolomics include various analytical techniques for measuring metabolite levels (Table 4.1.). Metabolomics application encompass various fields (Table 4.2.).
Table 4.1. Analytical techniques use for measurement of metabolite levels.
| Method | Application |
| Mass spectrometry (MS) | Allows accurate determination of the molecules mass and their composition. |
| Nuclear magnetic resonance (NMR) | Identifies and quantifies metabolites |
| Gas chromatography (GC) | Separates volatile and semi-volatile metabolites |
Table 4.2. Metabolomics application fields.
| Field | Application |
| Medicine |
|
| Pharmaceutical industry |
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| Agriculture |
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| Food industry |
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| Ecotoxicology |
|
1.2. Potential of environmental metabolomics
Environmental metabolomics is aimed at solving important problems related to the ecosystem and reveals great potential for:
- Identification of metabolic profiles that organisms produce in response to various environmental factors;
- Monitoring pollution after identifying and quantifying toxic substances in the environment. Analysis of metabolites in organisms indicates the presence of pollutants such as heavy metals, pesticides, and other chemicals.
- Developing new technologies for purifying water and soil from pollutants, as some bacteria can degrade toxic substances through their metabolic processes.
- Assessment of environmental stress and the influence of various factors such as climate, soil conditions, pollution, and other environmental stressors on the metabolism of plants, animals, and microorganisms in natural conditions.
- Identification of stress biomarkers to account for the response of organisms to environmental changes, such as physiological adaptations or toxicological effects. Identification of specific metabolites that serve as indicators of the ecosystem’s health.
- Identification of adaptation mechanisms – adaptation of the metabolism of organisms to survive in different environments, predicting their resilience to future climate change or other environmental challenges.
- Monitoring the ecosystems’ health by analyzing the metabolic profiles of different species, assessing the ecosystems’ overall health, and identifying environmental problems or threats, such as pollution or climate change.
Environmental metabolomics is still a relatively new field in Bulgaria, as in many other countries, but it has great potential for development and application in various scientific and practical contexts.
1.3. Challenges of environmental metabolomics in data interpretation
Environmental metabolomics is a powerful approach to studying the chemical interactions between organisms and their environment and generates large and diverse data sets. Data interpretation is often difficult for several reasons:
- Complexity and heterogeneity of samples – metabolomics analyses often identify thousands of metabolites and complex unknown compounds that are poorly studied. Environmental samples such as soil, water, or sediments are heterogeneous samples of complex mixtures of organic and inorganic compounds, making analysis difficult. Also, some metabolites are presented in low concentrations, making their detection and quantification challenging.
- Standardization and reproducibility – the application of different methodologies for data extraction, analysis, and processing can lead to incomparable results due to the lack of standardized protocols. Also, the application of diverse equipment and analytical methods impacts the accuracy and reliability of difficult-to-reproduce data. The equipment has different sensitivity and range. The background signals from other substances in the samples make it difficult to identify specific metabolites.
- Data interpretation – the existence of isomers with similar chemical properties and the lack of correspondences in the available databases complicates their differentiation.
- Integration with other “omics” data – determining the relationship between metabolites and environmental factors does not always lead to cause-effect relationships understanding. Therefore, metabolomics is integrated with other “omics” data, such as combining with genomics, proteomics, or transcriptomics. The integration of these different levels of data requires sophisticated bioinformatics approaches and correct interpretation.
- Presentation of results – the difficulty in presenting large volumes of data in a comprehensible and accessible way and the effective visualization of multidimensional data often requires specialized software and skills.
Potential solutions to these challenges include the use of better sensitive and high-throughput analytical technologies, databases and standardized protocols, multivariate statistical methods, and machine learning for better analysis and interpretation. The development of environmental metabolomics depends on overcoming these challenges, allowing for a better understanding of ecosystem interactions and their sustainable management.
2. METABOLOMIC DIVERSITY OF ECOSYSTEMS
Ecology is a science, a branch of biology, that studies the interactions between organisms as well as the environment in which they live. The main subject of study of ecology are ecosystems, interconnected networks of plants, animals, and other organisms in a given geographical area, depending on each other. Ecometabolomics analyzes the metabolome, the total number of metabolites, and its changes in response to environmental changes.
