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Molecules Targeting the Human Microbiome: Natural Products, Metabolites and Mechanisms
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Molecules Targeting the Human Microbiome: Natural Products, Metabolites and Mechanisms

A special issue of Molecules (ISSN 1420-3049).

Deadline for manuscript submissions: 30 September 2026 | Viewed by 1864

Editors

Dr. Juliana Garcia

E-Mail Website
Guest Editor
1. Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
2. AquaValor – Centro de Valorização e Transferência de Tecnologia da Água – Associação, Rua Dr. Júlio Martins n.º 1, 5400-342 Chaves, Portugal
Interests: biological activities of natural products; chemical characterization of biocompounds; multidrug-resistant pathogens; food and chemical toxicology; nutraceutical and medicinal value of agro-industrial by-products
Special Issues, Collections and Topics in MDPI journals
Dr. Irene Gouvinhas

E-Mail Website
Guest Editor
Centre for the Research and Technology of Agro-Environment and Biological Sciences (CITAB), Institute for Innovation, Capacity Building and Sustainability of Agri-Food Production (Inov4Agro), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
Interests: bioactivity; chemical characterization of natural products; identification, quantification, separation, and recovery of bioactive compounds from different food and agro-food byproducts; experimental design applied to extraction and process optimization of natural products
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The human microbiome is a major determinant of host physiology, shaping immunity, barrier function, metabolism, and inflammation through a dense chemical exchange of microbial metabolites and bioactive molecules.

This Special Issue will highlight advances in the discovery, characterization, and mechanistic understanding of molecules that modulate the microbiome and microbiome-derived functions. We aim to bring together contributions spanning natural products, dietary bioactives, prebiotics, postbiotics, and small molecules influencing microbial composition, interspecies interactions, and metabolic outputs (e.g., SCFAs, indoles, bile acid derivatives, phenolic metabolites). This Special Issue will welcome studies using targeted/untargeted metabolomics, molecular docking, in vitro gut models, microbial ecology, and host–microbe assays to connect chemical structure with functional outcomes. We particularly encourage submissions addressing structure–activity relationships, delivery strategies, safety assessment, and translational relevance for human health, including gut, skin, and respiratory microbiomes. Article types may include original research, systematic or narrative reviews, and methodological papers focused on analytical platforms and bioinformatics workflows supporting microbiome–metabolite research.

Dr. Juliana Garcia
Dr. Irene Gouvinhas
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 submissions that pass pre-check are 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 250 words) can be sent to the Editorial Office for assessment.

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly 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 2700 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.

Keywords

  • human microbiome
  • microbial metabolites
  • bioactive molecules
  • microbiomes

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Review

18 pages, 770 KB  
Review
Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host–Microbe Mechanisms and Paths to Clinical Translation
by Juliana Garcia, Jani Silva, Maria José Alves and Irene Gouvinhas
Molecules 2026, 31(13), 2229; https://doi.org/10.3390/molecules31132229 - 24 Jun 2026
Viewed by 247
Abstract
Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune [...] Read more.
Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption—often combined with persistent biofilm formation—drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host–microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools—advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance. Full article
(This article belongs to the Special Issue Molecules Targeting the Human Microbiome: Natural Products, Metabolites and Mechanisms)
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29 pages, 2912 KB  
Review
Advances in Scalp Microbiome Research: Molecular Insights into the Metabolism-Inflammation-Barrier Axis and Dandruff Pathogenesis
by Le Deng, Xiao Ling, Li Li, Youjie He and Miaomiao Guo
Molecules 2026, 31(12), 2093; https://doi.org/10.3390/molecules31122093 - 14 Jun 2026
Viewed by 1323
Abstract
Dandruff (DF) is a prevalent, recurrent inflammatory scalp disorder increasingly recognized as a complex state of functional dysbiosis rather than a simple Malassezia overcolonization. The scalp microbiome is predominantly shaped by Malassezia species (M. restricta and M. globosa), Cutibacterium, and [...] Read more.
Dandruff (DF) is a prevalent, recurrent inflammatory scalp disorder increasingly recognized as a complex state of functional dysbiosis rather than a simple Malassezia overcolonization. The scalp microbiome is predominantly shaped by Malassezia species (M. restricta and M. globosa), Cutibacterium, and Staphylococcus species. Recent multi-omics evidence indicates that DF pathogenesis is driven by the destabilization of microbial interaction networks and strain-level functional heterogeneity, characterized by the disruption of the C. acnes/S. epidermidis balance and the opportunistic expansion of Staphylococcus aureus. Mechanistically, Malassezia utilizes its lipolytic repertoire to hydrolyze host sebum into irritant free fatty acids and peroxides. Concurrently, oxidative metabolites like squalene peroxide (SQOOH) penetrate the stratum corneum to activate the NF-κB and aryl hydrocarbon receptor (AhR) pathways, triggering a pro-inflammatory cascade that overexpresses keratins (K6/16/17) and downregulates filaggrin. This molecular cascade drives abnormal keratinocyte turnover and lipidomic remodeling, establishing a self-perpetuating “metabolism–inflammation–barrier disruption” pathological cycle. This review systematically elucidates the molecular etiology of DF as an ecological disorder driven by a tripartite imbalance among the microbiome, host physiology, and the environmental niche. We propose that next-generation therapeutic paradigms must transcend traditional antifungal eradication, focusing instead on targeted molecular intervention and microecological restoration to recalibrate overall scalp homeostasis. Full article
(This article belongs to the Special Issue Molecules Targeting the Human Microbiome: Natural Products, Metabolites and Mechanisms)
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