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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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Gut Microbiota and Metabolic Disease Pathogenesis

edited by

Gerald Maarman

submission deadline 31 Dec 2025 | Viewed by 188 | 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)

Parasitic Diseases in Livestock, 2nd Edition

edited by

Aleksandra Uzelac

Luca Villa

and

Ivana Klun

submission deadline 31 Dec 2025 | Viewed by 185 | Submission Open

Keywords: epidemiology of parasitic diseases in the livestock industry; impact of parasites on herd economy; zoonotic parasites of livestock; molecular characterization and influence on virulence; implementation of innovative tools for diagnostics; treatment and drug resistance; control and prevention

(This special issue belongs to the Section Veterinary Microbiology)

Microbiome Innovations in Food Systems for a Green Future

edited by

and

submission deadline 31 Dec 2025 | Viewed by 180 | 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)

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

edited by

Cassandre Lazar

submission deadline 31 Dec 2025 | Viewed by 180 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Anaerobic Gut Fungi: Ecological Role and Biotechnological Potential

edited by Radwa Hanafy

submission deadline 31 Dec 2025 | Viewed by 178 | 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 Gut Microbiota)

Chemolithoautotrophic Microorganisms—Pioneers of Biospheric Evolution and Sustainable Biotechnology

edited by Lijing Jiang

submission deadline 31 Dec 2025 | Viewed by 173 | 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)

Bacterial Resistance and Adaptation in the Post-Antibiotic Ban Era

edited by

Abdelaziz Ed-Dra

and

Min Yue

submission deadline 31 Dec 2025 | Viewed by 170 | Submission Open

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

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

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 167 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

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 159 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

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

edited by

Dennis Cvitkovitch

submission deadline 31 Dec 2025 | Viewed by 159 | 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)

Breaking Barriers: The Breakdown of Epithelial Defenses by Pathogens

edited by

Karen Bohmwald

submission deadline 31 Dec 2025 | Viewed by 149 | 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)

Infectious Disease in Companion Animals

edited by

Olga Szalus̈-Jordanow

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

Keywords: companion animals; veterinary medicine; infectious diseases

(This special issue belongs to the Section Veterinary Microbiology)

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

edited by

Alejandro Speck-Planche

submission deadline 31 Dec 2025 | Viewed by 140 | 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)

Diagnostic and Molecular Epidemiology of Infectious Diseases in Veterinary Medicine

edited by Seyed Ali Ghorashi

submission deadline 31 Dec 2025 | Viewed by 135 | Submission Open

Keywords: ⁠veterinary medicine; ⁠veterinary science; ⁠veterinary pathology; ⁠molecular epidemiology; ⁠animal science; 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)

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 134 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

Engineering of Microbial Factories for the Production of Useful Compounds

edited by

Yun-Peng Chao

and

Chung-Jen Chiang

submission deadline 31 Dec 2025 | Viewed by 128 | Submission Open

Keywords: microbial factories; metabolic engineering; synthetic biology; sustainable bioprocess

(This special issue belongs to the Section Microbial Biotechnology)

Unraveling the Mysteries of Gut Microbiota to Advance Sustainable Aquaculture

edited by Qunlan Zhou

submission deadline 31 Dec 2025 | Viewed by 120 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

New Developments in Virus Detection and Disinfection in the Environment

edited by

Jinge Huang

and Xiuping Jiang

submission deadline 31 Dec 2025 | Viewed by 120 | Submission Open

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

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

Marine Agricultural Microorganisms

edited by

Donglin Zhao

submission deadline 31 Dec 2025 | Viewed by 118 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Sexually Transmitted Infections and Host Immune Response

edited by MacIej Pastuszczak

submission deadline 31 Dec 2025 | Viewed by 116 | Submission Open

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

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

Microbial Community Structure and Functions in Marine Sediments

edited by

Asunción Lago-Lestón

submission deadline 31 Dec 2025 | Viewed by 115 | 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)

Biofilms and Implantable Device-Related Infections

edited by

Felipe Francisco Tuon

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

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

(This special issue belongs to the Section Biofilm)

The Gut–CKD Axis: Thinking Outside the Box

edited by

Julie Kemp

Denise Mafra

and Marcia Ribeiro

submission deadline 31 Dec 2025 | Viewed by 99 | 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)

Environmental Microbes in Antimicrobial Resistance and Soil Pollution Mitigation

edited by Yan Wang

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

Keywords: antimicrobial resistance; genes; microbial bioremediation; soil; microbial communities; pollutant degradation; bioremediation