While species and genetic diversity are well-known concepts, metabolomic diversity remains relatively unexplored. It represents the diversity of small molecules (metabolites) in living organisms. Sources of metabolomic diversity are mainly microorganisms in soil, water, and plants, as well as plants and animals that produce secondary metabolites for protection, communication, and adaptation to the environment. Many factors influence metabolic profiles, such as climate, soil type, water availability, nutrients, etc.
Metabolomic diversity is the result of the complex interactions between different organisms in an ecosystem, their metabolic pathways, and the physicochemical conditions of the environment. Human activities, climate change, and other factors have a significant impact on the metabolomic diversity of ecosystems. For example, heavy metal pollution can lead to changes in the metabolism of plants and animals, and climate change can affect the distribution of certain metabolites in the ecosystem.
Metabolomic diversity is fundamental to the functioning of ecosystems and their ability to adapt to change. Studying it helps to better understand the interactions between species and the relationship between biotic and abiotic factors in the environment, to provide valuable information about the health of our planet and to develop more effective strategies for environmental protection (Fig. 4.2).
Figure 4.2. Ecosystem metabolomic diversity impacts.
3. METABOLOMICS AND ENVIRONMENTAL MICROBIOLOGY
3.1. Metabolomic studies of natural microbial communities 
Microorganisms are the most abundant life forms in almost every habitat on Earth. Despite their size, they can cause serious diseases, clean up contaminated soils and water, and alter global climate. The diversity of microorganisms is impressive, as is their metabolic diversity, but much remains unexplored. Some microorganisms thrive under extreme conditions. Ecological transcriptomic and proteomic studies have revealed metabolites active in extremophile communities. Metabolites directly related to their physiology are less well defined, as metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities, often relating to the environmental matrix.
Community proteomics and transcriptomics can provide insight into the potential function of coexisting microorganisms in situ. However, these analyses are not possible for small molecule metabolites that are fundamental to the physiological or phenotypic state of the organism. Natural microbial communities are complex ecosystems composed of billions of microorganisms interacting with each other and the environment. These communities play a key role in many natural processes, such as the decomposition of organic matter, nutrient cycling, and biogeochemical cycles. Various methods are used to understand the functioning of these communities, including metabolomics studies.
Advances in analytical techniques allow the study of this diversity by simultaneously measuring thousands of known and unknown microbial metabolites, thus giving rise to microbial metabolomics.
3.2. Analysis of the collective metabolome of microbial communities
Microbial metabolomics aims to study all aspects of microbial metabolism by measuring metabolites inside and outside microbes, whether they live in monocultures, in the laboratory, or in complex ecological communities. Applying metabolomic studies to natural microbial communities allows us to obtain information about the biochemical processes and metabolic pathways active in the community, the interactions between microorganisms in different microbial species, and the changes in community metabolism in response to environmental changes.
Metabolomic studies of natural microbial communities represent a rapidly developing field of science that provides us with new opportunities to understand the complexity and diversity of the microbial world by:
- Discovering key intracellular and extracellular metabolites involved in cellular processes, such as ion homeostasis, redox status, nutrient cycling, energetics, and cell-cell signaling.
- Understanding ecosystem functions and how microbial communities contribute to ecosystem functioning.
- Discovering new bioactive compounds, as they are a rich source of new substances with potential applications in medicine, pharmacy, and biotechnology.
- Environmental monitoring through metabolomic profiles of microbial communities can be used as biomarkers for assessing environmental quality.
Metabolomic studies of microbial communities are used in:
- Studying soil microbiomes by characterizing the metabolic profile of soil microbiomes and assessing their impact on soil fertility and plant growth.
- Analysis of the gut microbiota for human health, the relationship between the composition of the gut microbiota and various diseases, such as obesity, diabetes, and inflammatory bowel diseases.
- Monitoring aquatic ecosystems to assess the impact of their pollution and to discover new biomarkers for monitoring water quality.
