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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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Exploring Foliar Plant–Bacterial Pathogen Interactions and Innovative Control Approaches

edited by

Yasuhiro Ishiga

and

Nanami Sakata

submission deadline 30 Nov 2025 | Viewed by 42 | Submission Open

Keywords: foliar bacterial interactions; virulence factors; host resistance mechanisms; bacterial pathogenesis; sustainable disease management; stomatal immunity; environmental impact on plant diseases; plant immunity; agricultural biotechnology

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

Advances in the Diagnosis and Management of Infectious Keratitis

edited by Ciro Costagliola,

Salvatore Troisi

, Francesco Matarazzo and

Mario Troisi

submission deadline 30 Nov 2025 | Viewed by 42 | Submission Open

Keywords: infectious keratitis; corneal infections; molecular diagnostics; antimicrobial resistance; biofilm-related infections; advanced imaging in ophthalmology; novel therapeutic strategies; ophthalmic microbiology; corneal ulcer management; pathogen identification

(This special issue belongs to the Section Medical Microbiology)

Emerging and Re-Emerging Infections in the Immunocompromised Host

edited by

Emanuele Palomba

submission deadline 30 Nov 2025 | Viewed by 36 | Submission Open

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

(This special issue belongs to the Section Medical Microbiology)

Gut Microbiota, Diet, and Gastrointestinal Cancer, 2nd Edition

edited by Flavio De Maio and

Marco Cintoni

submission deadline 30 Nov 2025 | Viewed by 25 | Submission Open

Keywords: gut microbiota; diet; nutrition; gastrointestinal cancer; colorectal cancer; probiotics; prebiotics; postbiotics; radiotherapy; chemotherapy

(This special issue belongs to the Section Gut Microbiota)

Beneficial Microorganisms for Sustainable Agriculture

edited by

Tim J. Dumonceaux

and

Christina Eynck

submission deadline 30 Nov 2025 | Viewed by 17 | Submission Open

Keywords: abiotic stress; biotic stress; biocontrol; biofertilizer; plant– microbe interaction

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

Probiotics: The Current State of Scientific Knowledge (2nd Edition)

edited by

Jacek Piatek

submission deadline 30 Nov 2025 | Viewed by 15 | Submission Open

Keywords: microbiota modification; microbiological techniques for identifying microorganisms; probiotics in therapy; probiotics and antibiotic resistance

(This special issue belongs to the Section Gut Microbiota)

Marine Microbial Systems: From Molecular Mechanisms to Biotechnological Innovations

edited by

Hainan Su

and

Yuqiang Zhang

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

Keywords: marine microorganisms; functional enzymes; bioactive secondary metabolites; bio-manufacturing; bio-pharmaceutical; bio-agriculture; environmental governance

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

Mycobacterial Research

edited by

Kaixia Mi

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

Keywords: mycobacterial biology; immune response; antimicrobial resistance; co-infections; microbiome interactions; therapeutic innovations

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

Emerging Pathogen Infections and Host Immune

edited by

Barbara Camilloni

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

Keywords: emerging pathogens; pathogen-associated molecular patterns; virulence factors; innate immunity; cellular response; humoral response; immunocompromised host

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

Pediatric Osteoarticular Infections: Diagnosis, Management, and Emerging Challenges

edited by

Ceroni Dimitri

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

Keywords: osteoarticular; joint; bone; infection; nucleic acid amplification assays; PCR; mNGS; management; surgery

(This special issue belongs to the Section Medical Microbiology)

Advances in Molecular Biology of Entamoeba histolytica

edited by Laurence A. Marchat

submission deadline 30 Nov 2025 | Submission Open

Keywords: Entamoeba histolytica; genome structure and function; protein structure and function; pathogenicity and virulence; bioinformatics; omics; relationships with host and microbiome; metabolism; gene expression; drug resistance

(This special issue belongs to the Section Medical Microbiology)

Respiratory Diseases and Microbiome Dysbiosis

edited by

Heleni Loutrari

and Paraskevi Katsaounou

submission deadline 30 Nov 2025 | Submission Open

Keywords: upper and lower airway disorders; microbiome; inflammation; immune response; infections; allergies; dysbiosis; gut– lung axis; metagenomics; multi-omics

(This special issue belongs to the Section Microbiomes)

Antimicrobial Resistance in Foodborne Pathogens: Surveillance, Mechanisms and Mitigation Strategies

edited by

Teresa Semedo-Lemsaddek

submission deadline 30 Nov 2025 | Submission Open

Keywords: antimicrobial resistance; foodborne pathogens; One Health; AMR surveillance; mobile genetic elements; antimicrobial usage; food safety; mitigation strategies