(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 94 | Submission Open

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

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

Molecular Mechanisms of Mammalian Intra-Amniotic Infection

edited by Matthew Jackson and Kevin Theis

submission deadline 31 Dec 2025 | Viewed by 87 | Submission Open

Keywords: intra-amniotic infections; microbes; pathogenic mechanisms

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

Gut Microbiome in Homeostasis and Disease, 3rd Edition

edited by

Michael Doulberis

submission deadline 15 Jan 2026 | 7 articles | Viewed by 6971 | Submission Open

Keywords: gut microbiome; dysbiosis; gut– brain axis; gut– liver axis; fecal microbiota transplantation; gut probiotics; commensal and non-commensal microorganisms; Helicobacter

(This special issue belongs to the Section Gut Microbiota)

Microbes for Sustainable Production

edited by

Yan Zhao

submission deadline 15 Jan 2026 | 1 articles | Viewed by 667 | Submission Open

Keywords: microbial biotechnology; microbial community; microbial diversity; microbial interactions; sustainable production; microbial bioremediation and circular economy

(This special issue belongs to the Section Microbial Biotechnology)

Microorganisms in Aquatic Environments: Emphasis on Computational, In Vitro and Ex Vivo Studies

edited by Jovanka Lukić

submission deadline 15 Jan 2026 | Viewed by 323 | Submission Open

Keywords: microbiota; aquaculture; open water; in vitro; ex vivo; sequencing; modeling

(This special issue belongs to the Section Veterinary Microbiology)

Infectious Disease Surveillance in Romania: Second Edition

edited by

Daniela Piţigoi

submission deadline 20 Jan 2026 | 2 articles | Viewed by 1913 | Submission Open

Keywords: surveillance; vaccine preventable diseases; antimicrobial resistance; health care associated infection; influenza; COVID-19; Romania

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

Advances in Human Infections and Public Health

edited by Katrin Gaardbo Kuhn

submission deadline 31 Jan 2026 | 8 articles | Viewed by 33114 | Submission Open

Keywords: human infections; public health; advances; preparedness; control; prevention

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

Current Pattern in Epidemiology and Antifungal Resistance

edited by

Carmen Rodríguez-Cerdeira

, Javier Araiza Santibáñez and

José Pereira Brunelli

submission deadline 31 Jan 2026 | 6 articles | Viewed by 21899 | Submission Open

Keywords: Candida albicans; Candida auris; Candida glabrata; Candida parapsilosis; Aspergillus fumigatus; Cryptococcus neoformans; Mucormycosis; emerging fungal infections; nosocomial transmission; determination of antifungal susceptibility; resistance to antifungal agents; adaptation; rate of mutation and reproduction; molecular methods to determine resistance; the study of new antifungal agents; genotypic characterization techniques; invasive infections caused by filamentous fungi; antimicrobial peptides with antifungal properties; antifungal resistance in dermatophytes

(This special issue belongs to the Section Medical Microbiology)

Helicobacter pylori and Related Gastrointestinal Diseases: Infection, Treatment, Prevention, and Beyond

edited by

Ping I. Hsu

submission deadline 31 Jan 2026 | 2 articles | Viewed by 10303 | Submission Open

Keywords: Helicobacter pylori (H. pylori); gastrointestinal diseases; infection; treatment; prevention; vaccination; pathogenesis

(This special issue belongs to the Section Medical Microbiology)

Challenges of Biofilm-Associated Bone and Joint Infections

edited by Christof Berberich and

Jaime Esteban

submission deadline 31 Jan 2026 | 7 articles | Viewed by 10169 | Submission Open

Keywords: diagnostics; prevention; antibiotic

(This special issue belongs to the Section Biofilm)

Animal Viral Infectious Diseases

edited by He Zhang

submission deadline 31 Jan 2026 | 8 articles | Viewed by 9468 | Submission Open

Keywords: animal viral infectious diseases; host– animal virus interactions; pathogenesis; strategies to combat infections; new drug development; diagnostic tools; virus detection; epidemiological investigation

(This special issue belongs to the Section Veterinary Microbiology)

Correlations Between the Gastrointestinal Microbiome and Diseases

edited by

Jilei Zhang

submission deadline 31 Jan 2026 | 5 articles | Viewed by 9255 | Submission Open

Keywords: gut microbes; microbiome; host health; diseases; gastroenterology

(This special issue belongs to the Section Microbiomes)

Advances in Agro-Microbiology

edited by

Yelizaveta Chernysh

Hynek Roubík

and

Tsuyoshi Imai

submission deadline 31 Jan 2026 | 7 articles | Viewed by 8810 | Submission Open

Keywords: microbial activity; sustainable agriculture; bio-based products; soil contamination; bioremediation; improve agricultural yields

