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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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Chlamydiae and Chlamydia-Like Infections

edited by

Servaas A. Morré

and Stephan Verweij

submission deadline 31 Dec 2025 | 5 articles | Viewed by 22083 | Submission Open

Keywords: Chlamydiales; Chlamydia infection; molecular and cell biology; genetics and genomics; host– pathogen interaction; diagnostics; vaccine development; epidemiology; prevention and policy; zoonosis; Chlamydia-like; model systems to study Chlamydiae and Chlamydia-like infections

(This special issue belongs to the Section Medical Microbiology)

Advances in Parvovirus Infection of Pets and Waterfowl

edited by

Chuanfeng Li

submission deadline 31 Dec 2025 | 5 articles | Viewed by 22074 | Submission Open

Keywords: parvovirus; genetic evolution; pathogenicity; parvovirus– host interaction; epidemiology; genetic characterization; phylogeny; detection methods; vaccine; diagnostic preparations

(This special issue belongs to the Section Veterinary Microbiology)

Advanced Research on Microbial Biofilms—a Themed Issue in Honor of Professor Gianfranco Donelli

edited by Jeffrey B. Kaplan, Steven L. Percival and

Lorenzo Drago

submission deadline 31 Dec 2025 | 11 articles | Viewed by 20949 | Submission Open

Keywords: microbial biofilms; antibiofilm; biofilm development; evolution of biofilms

(This special issue belongs to the Section Biofilm)

Microbial Safety and Beneficial Microorganisms in Foods

edited by

Theodoros Varzakas

submission deadline 31 Dec 2025 | 8 articles | Viewed by 20897 | Submission Open

Keywords: microbial safety; foodborne pathogens; beneficial microorganisms; food processing; fermentation-oriented foods; probiotics

(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 15495 | Submission Open

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

(This special issue belongs to the Section Medical Microbiology)

Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections (2nd Edition)

edited by

Hirokazu Kimura

and

Mitsuru Sada

submission deadline 31 Dec 2025 | 6 articles | Viewed by 13857 | Submission Open

Keywords: viral respiratory infections; molecular epidemiology; diagnostics; management

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

Prioritizing Diseases for Public Health in Emergency Contexts: A WHO Initiative

edited by

Luca Roncati

submission deadline 31 Dec 2025 | 6 articles | Viewed by 13452 | Submission Open

Keywords: coronavirus disease 2019 (COVID-19); severe acute respiratory syndrome (SARS); middle east respiratory syndrome (MERS); nipah virus; ebola hemorrhagic fever (EHF); marburg hemorrhagic fever (MHF); lassa hemorrhagic fever (LHF); crimean– congo hemorrhagic fever (CCHF); rift valley fever (RVF); zika fever; monkeypox; plague

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

Antimicrobial Testing (AMT), Third Edition

edited by

Suresh G. Joshi

submission deadline 31 Dec 2025 | 8 articles | Viewed by 12808 | Submission Open

Keywords: antibiogram; antibiotic susceptibility test; antimicrobial testing; bacterial resistance; biofilm-embedded bacteria; antifungal test; genotypic AMT; multidrug resistance; antimicrobial nanoparticle

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

Genomics and Epidemiology of Clinical Microorganisms

edited by

Addy Cecilia Helguera-Repetto

and

Moises Leon-Juarez

submission deadline 31 Dec 2025 | 6 articles | Viewed by 11528 | Submission Open

Keywords: infectious disease epidemiology; pathogen genomics; molecular characterization of microorganisms; clinical outcomes of infectious diseases; virulence determinants; antibiotic resistance; pathogen gene expression

(This special issue belongs to the Section Medical Microbiology)

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms, 3rd Edition

edited by

Adriana Calderaro

submission deadline 31 Dec 2025 | 5 articles | Viewed by 11233 | Submission Open

Keywords: MALDI-TOF MS; diagnosis; microorganism identification; bacteria; viruses; parasites; fungi; antimicrobial susceptibility testing

(This special issue belongs to the Section Medical Microbiology)

Intestine as a Hub for Host-Microbe Interactions and Its Impact on Local and Systemic Health

edited by

Helioswilton Sales-Campos

and

José Luiz de Brito Alves

submission deadline 31 Dec 2025 | 4 articles | Viewed by 10916 | Submission Open

Keywords: microbiota; gut pathogens; immune response; inflammation; dysbiosis; infection; nutritional status

