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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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The Host Response to Animal Virus Infection

edited by Liwei Li

submission deadline 31 Dec 2025 | 1 articles | Viewed by 201 | Submission Open

Keywords: respiratory virus; coronavirus; emerging pathogens in animals; host immune response; innate immunity; neutralizing antibody; non-coding RNA; viral infection; antiviral agents; antiviral strategy

(This special issue belongs to the Section Veterinary Microbiology)

Advances in Novel Antibacterial Agents, 2nd Edition

edited by Mariateresa Vitiello

submission deadline 31 Dec 2025 | Viewed by 145 | Submission Open

Keywords: bacterial infections; multidrug-resistant bacteria; antimicrobials; natural products; resistance mechanisms

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

Plant Microbiome: Pioneering Microbiome-Driven Strategies for Climate-Resilient Agriculture

edited by

Dilfuza Egamberdieva

submission deadline 31 Dec 2025 | Viewed by 138 | Submission Open

Keywords: plant– microbe interactions; climate change mitigation; carbon sequestration; soil health; greenhouse gas reduction; microbial inoculants; sustainable agriculture

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

Host–Microbiome Cross-Talk in Cancer Development and Progression

edited by Subhadeep Das

submission deadline 31 Dec 2025 | Viewed by 132 | Submission Open

Keywords: dietary factors; epigenetic responses; bioinformatic and deep learning techniques; therapy; tumor microenvironment; microbiome-targeted therapies

(This special issue belongs to the Section Microbiomes)

HIV Infections: Diagnosis and Drug Uses

edited by

Nompumelelo Mkhwanazi

submission deadline 31 Dec 2025 | Viewed by 131 | Submission Open

Keywords: HIV prevention and vaccines; drug resistance; HIV-1 coinfections; HIV diagnosis; natural products as antiviral agents; immunomodulation

(This special issue belongs to the Section Virology)

Diagnosis, Treatment, and Prevention of Biofilm Infections—How to Proceed?

edited by Niels Høiby and Claus Moser

submission deadline 31 Dec 2025 | Viewed by 100 | Submission Open

Keywords: biofilm; biofilm infections; chronic infections; foreign body infections; implant infections

(This special issue belongs to the Section Biofilm)

Microbiome Innovations in Food Systems for a Green Future

edited by

and

submission deadline 31 Dec 2025 | Viewed by 98 | Submission Open

Keywords: soil fertility; climate change; crop resilience; sustainable food processes; global food security; alternative protein production; dietary sustainability; food preservation; functional foods; human and animal health; waste management; circular economy; sustainable food policies and regulations

(This special issue belongs to the Section Microbiomes)

Advances in Plant–Soil–Microbe Interactions

edited by

Zelaya Molina Lily Xochilt

and

Sergio de los Santos Villalobos

submission deadline 31 Dec 2025 | Viewed by 96 | Submission Open

Keywords: plant– soil– microbe interactions; rhizosphere microbiome; sustainable agriculture; environmental stressors; microbial inoculants

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

Probiotic and Postbiotic Properties of Lactobacillus, 2nd Edition

edited by

Sang-Ho Baik

submission deadline 31 Dec 2025 | Viewed by 89 | Submission Open

Keywords: Lactobacillus; probiotics; postbiotics; novel probiotic properties; next-generation probiotics

(This special issue belongs to the Section Food Microbiology)

Microbiome- and Host-Mediated Effects of Prebiotics in Foods and Feeds

edited by

Ian Connerton

and Adam Lee

submission deadline 31 Dec 2025 | Viewed by 82 | Submission Open

Keywords: prebiotics; gut microbiota; gut health; gut architecture; gut immunomodulation; beneficial microbes; oligosaccharides; microbiome manipulation

(This special issue belongs to the Section Food Microbiology)

Bloodstream Infection: Common and Uncommon Pathogens

edited by Carola Mauri

submission deadline 31 Dec 2025 | Viewed by 71 | Submission Open

Keywords: bloodstream infection (BSI); pathogens; antibiotic resistance; new drugs