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

Microbial Safety and Molecular Detection in Food Production and Processing

edited by

Julio Parra-Flores

submission deadline 15 Dec 2025 | Viewed by 165 | Submission Open

Keywords: microbiological quality of foods; pathogens and opportunistic foodborne pathogens; molecular epidemiology of foodborne illness; molecular characterization of foodborne pathogens; biofilm; sanitizers; and control of pathogens in food production plants; virulence factors; antibiotic resistance

(This special issue belongs to the Section Food Microbiology)

Shiga-Toxin Producing Escherichia coli and the Animal Host

edited by

Indira Kudva

submission deadline 31 Dec 2025 | 4 articles | Viewed by 10969 | Submission Open

Keywords: E. coli; STEC; animal-host; interaction; colonization; pathogenicity; diagnosis; prevention; therapy; alternatives

(This special issue belongs to the Section Medical Microbiology)

Antimicrobial Resistance (AMR) Diagnostics and Genomic/Molecular Epidemiology of Multidrug-Resistant Isolates

edited by

Anna Baraniak

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2508 | Submission Open

Keywords: enterobacterales; antibiotic resistance; ß -lactamases; carbapenemases; multidrug-resistant isolates; epidemiology

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

State-of-the-Art Environmental Microbiology in China 2025

edited by

Zhiyong Li

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2246 | Submission Open

Keywords: structure and function of microbial communities; microbial community genetics; transcriptomics; proteomics and metabolomics; microbial interaction; microbial communication; microbial ecology; microbial population biology; biogeochemical processes (C; N; P; S cycles); microbial life in extreme environments; evolutionary processes of microbial communities; biofilm formation and the surfaces of microbes; metabolic flux analysis and stable isotope probing (DNA; RNA and protein); microbiome biology of environmental habitats (e.g.; soil; rhizosphere or aquifer); microbial treatment: microbial biodegradation; microbial bioremediation; microbial and waste recycling; microbial pesticide; microbial fertilizer; and others; microbial pollution: pathogenic microorganisms in the environment (water/soil/air/food); microbial metabolism; environmental pollution (e.g.; microbial toxin); and others; microbiological monitoring: testing method and monitoring technique development

(This special issue belongs to the Section Environmental Microbiology)

Feature Paper in Food Microbiology

edited by

Giuseppe Comi

Antonio Bevilacqua

and Francesca Coppola

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1207 | Submission Open

Keywords: new products; functional food; starter cultures and bioprotection; metagenomics and metabolomics; new identification methods; food waste recycling; novel pre-pro-syn-postbiotic applications; foodborne pathogens; innovations in traditional and new fermented foods; microorganisms in food ecosystems

(This special issue belongs to the Section Food Microbiology)

Accelerated Topics in Public Health Microbiology and Microbial Food Safety

edited by

Aliyar Fouladkhah

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1145 | Submission Open

Keywords: public health microbiology; microbial food safety; water safety; infectious disease; climate change

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

Gene Expression Profiling in Leishmania: From Basic Research to Vaccines and Drug Targets

edited by

Pedro José Alcolea

and Ana M. Alonso

submission deadline 31 Dec 2025 | Viewed by 503 | Submission Open

Keywords: Leishmania spp.; genomics; transcriptomics; proteomics; promastigotes; amastigotes; extracellular vesicles; vaccine candidates; drug target candidates; meta-analysis

(This special issue belongs to the Section Medical Microbiology)

The Interactions Between Nutrients and Microbiota

edited by

Renata Barczyńska-Felusiak

and

Agnieszka Rudzka

submission deadline 31 Dec 2025 | Viewed by 394 | Submission Open

Keywords: diet; nutrients; microbiota; human health

(This special issue belongs to the Section Food Microbiology)

Rare Human Pathogens

edited by Percy Schröttner

submission deadline 31 Dec 2025 | Viewed by 221 | Submission Open

Keywords: rare; pathogen; diseases; pathogenic bacteria

(This special issue belongs to the Section Medical Microbiology)

Plant-Microbe Interactome: The Green Dialogue Within the Plant Holobiont

edited by

Annamaria Bevivino

Alessia Fiore

and

Silvia Tabacchioni

submission deadline 31 Dec 2025 | Viewed by 203 | Submission Open

Keywords: soil microbiome; plant holobiont; one health; sustainable agriculture

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

Microbiota and Microbiomes in Plants, Animals and Environment: A One Heath Perspective—Second Edition

edited by Moussa Diarra and

Wen Chen

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

Keywords: microbiota/microbiome; antimicrobial; disease and health; environment; climate; One Health approach

Microbe-Plant-Environment Interactions over Time

edited by

Phatu Mashela

submission deadline 31 Dec 2025 | Viewed by 181 | Submission Open

Keywords: microbe– plant– environment interaction; crops; plant pathogen

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

The Host Response to Animal Virus Infection

edited by Liwei Li

submission deadline 31 Dec 2025 | Viewed by 138 | 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)