3.3. Natural microbial communities
Depending on the environment, microbial communities are adapted to different ecological niches. The diversity of ecological niches is great due to differences in light, temperature, and nutrient availability in the ecosystem. It is regulated naturally by flows, temperature fluctuations, and ultraviolet radiation. Microbial communities are critical for the maintenance of life and are closely related to the chemical and physical properties of the inhabited environment. The study of their ecological niches helps to understand global ecosystem processes. There is a great diversity of microbial communities in the natural environments, as autlined in table 4.3.
Table 4.3. Diversity of microbial communities in the natural environments.
| Microbial community | Types of microorganisms |
| Surface waters (rivers, lakes, seas and oceans) |
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| Groundwater: adaptated to nutrient – poor environments and limited access to oxygen and light |
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| Soil: the most diverse communities with a significant role in organic matter recycling, toxins decomposition, and elmemnts absorbtion |
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| Other environments |
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3.4. Uncovering the functional significance of microbiome diversity
Uncovering the functional significance of microbiome diversity and its associated metabolomic diversity requires integrated statistical approaches and specialized analysis tools. By using these methods and tools, it is possible to make a functional interpretation, as well as to summarize metabolomic diversity. Combining multi-omic data allows for a deeper understanding of the interactions between microorganisms and their environment. The main steps and approaches for characterizing and summarizing these data are:
- Data collection and pre-processing – for microbiome and metabolomic data
- Microbiome diversity assessment – Alpha-diversity (diversity within a sample), Beta-diversity (differences between samples).
- Metabolomic diversity characterization by identifying specific metabolomes and classification of metabolites, statistical analyses against functional groups, etc.
- Microbiome and metabolomic data integration using Canonical Correlation Analysis (CCA), Procrustes Analysis, or methods for connecting different data types and machine learning.
- Data summarization and visualization with heat maps for the relationships between microbes and metabolites and Network Analysis for functional interactions.
- Tools and software – QIIME 2 for microbiome analyses. MetaboAnalyst for metabolomic analyses (R packages such as phyloseq, vegan, mixOmics for statistical analyses) and Python packages, such as scikit-learn, seaborn, and matplotlib for modeling and visualization.
4. LABORATORY STUDIES OF ENVIRONMENTAL METABOLITES
Modelling laboratory studies of environmental metabolites is a powerful tool for understanding the complex biochemical processes occurring in natural ecosystems. By combining experimental data and mathematical models, we can obtain a more complete picture of metabolic networks and develop new strategies for environmental protection. Using mathematical models and computer simulations, we can simulate experimental conditions, analyze large amounts of data, and build hypotheses about the mechanisms underlying observed phenomena. Modelling laboratory studies provides several advantages, such as:
- Better understanding of complex ecosystems, in which modelling allows us to simulate interactions in nonlinear ways between multiple factors that influence metabolic processes.
- Optimization of experiments by planning and optimizing experiments by identifying the most appropriate conditions for observing certain processes.
- Prediction of future events by anticipating how environmental changes will affect metabolic processes and assessing the potential consequences of these changes.
- Big data analysis through modelling allows us to analyze the huge amounts of metabolome data generated and efficiently extract useful information.
- The different models developed to simulate laboratory studies of environmental metabolites are presented in Fig.4.3.
Figure 4.3. Different models simulating laboratory studies of environmental metabolites.
4.1. Categories of environmental metabolomic studies
The “metabolome” of an organism is its complete set of metabolites, the complete biochemical phenotype (or metabotype) of any biofluid, cell, tissue, or organism, both qualitatively and quantitatively.
By analyzing metabolomes, we can obtain valuable information about the biochemical processes occurring in the environment and develop new strategies for nature conservation. The main categories of ecological metabolomics are shown in Table 4.4.