(This special issue belongs to the Section Medical Microbiology)

Resource Utilization of Microorganisms: Fermentation and Biosynthesis

edited by Shoushuai Feng

submission deadline 31 Dec 2025 | Viewed by 61 | Submission Open

Keywords: industrial microorganisms resources; microbial physiological traits; fermentation optimization; synthetic biology; sustainability application

(This special issue belongs to the Section Microbial Biotechnology)

Research on Airborne Microbial Communities

edited by

Changliang Nie

submission deadline 31 Dec 2025 | Viewed by 58 | Submission Open

Keywords: atmospheric microorganisms; bioaerosol; microbial community; air pollutant; climate change

(This special issue belongs to the Section Environmental Microbiology)

The Microbial Pathogenesis

edited by

Tingting Wang

and Canfeng Hua

submission deadline 31 Dec 2025 | Viewed by 51 | Submission Open

Keywords: microbial pathogenesis; virulence factors; host– pathogen interactions; antibiotic resistance; immune evasion; bacterial genomics; fungal infections; viral pathogenesis; molecular microbiology; host immune response

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

Antibiotic Bans and Antimicrobial Resistance: Progress, Challenges, and Future Strategies

edited by

Abdelaziz Ed-Dra

and

Min Yue

submission deadline 31 Dec 2025 | Viewed by 49 | Submission Open

Keywords: impact of antibiotic bans; antibiotic use; antimicrobial resistance; antibiotic restrictions

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

Integrative Metabolic Modelling of Bacterial Systems in Microbiome Contexts: From Genomes to Community Functions

edited by Arianna Basile

submission deadline 31 Dec 2025 | Viewed by 49 | Submission Open

Keywords: microbiome; multi-omics; microbial communities; metabolic modelling; bioinformatics tools

(This special issue belongs to the Section Microbiomes)

Chemolithoautotrophic Microorganisms—Pioneers of Biospheric Evolution and Sustainable Biotechnology

edited by Lijing Jiang

submission deadline 31 Dec 2025 | Viewed by 47 | Submission Open

Keywords: chemolithoautotrophic microorganisms; ancient metabolic pathways; extreme environmental; microbial– mineral interactions; industrial applications; extraterrestrial life

(This special issue belongs to the Section Environmental Microbiology)

Gut Microbiota and Metabolic Disease Pathogenesis

edited by

Gerald Maarman

submission deadline 31 Dec 2025 | Viewed by 47 | Submission Open

Keywords: gut microbiota dynamics (structural/morphological/anatomical changes; eubiosis; and dysbiosis); exploring healthy gut microbiota; gut microbiota; host genetics; and epigenetics; gut microbiota shotgun metagenomics; single-cell sequencing; CRISPR editing; and spatial profiling; transcriptomics; proteomics; and metabolomics; mitochondrial bioenergetics and metabolism; mitochondrial signaling; personalized and precision microbiome therapies; microbial metabolites as therapeutics; gut– brain axis and neuroactive microbes; gut– brain axis in cardio-pulmonary vascular diseases; gut involvement in metabolic diseases; gut microbiota in immune-oncology and cancer

(This special issue belongs to the Section Gut Microbiota)

State of the Art of Gut Microbiota in Italy (2025, 2026)

edited by

Maddalena Rossi

and Francesco Candeliere

submission deadline 31 Dec 2025 | Viewed by 41 | Submission Open

Keywords: metagenomics; genomics; gut microbiota; probiotics; microbial ecology; microbial biotechnology

(This special issue belongs to the Section Gut Microbiota)

Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections

edited by

Vassiliki Pitiriga

submission deadline 31 Dec 2025 | Viewed by 40 | Submission Open

Keywords: infectious disease; laboratory diagnosis; epidemiology

(This special issue belongs to the Section Medical Microbiology)

