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Microorganisms publishes Special Issues to create collections of papers on specific topics, with the aim of building a community of authors and readers to discuss the latest research and develop new ideas and research directions. Special Issues are led by Guest Editors, who are experts on the topic and all Special Issue submissions follow MDPI's standard editorial process. The journal’s Editor-in-Chief and/or designated Editorial Board Member will oversee Guest Editor appointments and Special Issue proposals, checking their content for relevance and ensuring the suitability of the material for the journal. The papers published in a Special Issue will be collected and displayed on a dedicated page of the journal’s website. Further information on MDPI's Special Issue policies and Guest Editor responsibilities can be found here. For any inquiries related to a Special Issue, please contact the Editorial Office.

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Microbiome in Fish and Their Living Environment

edited by

Yongjun Chen

and

Gang Yang

submission deadline 10 Nov 2025 | 12 articles | Viewed by 11951 | Submission Open

Keywords: fish species; gut microbiome; dietary modification; water environment; immunity

(This special issue belongs to the Section Veterinary Microbiology)

Microorganisms in Functional Foods: 2nd Edition

edited by

Jadranka Frece

submission deadline 15 Nov 2025 | 3 articles | Viewed by 8028 | Submission Open

Keywords: functional food; probiotics; prebiotics; fermentation; food microbiology; health promotion; gut diversity

(This special issue belongs to the Section Food Microbiology)

Ticks and Tick-Borne Pathogens—from Understanding to Control

edited by

Larissa Almeida Martins

and

Andrea Fogaça

submission deadline 15 Nov 2025 | 2 articles | Viewed by 5556 | Submission Open

Keywords: tick biology; tick-borne pathogens; transmission-block vaccines; tick control; tick– host interactions; tick saliva; tick immunology; tick virus; tick microbiome; tick vaccine development

(This special issue belongs to the Section Public Health Microbiology)

Lactic Acid Bacteria in Food Fermentation and Biotechnology

edited by

Spiros Paramithiotis

submission deadline 15 Nov 2025 | 1 articles | Viewed by 1563 | Submission Open

Keywords: genomics; transcriptomics; metabolomics; cell factories; bioactive compounds

(This special issue belongs to the Section Food Microbiology)

Rhizosphere Microbial Community, 4th Edition

edited by

Taegun Seo

submission deadline 15 Nov 2025 | 2 articles | Viewed by 1327 | Submission Open

Keywords: rhizosphere; endophytes; plant-microbe interactions

(This special issue belongs to the Section Plant Microbe Interactions)

Advances in Magnetotactic Bacteria

edited by Hongmiao Pan

submission deadline 15 Nov 2025 | Viewed by 118 | Submission Open

Keywords: magnetotactic bacteria; multicellular magnetotactic prokaryotes; magnetically responsive protists; magnetosome; biomineralization; culture; genome; evolution; environmental adaptability strategy; ecological function; magnetofossil; metagenome assembled genomes

(This special issue belongs to the Section Environmental Microbiology)

Viral Diseases: Current Research and Future Directions

edited by

Sherif T.S. Hassan

submission deadline 30 Nov 2025 | 8 articles | Viewed by 26128 | Submission Open

Keywords: RNA viruses; DNA viruses; virus– host interactions; immune evasion strategies; host immune response; viral epidemiology; biology and pathogenesis; virus diagnosis; viral diseases; prevention; management and treatment strategies; antiviral therapeutics; vaccine development

(This special issue belongs to the Section Virology)

Recent Advances on Microbial Interactions with Materials and Their Applications

edited by

Ruiyong Zhang

Hongwei Liu

and Fang Guan

submission deadline 30 Nov 2025 | 6 articles | Viewed by 25101 | Submission Open

Keywords: microbiologically influenced corrosion; biofouling; biomineralization and bioleaching; elements cycle; microbial degradation.