(This special issue belongs to the Section Gut Microbiota)

Feature Papers in Food Microbiology

edited by

Giuseppe Comi

Antonio Bevilacqua

and Francesca Coppola

submission deadline 31 Dec 2025 | 5 articles | Viewed by 10767 | 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)

Advanced Research on Antimicrobial Activity of Natural Products

edited by

Anca Zanfirescu

and Corina Andrei

submission deadline 31 Dec 2025 | 7 articles | Viewed by 10530 | Submission Open

Keywords: antimicrobial resistance; antimicrobial activity; pathogens; infectious disorders; natural products; anti-infective agents

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

Pathogenic Biofilms: Physiology, Molecular Mechanisms and Counter Strategies

edited by

Domenico Franco

and

Laura Maria De Plano

submission deadline 31 Dec 2025 | 4 articles | Viewed by 9958 | Submission Open

Keywords: pathogenic biofilm; planktonic and sessile cells; antiadhesive and antifouling strategies; quorum sensing; quorum quenching; extracellular polymeric substances (EPSs); phage therapy

(This special issue belongs to the Section Biofilm)

The Central Role of Microbiota in Eye Health

edited by

Francesco Petrillo

and

Elisa Zanotto

submission deadline 31 Dec 2025 | 5 articles | Viewed by 9552 | Submission Open

Keywords: eye health; microbiota; next-generation sequencing; immune system

(This special issue belongs to the Section Medical Microbiology)

Persistence and Antimicrobial Resistance of Bacterial Pathogens in the Food Processing Environment

edited by Marios Mataragas,

Shuxiang Liu

and

Nikolaos D. Andritsos

submission deadline 31 Dec 2025 | 4 articles | Viewed by 9242 | Submission Open

Keywords: foodborne pathogens; pathogenic bacteria; Salmonella; Campylobacter; Listeria monocytogenes; microbial persistence; bacterial stresses; antimicrobial resistance; antibiotic susceptibility; quaternary ammonium compounds

(This special issue belongs to the Section Food Microbiology)

Bioproduction of Functional and Bioactive Ingredients: State of the Art and Technological Advances

edited by Gustavo Molina

submission deadline 31 Dec 2025 | 4 articles | Viewed by 9205 | Submission Open

Keywords: microbial metabolic engineering; upscale technology; bioprocess optimization; agroindustrial residues; functional ingredients; bioactive compounds; probiotics and prebiotics; antimicrobial peptides; vitamins and antioxidants; industrial biotechnology

(This special issue belongs to the Section Microbial Biotechnology)

Disinfection, Inactivation, and Sterilization of Pathogens and Biotoxins: Emerging Technologies and Strategies

edited by

Akikazu Sakudo

submission deadline 31 Dec 2025 | 3 articles | Viewed by 9030 | Submission Open

Keywords: disinfection technologies; pathogen inactivation; sterilization techniques; biotoxin degradation; advanced disinfection methods; public health

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

Diet, Supplements, Lifestyle and Human Microbiota: Impacts on Health and Disease

edited by

Valerio Pazienza

and

Concetta Finocchiaro

submission deadline 31 Dec 2025 | 3 articles | Viewed by 8461 | Submission Open

Keywords: human microbiome; dysbiosis; cancer; vaginal microbiota; sport; nutrition; lifestyle; pathological condition; infertility; IVF

(This special issue belongs to the Section Microbiomes)

Diagnosis, Treatment and Prevention of Viral Infections

edited by

Alexandro Guterres

submission deadline 31 Dec 2025 | 4 articles | Viewed by 8386 | Submission Open

Keywords: viral infections; molecular diagnostics; antiviral therapies; RNA-based vaccines; point-of-care testing; emerging viruses; drug resistance; immunotherapy; viral biomarkers; prevention strategies

(This special issue belongs to the Section Virology)

Water Microorganisms Associated with Human Health, 2nd Edition

edited by

Ana Machado

submission deadline 31 Dec 2025 | 7 articles | Viewed by 7554 | Submission Open

Keywords: drinking water; recreational water; microorganisms; biomarkers; emerging contaminants; risk assessment; waterborne diseases; One Health