Unraveling the Mysteries of Gut Microbiota to Advance Sustainable Aquaculture

edited by Qunlan Zhou

submission deadline 31 Dec 2025 | Viewed by 38 | Submission Open

Keywords: gut microbiota; functional probiotics; immunity; nutrition; multi-omics

(This special issue belongs to the Section Gut Microbiota)

Sexually Transmitted Infections and Host Immune Response

edited by MacIej Pastuszczak

submission deadline 31 Dec 2025 | Viewed by 37 | Submission Open

Keywords: host immune response; syphilis; gonorrhea; non-gonococcal infections; HIV; STI

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

Breaking Barriers: The Breakdown of Epithelial Defenses by Pathogens

edited by

Karen Bohmwald

submission deadline 31 Dec 2025 | Viewed by 35 | Submission Open

Keywords: epithelial barrier; blood– brain barrier; barrier breakdown; pathogen invasion; tight junctions; endothelial cells; mucosal immunity; host– pathogen interaction; epithelial remodeling; neuroinvasion; respiratory tract

(This special issue belongs to the Section Medical Microbiology)

Trichomonas vaginalis and Trichomoniasis: Biomarkers and Possible Pharmacological Alternatives

edited by

María Elizbeth Alvarez-Sánchez

, Julio César Torres-Romero and

Elisa Elvira Figueroa-Angulo

submission deadline 31 Dec 2025 | Viewed by 33 | Submission Open

Keywords: trichomoniasis in men; biomarkers; pharmaceutical alternatives

(This special issue belongs to the Section Medical Microbiology)

Fruit Wine Fermentation and Microbial Communities

edited by

Feifei Gao

submission deadline 31 Dec 2025 | Viewed by 30 | Submission Open

Keywords: fruit wine; fermentation; lactic acid bacteria; yeast; microbial diversity; flavor; volatile compounds; metabolites

(This special issue belongs to the Section Food Microbiology)

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

edited by

Alex Galanis

and

Aglaia Pappa

submission deadline 31 Dec 2025 | Viewed by 29 | Submission Open

Keywords: environmental microbiome; soil microbiome; rhizobiome; host– microbe interactions; microbiome manipulation; sustainable agriculture

(This special issue belongs to the Section Microbiomes)

Epidemiology, Prevention and Control of Foodborne Microbial Pathogens, Second Edition

edited by

Gabriel Augusto Marques Rossi

Marcia Nitschke

and

Juliano Gonçalves Pereira

submission deadline 31 Dec 2025 | Viewed by 27 | Submission Open

Keywords: biofilms; Clostridium spp.; Escherichia coli; foodborne; Listeria monocytogenes; outbreaks; parasites; prions; Salmonella spp.; Staphylococcus aureus; Vibrio spp.; viruses

(This special issue belongs to the Section Food Microbiology)

Biofilms and Implantable Device-Related Infections

edited by

Felipe Francisco Tuon

submission deadline 31 Dec 2025 | Viewed by 26 | Submission Open

Keywords: biofilm formation; implant-associated infections; medical devices; antimicrobial resistance; infection prevention

(This special issue belongs to the Section Biofilm)

New Developments in Virus Detection and Disinfection in the Environment

edited by

Jinge Huang

and Xiuping Jiang

submission deadline 31 Dec 2025 | Viewed by 25 | Submission Open

Keywords: virus; environmental surface; air; water; detection; disinfection

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

Microbial Nutrient Cycling Mechanisms

edited by

Jiawen Wang

submission deadline 31 Dec 2025 | Viewed by 25 | Submission Open

Keywords: microbes; nutrient cycling; mechanism; carbon; nitrogen; phosphorus; sulfur; environmental factors; biotechnology applications

(This special issue belongs to the Section Environmental Microbiology)

Antimicrobial Research: In Silico Strategies for Drug Discovery Against Microbial Infections

edited by

Alejandro Speck-Planche

submission deadline 31 Dec 2025 | Viewed by 24 | Submission Open

Keywords: antibacterial; antifungal; antiparasitic; antiviral; AI/machine learning; QSAR; complex network analysis; ligand-based drug discovery; structure-based drug discovery; de novo design; molecular modeling; chemoinformatics