(This special issue belongs to the Section Environmental Microbiology)

Genomics Approaches in Microbial Ecology

edited by Hugo César Ramírez-Saad and César Hernández-Rodríguez

submission deadline 30 Nov 2025 | 7 articles | Viewed by 18947 | Submission Open

Keywords: soil microorganisms; microbes associated with plants; microbes associated with animals; microbial ecology; omics approaches; microbiomes; microbial communities; microbial symbioses; bacteria; archaea; fungi; algae; protists; viruses

(This special issue belongs to the Section Molecular Microbiology and Immunology)

Feature Papers in Microbiomes

edited by

Pabulo Rampelotto

submission deadline 30 Nov 2025 | 9 articles | Viewed by 17597 | Submission Open

Keywords: human microbiome; animal microbiome; environmental microbiome; marine microbiome; plant microbiome; soil microbiome; bioinformatics and computational tools; microbial interactions and functions; microbiome-associated diseases; microbiome-omics technologies; multi-omics integration; microbial network; host– microbiome interactions; microbiome-based therapies; emerging trends

(This special issue belongs to the Section Microbiomes)

Research on Biology of Dinoflagellates

edited by

Marco Villanueva

, Tania Islas-Flores and Estefanía Morales-Ruiz

submission deadline 30 Nov 2025 | 7 articles | Viewed by 15972 | Submission Open

Keywords: dinoflagellate; molecular biology; genomics; transcriptomics; proteomics; metabolomic

(This special issue belongs to the Section Environmental Microbiology)

Gut Microbiota in Health and Diseases: The Role of Pro-/Pre-/Syn-/Post-Biotics in the Gut–Liver–Brain Axis

edited by Mohamad Khalil and

Piero Portincasa

submission deadline 30 Nov 2025 | 2 articles | Viewed by 15248 | Submission Open

Keywords: gut microbiome; gut– liver– brain axis; gastrointestinal tract; digestion; metabolism; immune function

(This special issue belongs to the Section Gut Microbiota)

Advances in Veterinary Microbiology

edited by

Simone Peletto

submission deadline 30 Nov 2025 | 14 articles | Viewed by 14882 | Submission Open

Keywords: African Swine Fever Virus; Bluetongue Virus; Arboviruses; Microbiota; Metagenomics; Brucellosis

(This special issue belongs to the Section Veterinary Microbiology)

Overview of Healthcare-Associated Infections

edited by

Tun-Chieh Chen

and

Yusen Eason Lin

submission deadline 30 Nov 2025 | 3 articles | Viewed by 14540 | Submission Open

Keywords: infection; healthcare; public health

(This special issue belongs to the Section Medical Microbiology)

Contemporary Perspectives on Bacterial Virulence Factors

edited by Matthew Jackson and Kevin Theis

submission deadline 30 Nov 2025 | 3 articles | Viewed by 12750 | Submission Open

Keywords: bacterial pathogens; virulence factors; immune response; staphylococcus aureus; pseudomonas aeruginosa

(This special issue belongs to the Section Molecular Microbiology and Immunology)

Ticks and Tick-Borne Diseases in Animals, 2nd Edition

edited by

Ángeles Sonia Olmeda

and

Félix Valcárcel

submission deadline 30 Nov 2025 | 5 articles | Viewed by 11395 | Submission Open

Keywords: tick ecology; identification; tick-borne pathogen; vectorial role and capacity; laboratory and field control; new acaricides

(This special issue belongs to the Section Veterinary Microbiology)

Microbial Nitrogen Cycle

edited by

Volker Brozel

submission deadline 30 Nov 2025 | 4 articles | Viewed by 11151 | Submission Open

Keywords: microbial nitrogen cycle; nitrogen fixation; nitrification; denitrification; ammonification

(This special issue belongs to the Section Environmental Microbiology)

Gut Microbiota of Food Animal

edited by

Benoit St Pierre

submission deadline 30 Nov 2025 | 6 articles | Viewed by 10142 | Submission Open

Keywords: food animals; gut health; microbiota; microbial ecology; metagenomics; bioinformatics; metabolomics; culturomics

(This special issue belongs to the Section Veterinary Microbiology)

Research on Diseases of Aquatic Organisms

edited by Geovana Dotta,

Guilherme Tavares

and

Fabiana Pilarski

submission deadline 30 Nov 2025 | 6 articles | Viewed by 10046 | Submission Open

Keywords: conservation and welfare of aquatic animals; ecotoxicology of aquatic environments; amphibian health and diseases; crustacean health and diseases; fish health and diseases; health and diseases of bivalve mollusks; health and diseases of other aquatic animals

