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Application of Microbial Metabolomics

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Microbial metabolomics seeks to analyze all metabolites in a biological system, so the emphasis is on retaining and reflecting as much information as possible about the total metabolites throughout the process. At present, microbial metabolomics has been widely used in many research fields.

In mutant screening and the study of functional genes, microbial metabolomics can be used to distinguish different pathogens of bacterial pneumonia in animals and for the early diagnosis of pediatric infectious shock. In food and nutrition, microbial metabolomics has been applied to reveal the degradation process of pathogens and toxins, as well as the detection of toxic substances in food, providing new methods for food safety monitoring. The use of genomics, transcriptomics, proteomics and metabolomics to explore the influence of lactic acid bacteria and other intestinal microorganisms on the gut is also one of the current research hotspots. Microbial metabolomics approaches are not only able to detect metabolite changes in the gut under the action of lactic acid bacteria, but also to elucidate the effects of lactic acid bacteria metabolic pathways on host cells. In addition, intestinal flora is also the focus of systems biology and metabolomics studies.

Microbial metabolome in the study of gut microbes

Microorganisms colonizing the host gut are an important part of the gastrointestinal ecosystem. Their function and metabolism are closely related to host health and disease, preventing pathogen infection, providing energy to the host through their own metabolism, enhancing body immunity and interacting with the host to regulate metabolic phenotypes.

Under normal conditions, the structure of the intestinal flora plays an important role in the prevention and control of diseases. However, dysbiosis of the gut flora and altered microbial biodiversity can have a number of adverse effects on the host, leading to the development of various gastrointestinal, metabolic and immune disorders. Many studies have been conducted to investigate the role of intestinal flora and host metabolites in host health and disease through metabolomics techniques.

Microbial regulation of host metabolism via gut hormone releaseFig 1. Microbial regulation of host metabolism via gut hormone release (Martin et al., 2019).

Microbial metabolome in the study of soil environmental microorganisms

The production and release of small molecule metabolites in soil microbial communities and the consumption of metabolic activities constitute a complex system of extracellular metabolites of soil microorganisms, which is a direct reflection of the metabolic state of microbial communities. Studying the extracellular metabolites of microbial communities under different conditions can guide us to better understand the stress response of microorganisms.

The complexity of the soil environment and the difficulty of processing and analyzing soil microbial metabolite samples are among the reasons for the lack of research on extracellular metabolites in the soil environment. The organic compounds that make up soil organic matter are present in different levels of soil structure and their bioavailability varies. Among them, dissolved organic matter is the most readily available to soil microorganisms. Most of the dissolved organic matter present in soils is derived from microbial metabolism and cellular decomposition. Therefore, studies on the correlation between soil organic matter and microbial metabolites can be established.

Application of soil metabolomicsFig 2. Application of soil metabolomics (Withers et al., 2020).

Microbial metabolome in food microbiology research

Food safety has always been of great importance to governments and people of all countries. Pathogens, toxins and by-products produced by microbial degradation of food are closely related to food safety issues. Microbial metabolomics provides new strategies for food safety evaluation and has been successfully applied to the detection of toxic substances in food. For example, fingerprinting of volatile metabolites associated with specific microbial contamination has been studied using GC-MS techniques, and microbial toxins in foods have been detected using LC-MS and NMR techniques.

In addition, microbial metabolomics has been applied to assess the effects of nutrient deficiencies and excesses on the metabolic homeostasis of the organism, to monitor more precisely the effects of diet on the organism, and to reduce the interference of confounding factors such as age, gender, physiological status and lifestyle.

Microbial metabolomics in the study of pathogenic bacteria

Mass spectrometry is the most commonly used technique for metabolomic analysis in the study of fungal phytopathogenic fungi and is widely used for the analysis of mutations and detection and screening of secondary metabolites in pathogenic bacteria. In addition, microbial metabolomics has been applied to the diagnosis of diseases caused by pathogenic bacterial infections. For example, GC-MS analysis of volatile organic compounds in feces reveals that metabolomics techniques can be used to differentiate diarrhea caused by different pathogenic bacteria.


  1. Martin, A. M., Sun, E. W., Rogers, G. B., & Keating, D. J. (2019). The influence of the gut microbiome on host metabolism through the regulation of gut hormone release. Frontiers in physiology, 10, 428.
  2. Withers, E., Hill, P. W., Chadwick, D. R., & Jones, D. L. (2020). Use of untargeted metabolomics for assessing soil quality and microbial function. Soil Biology and Biochemistry, 143, 107758.

Related Sections

Microbial Metabolomics Service

Food Metabolomics Service

Metabolomic Approaches for Microbial Research

For Research Use Only. Not for use in diagnostic procedures.


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