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

The Epidemiology, Clinical Aspects, Treatment and Preventive Strategies for Infectious Diseases in the Era of Antimicrobial Resistance (AMR)

edited by Victoria Birlutiu

submission deadline 31 Dec 2025 | Viewed by 24 | Submission Open

Keywords: antimicrobial resistance (AMR); multidrug-resistant bacteria; antifungal resistance; infectious disease epidemiology; clinical microbiology; rapid diagnostics; biofilm-related infections; antimicrobial stewardship; infection prevention; resistance surveillance

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

Diagnostic Innovations and Molecular Epidemiology of Infectious Diseases in Veterinary Medicine

edited by Seyed Ali Ghorashi

submission deadline 31 Dec 2025 | Viewed by 23 | Submission Open

Keywords: veterinary diagnostics; molecular diagnostics; infectious diseases; point-of-care testing; animal pathogens; zoonotic diseases; molecular typing; surveillance and monitoring; veterinary microbiology; diagnostic assay development; rapid diagnostics; veterinary pathogens; wildlife microbiology

(This special issue belongs to the Section Veterinary Microbiology)

Marine Agricultural Microorganisms

edited by

Donglin Zhao

submission deadline 31 Dec 2025 | Viewed by 22 | Submission Open

Keywords: marine agricultural microorganisms; natural products; microbial pesticides; microbial fertilizers; microbial stimulants

(This special issue belongs to the Section Environmental Microbiology)

The Gut-CKD Axis: Thinking Outside the Box

edited by

Julie Kemp

, Denise Mafra and Marcia Ribeiro

submission deadline 31 Dec 2025 | Viewed by 20 | Submission Open

Keywords: gut microbiota; cardiometabolic diseases; cardiovascular disease; diabetes; kidney disease; immune responses; host metabolism; microbiota-targeted therapies

(This special issue belongs to the Section Gut Microbiota)

Microbiological Approaches to Water Pollution Control and Water Ecological Restoration

edited by

Haiya Zhang

Weigao Zhao

and

Xiaoou Wang

submission deadline 31 Dec 2025 | Viewed by 19 | Submission Open

Keywords: microbial bioremediation; aquatic microbiome; nutrient removal (nitrogen/phosphorus); biofilm-mediated purification; artificial wetland microbiology; biochar-enhanced wastewater treatment; microbial fuel cells (MFCs); emerging contaminants degradation; microbial ecology in water distribution systems; climate-resilient water restoration

(This special issue belongs to the Section Microbial Biotechnology)

Algae-Bacteria Interactions in Environment

edited by LiXiao Ni

submission deadline 31 Dec 2025 | Viewed by 18 | Submission Open

Keywords: algal– bacterial interactions; algal– bacterial symbiosis; cyanobacterial blooms; quorum sensing; biogeochemical cycling; wastewater treatment; ecological networks

(This special issue belongs to the Section Environmental Microbiology)

Nanoparticle-Based Vaccines and Therapeutics for Multidrug-Resistant Pathogens

edited by

Victor Nizet

and Elisabet Bjånes

submission deadline 31 Dec 2025 | Viewed by 16 | Submission Open

Keywords: antimicrobial resistance; nanotherapeutic; nanovaccine; nanomedicine; pathogen; multidrug resistance

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

Advances in Microbial Biofilm Formation (2nd Edition)

edited by

Ute Römling

submission deadline 31 Dec 2025 | Viewed by 15 | Submission Open

Keywords: commensal; environment; metabolism; multi-disciplinarity; pathogen; second messenger signaling

(This special issue belongs to the Section Biofilm)