(This special issue belongs to the Section Veterinary Microbiology)

Molecular Ecology of Microalgae and Cyanobacteria

edited by

Burkhard Becker

, Karin Glaser and Ekaterina Pushkareva

submission deadline 30 Nov 2025 | 4 articles | Viewed by 9974 | Submission Open

Keywords: microalgae; cyanobacteria; molecular omics

(This special issue belongs to the Section Environmental Microbiology)

Advances in Research on Waterborne Pathogens

edited by Ashwini S. Kucknoor

submission deadline 30 Nov 2025 | 5 articles | Viewed by 9923 | Submission Open

Keywords: waterborne pathogens; pathogen detection; antimicrobial resistance; public health

(This special issue belongs to the Section Environmental Microbiology)

Healthcare-Associated Infections and Antimicrobial Therapy—2nd Edition

edited by

Diamantis P. Kofteridis

and

Petros Ioannou

submission deadline 30 Nov 2025 | 6 articles | Viewed by 9207 | Submission Open

Keywords: clinical microbiology; healthcare-associated infections; antimicrobial therapy

(This special issue belongs to the Section Medical Microbiology)

Legionella pneumophila: A Microorganism with Thousand Faces, 2nd Edition

edited by

Teresa Maria Assunta Fasciana

submission deadline 30 Nov 2025 | 4 articles | Viewed by 9110 | Submission Open

Keywords: Legionella pneumophila; virulence factors; biofilm; disinfection strategy

(This special issue belongs to the Section Medical Microbiology)

Nutrition and Gut Microbiome

edited by

Giuseppe Merra

submission deadline 30 Nov 2025 | 3 articles | Viewed by 8473 | Submission Open

Keywords: nutrition; gut microbiome; diet; microbial diversity; pro-; pre- and post-biotics

(This special issue belongs to the Section Gut Microbiota)

Advances in Viral Disease Epidemiology and Molecular Pathogenesis

edited by

José Arellano-Galindo

submission deadline 30 Nov 2025 | 4 articles | Viewed by 8449 | Submission Open

Keywords: epidemiology; molecular pathogenesis; host– virus interactions; genetic variation; viral transmission; vaccines and antivirals; zoonotic viruses; environmental reservoirs.

(This special issue belongs to the Section Molecular Microbiology and Immunology)

Fungal Metabolites: Powering Pharmacological and Agricultural Frontiers

edited by

Maja Karaman

and

Ewa Zapora

submission deadline 30 Nov 2025 | 6 articles | Viewed by 8267 | Submission Open

Keywords: fungi; fungal metabolites; polysaccharides; pharmacological applications; agricultural innovations; crop productivity; stress tolerance

(This special issue belongs to the Section Environmental Microbiology)

Chemical Communication in Plant–Microbe Beneficial Interactions Between Plants and Rhizosphere Microorganisms

edited by Haichao Feng and Yunpeng Liu

submission deadline 30 Nov 2025 | 4 articles | Viewed by 8152 | Submission Open

Keywords: plant growth-promoting rhizobacteria (PGPR); root exudates; colonization; chemotaxis; attachment; biofilm; rhizomicrobiome; plant health; recruitment; biocontrol

(This special issue belongs to the Section Plant Microbe Interactions)

Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition

edited by

José David Flores-Félix

submission deadline 30 Nov 2025 | 6 articles | Viewed by 7931 | Submission Open

Keywords: rhizobacteria; endophytes; epiphytes; rhizosphere; phyllosphere; plant growth-promoting bacteria; plant microbiome; plant– microbe transcriptomic; plant– microbe interactions; culturomic microbiote; quorum sensing

(This special issue belongs to the Section Plant Microbe Interactions)

Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition

edited by

Blanca R. López

and

Luz De-Bashan

submission deadline 30 Nov 2025 | 5 articles | Viewed by 7751 | Submission Open

Keywords: plant growth-promoting bacteria; endophytes; environmental stress; nitrogen fixing bacteria; P and K solubilizing bacteria; mechanisms of plant growth; PGPB-plant interaction soil microbial communities; soil rehabilitation; bacterial inoculants and biosafety

(This special issue belongs to the Section Plant Microbe Interactions)

