Special Issue "Microbiome and Metabolome"

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Environmental Science".

Deadline for manuscript submissions: 30 November 2020.

Special Issue Editors

Dr. Laura-Isobel McCall
Guest Editor
University of Oklahoma, Department of Chemistry and Biochemistry
Interests: metabolomics; chemical cartography; host–microbe interactions; LC–MS; microbiome
Dr. Hosein Mohimani
Guest Editor
Computational Biology Department, School of Computer Science, Carnegie Mellon University, PA, USA
Interests: computational metabolomics and metagenomics; natural product discovery; microbiome analysis
Special Issues and Collections in MDPI journals
Dr. Andrés Mauricio Caraballo-Rodríguez
Guest Editor
Skaggs School of Pharmacy & Pharmaceutical Sciences, San Diego, United States
Interests: natural products; small molecules; metabolomics; mass spectrometry; chemical ecology
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The microbiota, the community of microorganisms living on or in a given environment, is now widely acknowledged as a key determinant of health, disease, and organismal and ecosystem function. However, the mechanisms by which it does so remain poorly understood. Several small-molecule signals have been identified as mediators of this interaction, including short-chain fatty acids, secondary bile acids, amino acid metabolites, etc., but additional signals are clearly involved. Metabolomics is thus uniquely poised to define the chemical signals through which host and microbiota interact. Likewise, community living requires significant metabolic adaptations within microorganisms and considerable collaborative and competitive metabolic interactions between microbiota members in the environment and in hosts. This Special Issue of Metabolites, “Microbiome and Metabolome”, is dedicated to studies using metabolomics approaches to address these issues, and on novel data analysis approaches used to generate insight into these interactions. Multi-omics approaches integrating metabolomics with metagenomics, metatranscriptomics, or metaproteomics are of particular interest.

Dr. Laura-Isobel McCall

Dr. Hosein Mohimani

Dr. Andrés Mauricio Caraballo-Rodríguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • metabolomics
  • microbiome
  • microbiota
  • multi-omics
  • environmental microbiota
  • host-associated microbiota
  • cross-species communication
  • microbial community metabolism
  • metabolic adaptation
  • secondary metabolites

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Microbial amino acid metabolism tunes host immunity, metabolism and extraintestinal disorders

Rampanelli E  1;Nieuwdorp M 2; de Vos WM 3,4

1 Department of Experimental Vascular Medicine, Amsterdam University Medical Centers (AUMC, location AMC), Amsterdam, The Netherlands.

2 Department of Internal and Vascular Medicine, Amsterdam University Medical Centers (AUMC), Amsterdam, The Netherlands.

 3 Laboratory of Microbiology, Wageningen University,  Wageningen, The Netherlands.

Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Finland


The trillions of commensal microorganisms comprising the gut microbiota have gained growing attention owing to their impact on host physiology. Many microbial metabolites serve as messengers in the complex dialogue between commensals and host immune and endocrine cells, thereby influencing immune and metabolic responses. In this review, we highlight the importance of microbial amino acid metabolism in host health, with a focus on bacterial catabolism of tryptophan and the actions of its derivatives. Recent advances in our understandings of the host-microbiota crosstalk support a pivotal role of tryptophan catabolites in various physiological processes, from enhancing intestinal functions to promoting immune and metabolic homeostasis. Herein, we discuss the latest evidence on the effects of tryptophan-derived metabolites and their mechanisms of action and discourse how perturbations of tryptophan metabolism may affect host susceptibility to intestinal and extraintestinal disorders and impact the course of disease. Finally, we explore microbiota-based therapeutic interventions to restore microbial homeostasis and tryptophan metabolism, and hence improve clinical outcomes.

Title: The link between obesity, microbiota dysbiosis, and neurodegenerative pathogenesis

Emanuel Vamanu


Abstract: A current research direction of neurodegenerative pathologies establishes a link between their
occurrence, microbiota dysbiosis, and the incidence of obesity. Food digestion and assimilation of bioactive components will modulate the body's response to the different physicochemical factors. Oxidative stress is one of the major factors that shows a direct effect on the functioning of the human microbiota. The reaction of the body to this imbalance is crucial in the progression of inflammatory processes based on molecular mechanisms. Disturbance of the microbial pathway will result in a possibly permanent alteration in the expression of the physiological response. This review aims to highlight recent contributions to alleviating human dysbiosis in the case of degenerative diseases, especially for neurodegenerative pathologies, based on the rising prevalence of obesity. We discuss  the significance of microbiota modulation and sustain an alleviation of pathologies by a possible regenerative function. Thus, probiotics and prebiotics (including phenolic compounds with prebiotic effect) are an effective alternative that can support the modulation of the microbiota pattern over time and the attenuation of indirect causes that cause dysbiosis. Molecular aspects were presented in support of the modulating role of the microbiota following the use of probiotics.


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