Table 4.4. Ecological metaboomics types.
| Metabolomic type | Characteristics |
| Soil metabolomics |
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| Aquatic ecosystem metabolomics |
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| Air metabolomics |
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| Extreme environment metabolomics |
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| Organism-to-organism interaction metabolomics |
|
5. METABOLOMICS AND ENVIRONMENTAL STRESS RESISTENCE
5.1. Studying the body’s responses to environmental stressors
Environmental metabolomics provides powerful tools for studying the responses of organisms to stressors. By analyzing metabolomic profiles, we can obtain valuable information about the mechanisms of stress, identify biomarkers for early diagnosis of diseases, and develop new strategies for protecting the environment and human health. Environmental metabolomics is widely used for:
- Uncovering the stress mechanisms through metabolomic profiles’ analysis and identifying the specific stress-affected metabolic pathways. It allows for a better understanding of the mechanisms underlying the stress response.
- Assessing the effects of interventions aimed at reducing stress. It is possible to compare the metabolomic profiles of organisms subjected to a particular stress before and after therapy application. Metabolic profiles of organisms can serve as sensitive biomarkers for assessing stress. Changes in the levels of metabolites can signal an imbalance in metabolism resulting from stress exposure. Assessing the effects of stress on human health is an essential part of identifying biomarkers for early diagnosis of stress-related diseases. It is the basis for developing new therapeutics, such as discovering new drug targets and developing personalized therapies.
- Assessing the impact of pollutants by identifying biomarkers for pollution with heavy metals, pesticides, and other toxic substances.
- Studying climate change and the responses of plants and animals to changes in temperature, humidity, and other climatic factors.
Despite its great potential, environmental metabolomics still has some challenges. Nevertheless, the future of environmental metabolomics looks promising. With the development of new technologies and algorithms, this field will continue to play an increasingly important role in understanding the interactions between organisms and their environment.
5.2 Analyses of microbial responses to oxidative stress
Oxidative stress is a condition in which there is an imbalance between the generation of reactive oxygen species (ROS) and the cell’s ability to neutralize them. It is one of the main factors contributing to cell damage and the development of various diseases. Microorganisms, like larger organisms, are exposed to oxidative stress and have developed mechanisms to cope with it. Metabolomic analyses offer powerful tools to study these mechanisms at the molecular level, including primary and secondary oxidative stress responses.
Primary oxidative stress responses involve the damage of biomolecules such as DNA, proteins, and lipids by ROS. Metabolomic analyses can identify the products of this damage, such as oxidized lipids, carbonyl groups in proteins, and oxidized bases in DNA. The next stage of oxidative stress is the secondary reactions, which are associated with various signaling pathways and regulatory mechanisms, the activation that attempts to restore homeostasis. Metabolomic analyses can identify changes in metabolic profiles that reflect these responses in detail.
Metabolomic analyses provide powerful tools for studying microbial responses to oxidative stress. By identifying changes in metabolic profiles, we can gain a deeper understanding of the mechanisms underlying these responses. This information can be used to develop new strategies to combat infectious diseases and improve human health.
- Metabolomic analyses involve the identification of biomarkers, which are specific metabolites that can serve as biomarkers for oxidative stress. By analyzing changes in metabolic profiles, the metabolic pathways most affected by oxidative stress can be identified. These analyses can be used to evaluate the effectiveness of various antioxidants and other interventions to reduce oxidative stress. The application of metabolomic analyses in studying oxidative stress in microorganisms aims at:
- Studying the resistance of pathogenic microorganisms to antibiotics, whereby oxidative stress can contribute to the development of antibiotic resistance.
- Studying the adaptation of microorganisms inhabiting extreme environments to these conditions. Microorganisms exposed to high oxidative stress develop unique mechanisms to cope with it.
- Development of new antimicrobial agents based on new targets identification for antimicrobial agents and the metabolic pathways involved in the response to oxidative stress.
5.3. Metabolic stress in bacteria caused by metal pollution
Environmental pollution with heavy metals is a serious threat to all living organisms, including bacteria. These microorganisms are adaptable and can colonize different environments, even those with high concentrations of toxic substances. However, exposure to metals leads to significant changes in the metabolism of bacteria, referred to as metabolomic stress. Metabolomic stress caused by metal pollution is of great interest to scientists, with metabolomic analyses providing powerful tools to study the mechanisms of action of heavy metals on bacteria and to develop strategies to address this problem. The basis of metabolomic stress is to establish the mechanisms of action of heavy metals such as lead, cadmium, mercury, and arsenic, which can affect bacterial cells in different ways:
In oxidative stress, metals can generate reactive oxygen species (ROS) and damage DNA, proteins, and lipids. Damage to DNA leads to mutations and genetic instability. Heavy metals can bind to phospholipids in the cell membrane, disrupting its permeability and stability. Metals can also bind to enzymes and inhibit their activity, disrupting essential metabolic processes.