Editorial Board Members’ Collection Series: Hepatitis Viruses: Who They Are and Consequences

edited by

Isabelle Chemin

and

Flor Helene Pujol

submission deadline 30 Nov 2025 | 2 articles | Viewed by 7610 | Submission Open

Keywords: viral hepatitis; liver; pathogenesis; cancer; fibrosis; natural history; treatments; epidemiology; vaccine; genotypes

(This special issue belongs to the Section Virology)

Advances in Microbial Cell Factories, 3rd Edition

edited by

Thomas Brück

and

Dania Awad

submission deadline 30 Nov 2025 | 6 articles | Viewed by 7010 | Submission Open

Keywords: sustainability; biotechnology; bioengineering; biocatalysis; fermentation

(This special issue belongs to the Section Microbial Biotechnology)

Potential Antimicrobial Synergistic Interactions of Natural Products

edited by

Antonio Rosato

and Alexia Barbarossa

submission deadline 30 Nov 2025 | 2 articles | Viewed by 6952 | Submission Open

Keywords: antimicrobial resistance; synergistic effect; natural substances

(This special issue belongs to the Section Antimicrobial Agents and Resistance)

Phenotyping the Athletic Gut Microbiota: The Basis of Health and Physical Performance?

edited by Jesús Álvarez-Herms

submission deadline 30 Nov 2025 | 3 articles | Viewed by 6833 | Submission Open

Keywords: physiology; gut microbiota; exercise; hypoxia; nutrition; hyperthermia

(This special issue belongs to the Section Gut Microbiota)

Antimicrobial Stewardship: Strategies for Optimizing Antimicrobial Use and Combating Resistance

edited by

Viorica Railean

submission deadline 30 Nov 2025 | 3 articles | Viewed by 6551 | Submission Open

Keywords: antimicrobial stewardship; antimicrobial agent; antimicrobial therapy; dosing optimization; healthcare; antimicrobial surveillance and monitoring; human medicine; veterinary medicine; multidisciplinary; stewardship programs

(This special issue belongs to the Section Antimicrobial Agents and Resistance)

Sustainable Waste Biotechnologies: Biodegradation, Biotransformation, and Bioconversion

edited by

Xin Zhao

and Lei Zhang

submission deadline 30 Nov 2025 | 5 articles | Viewed by 5585 | Submission Open

Keywords: waste biotechnologies; waste management; biodegradation; biotransformation; bioconversion

(This special issue belongs to the Section Environmental Microbiology)

Climate-Driven Effects on the Human Microbiome and Public Health

edited by

Panos Zanos

and Anna Onisiforou

submission deadline 30 Nov 2025 | 1 articles | Viewed by 5547 | Submission Open

Keywords: climate change; human microbiome; public health

(This special issue belongs to the Section Medical Microbiology)

Feature Papers in Plant–Microbe Interactions in North America

edited by

Nazrul Islam

and

Susmita Das Nishu

submission deadline 30 Nov 2025 | 4 articles | Viewed by 5413 | Submission Open

Keywords: plant– microbe interaction; plant-associated microbes; biotic and abiotic stresses; agricultural sustainability

(This special issue belongs to the Section Plant Microbe Interactions)

Pathobiology, Infection Biology and Control of Protozoan Parasites—the ONE HEALTH Approach

edited by

Cláudia Marques

Maria João Gouveia

and Susana R. Sousa

submission deadline 30 Nov 2025 | 3 articles | Viewed by 5411 | Submission Open

Keywords: protozoan parasites; host– parasite interactions; pathobiology; disease control; ONE HEALTH

(This special issue belongs to the Section Veterinary Microbiology)

Research on Leishmania and Leishmaniasis: Second Edition

edited by

Mãrcia Dalastra Laurenti

and

Luiz Felipe Domingues Passero

submission deadline 30 Nov 2025 | 2 articles | Viewed by 4547 | Submission Open

Keywords: leishmania; leishmaniasis; drug treatment; vaccine; host-parasite interaction

(This special issue belongs to the Section Medical Microbiology)

Epidemiology of Zoonotic Pathogens

edited by

Mirela Imre

and

Marius Stelian Ilie

submission deadline 30 Nov 2025 | 5 articles | Viewed by 4503 | Submission Open

Keywords: zoonotic; pathogen; infection

(This special issue belongs to the Section Veterinary Microbiology)

