Research Topic

Microbial Metabolomics

About this Research Topic

The microbial metabolome is a reflection of a microbe’s metabolism, defined by the biosynthetic pathways and networks encoded in its genome and regulated by its host and environmental context. The analysis of the metabolome provides an assessment of the cellular state and gene function in a microbial system, revealing regulatory mechanisms and providing a deeper insight into cellular physiology, a better understanding of environmental effects on system function, and an assessment of the global outcome of interactions between microbial cells, their (human) host and their environment. Moreover, metabolomics permits identifying specific biomarker molecules associated with structural and metabolic states. Microbial metabolomics is an essential component of the ‘omics’ approaches applied in system biology, the metabolomic data offering essential input to metabolic models that are helping to better describe the microbial metabolic plasticity and regulation.

This article collection aims to address the most relevant current research on the application of microbial metabolomics to challenges in microbial physiology, secondary metabolite expression and regulation, biosynthesis of natural products, and metabolic modeling and engineering. Contributions on the metabolomic characterization of complex microbial communities, including the interaction between the human microbiome and its host, are also welcome, as are discussions of the computational tools and concepts used for the integrative interpretation of the rich datasets generated by modern metabolite profiling methods.

Please note that Systems Microbiology does not consider descriptive studies that are solely based on amplicon (e.g., 16S rRNA) profiles, unless they are accompanied by a clear hypothesis and experimentation and provide insight into the microbiological system or process being studied.


Keywords: Microbial Metabolomics, microbe’s metabolism, biosynthetic pathways, human microbiome, computational tools


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

The microbial metabolome is a reflection of a microbe’s metabolism, defined by the biosynthetic pathways and networks encoded in its genome and regulated by its host and environmental context. The analysis of the metabolome provides an assessment of the cellular state and gene function in a microbial system, revealing regulatory mechanisms and providing a deeper insight into cellular physiology, a better understanding of environmental effects on system function, and an assessment of the global outcome of interactions between microbial cells, their (human) host and their environment. Moreover, metabolomics permits identifying specific biomarker molecules associated with structural and metabolic states. Microbial metabolomics is an essential component of the ‘omics’ approaches applied in system biology, the metabolomic data offering essential input to metabolic models that are helping to better describe the microbial metabolic plasticity and regulation.

This article collection aims to address the most relevant current research on the application of microbial metabolomics to challenges in microbial physiology, secondary metabolite expression and regulation, biosynthesis of natural products, and metabolic modeling and engineering. Contributions on the metabolomic characterization of complex microbial communities, including the interaction between the human microbiome and its host, are also welcome, as are discussions of the computational tools and concepts used for the integrative interpretation of the rich datasets generated by modern metabolite profiling methods.

Please note that Systems Microbiology does not consider descriptive studies that are solely based on amplicon (e.g., 16S rRNA) profiles, unless they are accompanied by a clear hypothesis and experimentation and provide insight into the microbiological system or process being studied.


Keywords: Microbial Metabolomics, microbe’s metabolism, biosynthetic pathways, human microbiome, computational tools


Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.

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Submission Deadlines

31 October 2021 Abstract
12 January 2022 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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Topic Editors

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Submission Deadlines

31 October 2021 Abstract
12 January 2022 Manuscript

Participating Journals

Manuscripts can be submitted to this Research Topic via the following journals:

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