Very often, metabolomic changes are observed in bacteria exposed to heavy metals. The metabolomic analysis allows specific changes in the metabolic profile of bacteria identification in response to metal exposure. These changes may include the accumulation of metabolites in bacteria as a detoxification mechanism or as a response to cell damage or depletion of metabolites resulting from increased consumption or inhibition of synthesis. Metals can disrupt the regulation of various metabolic pathways, leading to changes in energy production, biomolecule synthesis, and other processes. The applications of metabolomic analysis are of great importance for:
- Assessment of metal toxicity by comparing the metabolomic profiles of bacteria exposed to different concentrations of metals and determining their toxicity.
- Biomarkers identification through metabolomic analyses of specific metabolites that can serve as biomarkers for metal exposure.
- Development of bioremediation strategies resulting from metabolomic analyses that can help the development of new strategies for bioremediation of soils and waters contaminated with heavy metals.
6. METHODOLOGICAL AND TECHNICAL DEVELOPMENTS
6.1. Achievements of metabolomics in aquatic ecotoxicology
In aquatic ecotoxicology, metabolomics has proven to be a particularly valuable tool for assessing the impact of pollutants on aquatic organisms. It provides a “snapshot” of the metabolic profile of an organism, which provides not only genetic information but also reflects the influence of the environment and all biochemical processes occurring in the organism. It makes it an extremely sensitive tool for detecting early changes induced by exposure to toxic substances. Metabolomics allows for the identification of early biomarkers of toxicity, revealing the mechanisms of action of pollutants and developing more effective strategies for water resources protection. It also provides new methods for assessing the pollutants’ impact on aquatic organisms and ecosystems. Several key achievements and applications of metabolomics in this field are related to the discovery of specific metabolites that change in response to exposure to toxic substances in water. These metabolites can serve as biomarkers of toxicity and help in the early detection of harmful effects. Also, by analyzing metabolic profiles, it is possible to understand how certain pollutants affect the metabolism of aquatic organisms. It helps to reveal the mechanisms of toxicity and to develop strategies for the protection of aquatic ecosystems.
The impact on aquatic organisms’ assessment is an important part of the research.
Metabolomics allows the creation of models that predict the impact of pollutants on aquatic organisms. These models can be used for risk assessment for the development of regulatory standards and modeling of ecotoxicological effects.
The chemicals’ relative toxicity can be assessed, and pollution control efforts can be prioritized by studying different types of pollutants and comparing the metabolic profiles of organisms exposed to pollutants.
The application of metabolomics in the field of aquatic ecotoxicology is related to water quality monitoring, which is:
- Real-world monitoring of water bodies, used to monitor water quality in real time. By analyzing the metabolic profiles of aquatic organisms, changes are detected that indicate the presence of pollutants and what corrective actions should be taken.
- Long-term monitoring of metabolic profiles can provide information on the chronic effects of pollutants on aquatic ecosystems and help develop long-term water resource management strategies.
New technologies and methods are being developed and integrated with other “omics” technologies. Metabolomics is often combined with genomics, proteomics and transcriptomics to obtain a more complete picture of biological responses to pollutants. This integration allows for a more precise understanding of the complex interactions between genetics, proteins and metabolites. New analytical techniques and tools are also being developed that improve the accuracy and sensitivity of measurements. This includes advanced methods for spectroscopy, chromatography and statistical analysis.
Metabolomics is a powerful tool in the field of aquatic ecotoxicology, which allows for a detailed study of the impact of pollutants on aquatic organisms and ecosystems. By identifying biomarkers, understanding mechanisms of toxicity, and developing new technologies, metabolomics contributes significantly to the conservation of water resources and the health of aquatic ecosystems.
