Microbiome Research for Animal, Plant and Environmental Health: Second Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbiomes".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 812

Special Issue Editors


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Guest Editor
Department of Molecular Biology and Genetics, Faculty of Health Sciences, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: probiotics; microbiota; microbiome; beneficial microbes; multi-omics; lactic acid bacteria
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
Department of Molecular Biology & Genetics, Democritus University of Thrace, 68100 Alexandroupolis, Greece
Interests: natural products; probiotics; microbiome; rhizobiome; cellular stress responses
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Microbiome Research for Animal, Plant and Environmental Health” (https://www.mdpi.com/si/195604).

Microbial communities play an integral role in the homeostasis and physiology of macro- and micro-ecosystems. Accumulating evidence demonstrates the critical impact of human microbiota on health and disease. In this context, it is recognized that the host microbiota contributes to crucial processes, such as nutrient synthesis and digestion, immunomodulation, intestinal barrier integrity, and protection against pathogenic insults, while exerting extraintestinal and systemic effects. By extension, microbiota research is of great interest because of its potential applications in the field of agriculture and animal husbandry. Indeed, the soil microbiome, as well as the plant microbiome and the rhizosphere microbiome (rhizobiome), can influence plant health, nutritional value, and the ability of plants to adapt to and withstand extreme environmental conditions, thus having major ecological and economic implications. In addition, the correlation between microbiota composition and the spread of pathogens to animals and the food chain is gaining increasing attention in the context of the “One Health” approach. Manipulating the composition of microbiota in these ecosystems can have a significant impact on human and animal health whilst also contributing to sustainable agriculture.

As Guest Editors of this Special Issue, we would like to invite you to submit original research articles, review articles, and short communications on various aspects of animal, plant, environmental, or soil microbiome research, new mechanistic insights into host–microbe interactions, methods of microbiome manipulation, and innovative technologies for sustainable livestock and agri-food production.

Dr. Alex Galanis
Dr. Aglaia Pappa
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 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. Microorganisms 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 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

  • environmental microbiome
  • soil microbiome
  • rhizobiome
  • host–microbe interactions
  • microbiome manipulation
  • sustainable agriculture

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Published Papers (2 papers)

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Research

32 pages, 3540 KB  
Article
Geographic Provenances Outweigh Tissue Compartments in Bacteriome Assembly of the Ectomycorrhizal, Edible, and Hallucinogenic if Undercooked, Lanmoa asiatica (Boletaceae, Boletales) Mushroom from Yunnan China
by Man Guo, Dong Liu, Zhilan Xia, Tao Xie, Luofeng Su, Jesus Pérez-Moreno and Fuqiang Yu
Microorganisms 2025, 13(11), 2431; https://doi.org/10.3390/microorganisms13112431 - 23 Oct 2025
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Abstract
Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. [...] Read more.
Ectomycorrhizal fungal sporomes represent complex microuniverses harboring structurally and functionally eclectic microbiomes with significant ecological roles and potential anthropogenic applications. Nevertheless, the factors governing the assembly of these microbial communities remain poorly understood, and numerous fungal taxa, including many ectomycorrhizal species, remain uninvestigated. This study characterizes the bacteriome of the socioculturally and economically important yet hallucinogenic-if-raw ectomycorrhizal bolete Lanmoa asiatica. We analyzed 36 basidiomata from four geographic locations within China, partitioning each into pileus, stipe, and hymenophore tissues, and sequenced the V5–V7 region of the bacterial 16S rRNA gene. Proteobacteria dominated (>85%), with Pantoea, Sphingomonas, and the Burkholderia complex identified as core genera. Contrary to expectations, α-diversity was highest in the stipe (Chao1 index up to 1934) rather than the exposed hymenophore. PERMANOVA indicated that geographic origin (R2 = 0.46, p < 0.001) was a stronger structuring force than tissue type (R2 = 0.28, p < 0.01). Functional prediction via PICRUSt2 revealed enrichments in lipid metabolism, antimicrobial resistance, and apoptosis pathways across sites, while tissue-specific functions involved carbohydrate and nitrogen metabolism. These findings support a hierarchical model of bacteriome assembly where broad-scale environmental filters override micro-niche differentiation, providing a biogeographic framework for the conservation of this highly valued edible mushroom. Full article
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24 pages, 3029 KB  
Article
Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding
by Maria Tokamani, Panagiotis Liakopoulos, Konstantinos Tegopoulos, Aristea-Marina Zigkou, George Triantaphyllidis, Nikolaos Kamidis, Maria E. Grigoriou, Raphael Sandaltzopoulos and Petros Kolovos
Microorganisms 2025, 13(10), 2373; https://doi.org/10.3390/microorganisms13102373 - 15 Oct 2025
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Abstract
The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing [...] Read more.
The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea. Full article
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