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

Research in Hospital Infection Control (3rd Edition)

edited by

Brian Crook

and Claire C. Bailey

submission deadline 31 Jan 2026 | 1 articles | Viewed by 8627 | Submission Open

Keywords: hospital infection control; hospital-acquired infection; healthcare worker; personal protective equipment and hygiene; disease transmission; disinfection; COVID-19

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

Advances in Microbial Cell Factories, 3rd Edition

edited by

Thomas Brück

and

Dania Awad

submission deadline 31 Jan 2026 | 7 articles | Viewed by 8292 | Submission Open

Keywords: sustainability; biotechnology; bioengineering; biocatalysis; fermentation

(This special issue belongs to the Section Microbial Biotechnology)

Advances in Halophilic Microorganisms

edited by

Maria del Rayo Sanchez-Carbente

submission deadline 31 Jan 2026 | 3 articles | Viewed by 8095 | Submission Open

Keywords: halophilic; microbe; extremophiles; biotechnology; taxonomy and biodiversity

(This special issue belongs to the Section Environmental Microbiology)

Method and Model Development Supporting Vaccines and Therapeutics Against Viral and Bacterial Pathogens and Toxins

edited by Chris M. Cirimotich

submission deadline 31 Jan 2026 | 3 articles | Viewed by 7192 | Submission Open

Keywords: vaccines; animal model; microphysiological

(This special issue belongs to the Section Medical Microbiology)

Microbial Infections and Host Immunity

edited by

Andrew Foey

submission deadline 31 Jan 2026 | 5 articles | Viewed by 6516 | Submission Open

Keywords: microbial pathogens; host immunity; infections; mechanisms; treatment strategies

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

Ticks and Threats: Insights on Tick-Borne Diseases

edited by Giovanni Sgroi and

Kandai Doi

submission deadline 31 Jan 2026 | 5 articles | Viewed by 6019 | Submission Open

Keywords: public health; ticks; tick-borne disease; tick-borne pathogens

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

Exploring Foodborne Pathogens: From Molecular to Safety Perspectives

edited by

Martina Srajer Gajdosik

and Hongsheng Huang

submission deadline 31 Jan 2026 | 3 articles | Viewed by 5458 | Submission Open

Keywords: food safety; foodborne pathogens; pathogen detection; molecular mechanisms; stress responses; antimicrobial resistance; virulence; foodborne diseases

(This special issue belongs to the Section Food Microbiology)

Drug Resistance and Molecular Research of Staphylococcus spp.

edited by

Jaime Bustos-Martínez

submission deadline 31 Jan 2026 | 1 articles | Viewed by 3587 | Submission Open

Keywords: immunotherapeutic strategies; Staphylococcus spp.; Staphylococcus infection; genomics; antimicrobial; resistance mechanisms; new antibacterials

(This special issue belongs to the Section Medical Microbiology)

Advances in Antimicrobial Treatment

edited by

Luis Adrián De Jesús-González

and

Moises Leon-Juarez

submission deadline 31 Jan 2026 | 2 articles | Viewed by 3244 | Submission Open

Keywords: antimicrobial resistance; novel therapies; drug repurposing; antiviral agents; antibacterial agents; antifungal agents; microbial pathogens; host– pathogen interactions; omics technologies; phage therapy

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

Microbial Food Webs

edited by Wuchang Zhang

submission deadline 31 Jan 2026 | 1 articles | Viewed by 2606 | Submission Open

Keywords: microbial food web; ciliates; flagellates; prokaryote; taxonomy; ecology; global change

(This special issue belongs to the Section Environmental Microbiology)

Fungal Biology and Interactions—3rd Edition

edited by

Renato Graciano de Paula

and

Roberto Nascimento Silva

submission deadline 31 Jan 2026 | 3 articles | Viewed by 2532 | Submission Open

Keywords: fungi; molecular biology; filamentous fungi

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

Lectins and Human Pathogenic Microorganisms: Mechanisms and Applications

edited by Rômulo F. Carneiro and Mayron Alves de Vasconcelos

submission deadline 31 Jan 2026 | 2 articles | Viewed by 2273 | Submission Open

Keywords: microorganism-derived lectins; human infection; therapeutics; biotechnology

(This special issue belongs to the Section Medical Microbiology)

Role of Microorganisms in Functional Dairy Products

edited by

Jasna Đorđević

submission deadline 31 Jan 2026 | 1 articles | Viewed by 2229 | Submission Open

Keywords: functional foods; probiotics; lactic acid bacteria; fermentation; dairy biotechnology; sustainability

(This special issue belongs to the Section Food Microbiology)

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