Emerging and Re-Emerging Infections in the Immunocompromised Host

edited by

Emanuele Palomba

submission deadline 30 Nov 2025 | 2 articles | Viewed by 4330 | Submission Open

Keywords: opportunistic infections; immunocompromised host; solid organ transplant; HIV; AIDS; oncohematologic malignancies

(This special issue belongs to the Section Medical Microbiology)

New Progress in Animal Herpesviruses

edited by Angélica Cristine de Almeida Campos

submission deadline 30 Nov 2025 | 2 articles | Viewed by 4206 | Submission Open

Keywords: herpesvirus; immunology of herpesvirus; new herpesviruses and new hosts; host x virus interaction; genetic evolution of herpesvirus; oneHealth; new techniques and diagnosis; animal herpesvirus surveillance; zoonotic potential of herpesvirus

(This special issue belongs to the Section Veterinary Microbiology)

Latest Research on Clostridioides difficile

edited by

George Broukhanski

submission deadline 30 Nov 2025 | 2 articles | Viewed by 4049 | Submission Open

Keywords: Clostridioides difficile; biology; epidemiology; pathogenicity; detection; treatment; infection control

(This special issue belongs to the Section Medical Microbiology)

Bacterial Infections and Antibiotic Resistance in Veterinary Medicine, 2nd Edition

edited by

Andrea Micke Moreno

and

Luisa Zanolli Moreno

submission deadline 30 Nov 2025 | 3 articles | Viewed by 3917 | Submission Open

Keywords: veterinary microbiology; bacterial infection; One Health; antimicrobial resistance

(This special issue belongs to the Section Veterinary Microbiology)

Microbial Communities in Soil: Drivers of Terrestrial Ecosystem Processes

edited by Xiawei Peng

submission deadline 30 Nov 2025 | 3 articles | Viewed by 3576 | Submission Open

Keywords: soil microbiome assembly; microbial functional traits; ecological networks; metagenomics; plant– soil feedback; climate change adaptation; microbiome engineering; ecosystem services; sustainable land management; soil biodiversity conservation

(This special issue belongs to the Section Environmental Microbiology)

Crosstalk Between Host and Pathogen: Innate Immunity, Infection and Metabolic Reprogramming

edited by Lei Xu

submission deadline 30 Nov 2025 | 3 articles | Viewed by 3124 | Submission Open

Keywords: host-pathogen interaction; bacterial infection; bacterial secretion systems; immunometabolites; innate immunity

(This special issue belongs to the Section Medical Microbiology)

Fungal Infections and Antifungal Agents

edited by

Stefanie Bressan Waller

submission deadline 30 Nov 2025 | 2 articles | Viewed by 2770 | Submission Open

Keywords: fungal infections; antifungal agents; antifungal drug discovery

(This special issue belongs to the Section Antimicrobial Agents and Resistance)

Effects of Diet and Nutrition on Gut Microbiota

edited by Heng Yuan and

Sunmin Park

submission deadline 30 Nov 2025 | 2 articles | Viewed by 2759 | Submission Open

Keywords: gut microbiota; nutrition; MASLD; functional food; hypertension; metabolism

(This special issue belongs to the Section Gut Microbiota)

Bacterial Virulence and Biosurfactants

edited by

Juliana Luna

submission deadline 30 Nov 2025 | 1 articles | Viewed by 2752 | Submission Open

Keywords: multi-resistant bacteria (MDR); resistance mechanisms; antibiotics; antimicrobial agents; drug susceptibility; green surfactants; medicinal plants; microbial nanoparticles

(This special issue belongs to the Section Antimicrobial Agents and Resistance)

Inflammatory Bowel Disease (IBD) and Microbiome: Etiopathogenesis, Diagnosis, and Therapeutic Advances

edited by

Michael Doulberis

submission deadline 30 Nov 2025 | 1 articles | Viewed by 2579 | Submission Open

Keywords: inflammatory bowel disease; microbiome-immune interactions; microbiome modulation; gut– brain axes; gut– liver axes

(This special issue belongs to the Section Medical Microbiology)

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