6.2. New statistical challenges – bioinformatics
Bioinformatics and metabolomics are two rapidly developing fields of science that, when combined, offer powerful tools for understanding complex biological systems. Combining bioinformatics and metabolomics creates a synergistic effect that allows:
- Identify new biomarkers by integrating genomic, transcriptomic, and metabolomic data, which can be used to discover new biomarkers for diagnosis and monitoring of various diseases.
- Uncover disease mechanisms by analyzing metabolomic changes associated with diseases, and identifying key metabolic pathways that are disrupted.
- Develop new therapeutics by understanding metabolic changes induced by diseases, and developing new drug molecules that restore normal metabolic function.
- Optimize biotechnological processes by analyzing metabolomic profiles of microorganisms, which can be used to optimize fermentation and production processes for biological products.
Bioinformatics and metabolomics are used in various fields of medicine in identifying biomarkers for cancer, diabetes, and other diseases; developing personalized medicine; discovery of new medicinal substances in pharmacy; in assessing the effectiveness and safety of drugs; in the food industry for food quality assessing, developing new functional foods; in agronomy for improving crop yields and sustainability, developing new plant varieties and in ecology for monitoring environmental pollution, assessing the impact of climate change.
Despite the great potential, the combination of bioinformatics and metabolomics is still associated with some challenges, such as the analysis of large and complex data, data standardization, and complexity in integrating genomic, transcriptomic, proteomic, and metabolomic data. Despite these challenges, the future of bioinformatics and metabolomics looks promising. As new technologies and algorithms develop, these two fields will continue to play an increasingly important role in understanding biological processes and developing new therapies and technologies.
7. CHALLENGES AND PROSPECTS
Ecological metabolomics is the integration of metabolomics and ecology to study the interactions between organisms and the environment through the study of metabolic profiles. Ecological metabolomics is a bridge between organisms and the environment. This field is rapidly developing. However, it faces several challenges and offers unique perspectives.
Despite the great potential of ecological metabolomics, it still faces several challenges, such as the complexity of ecological systems and dynamics, which makes it difficult to identify and quantify all metabolites. Databases with metabolic profiles of different organisms and ecosystems are still underdeveloped; the analysis of metabolomic data requires expensive equipment and specialized software tools, and the lack of standardized methods for sampling, extraction and analysis of metabolites makes it difficult to compare results.
7.1. Application of microbial metabolomics – creative proteomics
Microbial metabolomics and creative proteomics are two powerful tools in modern microbiology that allow us to better understand the complex processes occurring in microorganisms. These research areas are of great importance for several applications ranging from medicine and pharmacy to biotechnology and environmental protection.
Creative proteomics is a relatively new field dealing development and application of new methods for protein analysis. The goal is to overcome the limitations of traditional proteomic methods and obtain a more complete picture of the proteome of a given organism.
Integrating microbial metabolomics and creative proteomics in research provides an opportunity for a deeper understanding of cellular processes. By comparing changes in metabolomes and proteomes, it is possible to determine how changes in gene expression affect the cell metabolism. Microbial metabolomics and creative proteomics are powerful tools that have the potential to revolutionize various fields of science and technology. By combining these two fields, new drugs can be discovered, more efficient biotechnologies can be developed, and important environmental problems can be solved. Key areas of application of microbial metabolomics and creative proteomics are:
- Identification and differentiation of microbial strains by analyzing the unique metabolic profiles of different strains of microorganisms. Creative proteomics helps to identify and differentiate closely related strains. It has important implications for food safety, environmental microbiology, and clinical diagnostics.
- Microbial metabolomics provides a comprehensive overview of the metabolic pathways active in a microorganism. This information can be used to understand how microorganisms interact with their environment, respond to stress, and produce valuable metabolites.
- Creative proteomics helps identify potential drug targets by analyzing metabolic changes induced by antimicrobial compounds and evaluate the effectiveness of new antibiotics.
- Microbial metabolomics can be used in industrial biotechnology to optimize fermentation processes, improve the production of biofuels and other bioproducts, and engineer microorganisms for specific industrial applications.