Molecular Mechanisms of Mammalian Intra-Amniotic Infection

edited by Matthew Jackson and Kevin Theis

submission deadline 31 Dec 2025 | Viewed by 14 | Submission Open

Keywords: intra-amniotic infections; microbes; pathogenic mechanisms

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

Advances in the Human Oral Microbiome: From Ecology to Precision Therapeutics

edited by

Dennis Cvitkovitch

submission deadline 31 Dec 2025 | Viewed by 13 | Submission Open

Keywords: oral microbiome; biofilm ecology; multi-omics profiling; host– microbe interactions; precision therapeutics; salivary diagnostics; dysbiosis and disease; probiotics and phage therapy; spatial imaging; oral– systemic axis

(This special issue belongs to the Section Microbiomes)

Bioinformatics and Omic Data Analysis in Microbial Research, 2nd Edition

edited by

Douglas D. Rhoads

submission deadline 31 Dec 2025 | Viewed by 13 | Submission Open

Keywords: bioinformatics; microorganisms; genomics; proteomics; metabolomics; software pipelines

(This special issue belongs to the Section Microbiomes)

Anaerobic Gut Fungi: Ecological Role and Biotechnological Potential

edited by Radwa Hanafy

submission deadline 31 Dec 2025 | Viewed by 12 | Submission Open

Keywords: anaerobic gut fungi; neocallimastigomycota; CAZymes; rumen microbiome; microbial symbiosis; methanogenesis; host– microbe interaction; bioenergy; fungal biotechnology

(This special issue belongs to the Section Microbial Biotechnology)

Exploring the Gut-Brain Axis in Dementia: Biomarkers, Microbiota, and Machine Learning Approaches

edited by

Bing-Mu Hsu

submission deadline 31 Dec 2025 | Viewed by 11 | Submission Open

Keywords: gut-brain axis; microbiota; biomarkers; machine learning; dementia

(This special issue belongs to the Section Gut Microbiota)

Soil Health and Plant Microbiome–Bioeffectors Relationship in Sustainable Agriculture, 2nd Edition

edited by

Nikolay Vassilev

and

Stefan Shilev

submission deadline 31 Dec 2025 | Viewed by 11 | Submission Open

Keywords: plant-associated microbiome; plant– microbiome bioeffectors; microbial diversity; soil health; sustainable agriculture; circular bioeconomy

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

State-of-the-Art Environmental Microbiology in Canada 2025, 2026

edited by

Cassandre Lazar

submission deadline 31 Dec 2025 | Viewed by 11 | Submission Open

Keywords: microorganisms; environment; microbial communication; microbial ecology; biodegradation; bioremediation

(This special issue belongs to the Section Environmental Microbiology)

Microbial Community Structure and Functions in Marine Sediments

edited by

Asunción Lago-Lestón

submission deadline 31 Dec 2025 | Viewed by 10 | Submission Open

Keywords: sediment microbiome; marine microbial ecology; deep-sea sediments; coastal sediments; biogeochemical cycles; metagenomics

(This special issue belongs to the Section Environmental Microbiology)

Role of Microbes in the Remediation of Pollutants in the Environment, 2nd Edition

edited by Lilan Zhang and Xiaowei Liu

submission deadline 31 Dec 2025 | Viewed by 10 | Submission Open

Keywords: bioremediation; bacteria; archaea; fungi; microalgae; viruses; petroleum hydrocarbons; heavy metals; emerging pollutants; experimental biostimulation and bioaugmentation; bioindicators and biosensors; microbial and microbiome engineering; biosurfactants; hydrocarbon-degrading enzymes

(This special issue belongs to the Section Environmental Microbiology)

Novel Sequencing Technologies for the Characterization of Multidrug-Resistant Bacteria

edited by

Costas C. Papagiannitsis

submission deadline 31 Dec 2025 | Viewed by 10 | Submission Open

Keywords: antimicrobial resistance (AMR) genomics; next-generation sequencing (NGS); mobile genetic elements (plasmids/transposons); resistome profiling; One Health surveillance; metagenomic AMR detection; long-read sequencing (e.g.; Nanopore/PacBio); bioinformatic pipelines for AMR; nosocomial pathogen transmission; precision antimicrobial stewardship

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

Engineering of Microbial Factories for the Production of Useful Compounds

edited by