New Trends in Medical Bacteriology: Diagnosis, Treatment and Prevention—Second Edition

edited by

Norma Velazquez-Guadarrama

and Ma. Guadalupe Aguilera-Arreola

submission deadline 31 Dec 2025 | Viewed by 113 | Submission Open

Keywords: medical bacteria; diagnosis; treatment; prevention

(This special issue belongs to the Section Medical Microbiology)

Host–Microbiome Cross-Talk in Cancer Development and Progression

edited by Subhadeep Das

submission deadline 31 Dec 2025 | Viewed by 99 | 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)

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

edited by

Dilfuza Egamberdieva

submission deadline 31 Dec 2025 | Viewed by 99 | 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)

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

edited by Niels Høiby and Claus Moser

submission deadline 31 Dec 2025 | Viewed by 86 | Submission Open

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

(This special issue belongs to the Section Biofilm)

Beneficial Microbes: Food, Mood and Beyond—Third Edition

edited by

Mohamed Zommiti

and

Marc G. J. Feuilloley

submission deadline 31 Dec 2025 | Viewed by 70 | Submission Open

Keywords: prebiotics; probiotics; postbiotics; parabiotics; psycho-biotics; food; mood; benefactions; safety; antibiotics; neurotransmitters; humans; animals

(This special issue belongs to the Section Food Microbiology)

Microbiome Innovations in Food Systems for a Green Future

edited by

and

submission deadline 31 Dec 2025 | Viewed by 66 | 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)

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 41 | 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)

Probiotic and Postbiotic Properties of Lactobacillus, 2nd Edition

edited by

Sang-Ho Baik

submission deadline 31 Dec 2025 | Viewed by 39 | Submission Open

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

(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 32 | Submission Open

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

(This special issue belongs to the Section Medical Microbiology)

Chemolithoautotrophic Microorganisms—Pioneers of Biospheric Evolution and Sustainable Biotechnology

edited by Lijing Jiang

submission deadline 31 Dec 2025 | Viewed by 23 | 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)

Research on Airborne Microbial Communities

edited by

Changliang Nie

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

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

(This special issue belongs to the Section Environmental Microbiology)

Unraveling the Mysteries of Gut Microbiota to Advance Sustainable Aquaculture

edited by Qunlan Zhou

submission deadline 31 Dec 2025 | Viewed by 17 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

Biofilms and Implantable Device-Related Infections

edited by

Felipe Francisco Tuon

submission deadline 31 Dec 2025 | Submission Open

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

(This special issue belongs to the Section Biofilm)

Gut Microbiome in Homeostasis and Disease, 3rd Edition

edited by

Michael Doulberis

submission deadline 15 Jan 2026 | Viewed by 13 | 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)

Artificial Intelligence as a Tool for Combating Antimicrobial Resistance

edited by

Sergi Maicas

and

Jaume Segura-Garcia

submission deadline 31 Jan 2026 | Viewed by 54 | Submission Open

Keywords: AI; AMR; drug discovery; datasets; antibiotics

(This special issue belongs to the Section Microbial Biotechnology)

Advances in Microbial Biotechnological Approaches for Carbohydrate Biosynthesis

edited by Haining Tan, Yuhui Wang and

Lele Liu

submission deadline 31 Jan 2026 | Viewed by 16 | Submission Open

Keywords: microbial carbohydrate biosynthesis; glycoengineering; synthetic biology; enzyme engineering; glycoconjugate vaccines

(This special issue belongs to the Section Microbial Biotechnology)

Fungal Biology and Interactions—3rd Edition

edited by

Renato Graciano de Paula

and

Roberto Nascimento Silva

submission deadline 31 Jan 2026 | Viewed by 12 | Submission Open

Keywords: fungi; molecular biology; filamentous fungi

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

Salmonella Infections: Trends and Updates

edited by

Taseen Desin

submission deadline 28 Feb 2026 | 5 articles | Viewed by 6777 | Submission Open

Keywords: salmonellosis; epidemiology and surveillance; molecular biology and pathogenesis; antimicrobial resistance; one-health perspectives; prevention and control strategies

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

Probiotics, Prebiotics, and Synbiotics in Animal Nutrition and Health, and Food Safety

edited by María Esther Ortega-Cerrilla

submission deadline 28 Feb 2026 | 4 articles | Viewed by 6667 | Submission Open

Keywords: probiotics; prebiotics; synbiotics; animals; food safety

(This special issue belongs to the Section Food Microbiology)

Human Respiratory Syncytial Virus—Biology, Diagnosis and Prevention

edited by

Yurong Tan

submission deadline 28 Feb 2026 | 3 articles | Viewed by 5907 | Submission Open

Keywords: human respiratory syncytial virus; medical microbiology; molecular biology; virus diagnosis; infection prevention

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