- Analysis of the microbial metabolome in environmental samples helps assessment of the impact of pollutants on microbial communities and monitoring the ecosystems health.
The advantages of creative proteomics are the high expertise of scientists specializing in microbial metabolomics, access to modern analytical instruments, and the latest technologies, allowing for individual solutions to specific needs. Harnessing the power of microbial metabolomics creative proteomics helps researchers unlock the potential of microorganisms and solve essential problems in various fields, including medicine, agriculture, and ecology.
7.2. Characterizing the toxicity of environmental pollutants and disease risks
When an organism is exposed to a toxic agent, its metabolism changes, which leads to changes in the concentrations of various metabolites. Metabolomic analysis can identify these changes and provide information about the mechanisms of toxicity of the pollutant for damage to the organism at the cellular level. It also identifies specific metabolites that serve as exposure to a particular toxicant and doses indicators responsible for the damage. Information about the impact of increasing the concentration of the pollutant on the metabolic profile of the organism and which organs and systems it affects is essential.
Figure 4.4. Changes in the metabolic profile in response to pollutant exposure Gene expression profile after exposure of RAW 264.7 cells to the standard particulate matter (PM) material, NIST1648a, and PM with a reduced organic matter content, LAp120, in comparison to the effects of lipopolysaccharide (LPS).
The application of metabolomics and creative proteomics in the field of environment and health provides essential information for assessing the risk to human health associated with exposure to environmental pollutants, such as heavy metals, pesticides, and industrial chemicals. It can also be understood how pollutants accumulate in organisms and how this affects their metabolism. New pollutants that cause changes in metabolism can be identified. These metabolomic changes, associated with pollutant exposure, can be used to develop biomarkers for the early detection of environmentally related diseases. Another essential role is to be used to evaluate the effectiveness of different methods for the remediation of contaminated soils and waters.
- Exposure to environmental pollutants can significantly alter the human metabolome, leading to various health problems. Key metabolic changes can be markers for several human diseases, such as:
- Pollutants such as particulate matter (PM2.5) and ozone (O3) can induce oxidative stress, leading to increased levels of reactive oxygen species (ROS). This can damage lipids, proteins, and DNA, leading to increased lipid peroxidation products (e.g. malondialdehyde), protein oxidation products, and DNA adducts.
- Activation of inflammatory pathways, leading to increased levels of inflammatory cytokines (e.g. TNF-α, IL-6) and chemokines. These molecules can further contribute to oxidative stress and tissue damage.
- Disruption of energy metabolism, leading to changes in glucose, lipid, and amino acid metabolism, which alters blood glucose, fatty acid, cholesterol, and amino acid levels.
- Affect neurotransmitter metabolism leading to changes in levels of neurotransmitters such as dopamine, serotonin, and glutamate, leading to neurological and psychiatric disorders.
- Interfere with hormone signaling leading to changes in levels of hormones such as estrogen, testosterone, and thyroid hormones and significantly impacting reproductive health and development.
- Alterations in lipid metabolism and oxidative stress can increase the risk of atherosclerosis and cardiovascular disease.
- Induce inflammation and oxidative stress in the lungs, leading to respiratory diseases such as asthma and chronic obstructive pulmonary disease (COPD).
- Alterations in neurotransmitter metabolism can contribute to neurodegenerative diseases such as Alzheimer’s and Parkinson’s disease, as well as psychiatric disorders such as depression and anxiety.
- Some pollutants can directly damage DNA, leading to mutations that can contribute to cancer development.
- Exposure to pollutants during pregnancy and early childhood can have adverse effects on fetal and child development, including impaired cognitive function and respiratory development.
Accurate assessment of pollutant exposure is crucial for understanding the health impacts of pollution. Reducing pollutant emissions through regulations and technological advances is essential to mitigate the health risks associated with pollution.
Metabolomics is proving to be a powerful tool for studying the effects of pollutants on living organisms. By analyzing metabolic changes, scientists can gain valuable information about the mechanisms of toxicity, identify biomarkers of exposure, and assess human health risks. In the future, metabolomics will play an increasingly important role in developing effective strategies to protect the environment and improve human health.
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