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

Probiotics, Prebiotics, and Gut Microbes—Second Edition

edited by

Oleg Paliy

submission deadline 31 Dec 2025 | 3 articles | Viewed by 7447 | Submission Open

Keywords: probiotics; prebiotics; gut microbes; host health

(This special issue belongs to the Section Gut Microbiota)

Pathogens in Aquaculture Environments

edited by Eduardo Quiroz-Gúzman

submission deadline 31 Dec 2025 | 2 articles | Viewed by 6708 | Submission Open

Keywords: bacterial pathogens; bacterial pathogen database; aquaculture; disease; bacterial fish pathogens; bacterial shrimp pathogens; bacterial adhesion; bacterial colonization; virulence factor; pathogen– host interaction

(This special issue belongs to the Section Environmental Microbiology)

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

edited by

Anna Baraniak

submission deadline 31 Dec 2025 | 4 articles | Viewed by 6588 | Submission Open

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

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

Biofilm: Formation, Control, and Applications

edited by Huan Gu

submission deadline 31 Dec 2025 | 4 articles | Viewed by 6401 | Submission Open

Keywords: biofilm formation; material properties; cell-to-cell interactions; prevention; removal; control

(This special issue belongs to the Section Biofilm)

Advancing Microbial Taxonomy and Genomics: Bridging Diversity and Functionality

edited by

Sathiyaraj Srinivasan

submission deadline 31 Dec 2025 | 3 articles | Viewed by 6350 | Submission Open

Keywords: microbial taxonomy; genomics; extremophiles; unculturable microorganisms; hybrid sequencing; microbial communities; functional genomics; culture-independent methods; comparative genomics; prokaryotic and eukaryotic microbes

(This special issue belongs to the Section Microbiomes)

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

edited by

Zhiyong Li

submission deadline 31 Dec 2025 | 4 articles | Viewed by 6333 | 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)

Research on Mosquito-Borne Pathogens

edited by

Diego Peres Alonso

and Paulo Eduardo Martins Ribolla

submission deadline 31 Dec 2025 | 6 articles | Viewed by 6195 | Submission Open

Keywords: mosquito vector; mosquito pathogens; genetics; developmental biology; mosquito– pathogen interactions

(This special issue belongs to the Section Medical Microbiology)

Microbes in Aquaculture

edited by

Jiasong Zhang

submission deadline 31 Dec 2025 | 6 articles | Viewed by 5674 | Submission Open

Keywords: aquaculture microbiomes; probiotics in aquaculture; gut microbiota; disease management; pathogen and host interaction; water quality

(This special issue belongs to the Section Environmental Microbiology)

Advances in Plant–Soil–Microbe Interactions

edited by

Zelaya Molina Lily Xochilt

and

Sergio de los Santos Villalobos

submission deadline 31 Dec 2025 | 3 articles | Viewed by 5358 | 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)

Advances in Toxoplasma gondii and Toxoplasmosis

edited by

Maria Luz Galván-Ramírez

and Jorge Enrique Gómez Marín

submission deadline 31 Dec 2025 | 3 articles | Viewed by 5161 | Submission Open

Keywords: Toxoplasma gondii; toxoplasmosis; immune response; diagnosis; treatment; epidemiology

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

The Vaginal Microbiome in Health and Disease

edited by

Zohar Nachum

and

Enav Yefet

submission deadline 31 Dec 2025 | 4 articles | Viewed by 5059 | Submission Open

Keywords: vaginal flora; pathogenesis; therapeutic approaches; health

(This special issue belongs to the Section Medical Microbiology)

Fungus: Diversity, Genomics and Genetics

edited by

Isabel Antonieta Iturrieta-González

and Patrício Christian Godoy-Martínez

submission deadline 31 Dec 2025 | 3 articles | Viewed by 4908 | Submission Open

Keywords: fungal diversity; fungal genomics; phylogenetics; fungal taxonomy; Ascomycota; Basidiomycota; phylogeny; cryptic species; taxonomy; phytopathogenic fungi

(This special issue belongs to the Section Environmental Microbiology)

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

edited by

Nikolay Vassilev

and

Stefan Shilev

submission deadline 31 Dec 2025 | 1 articles | Viewed by 4147 | 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)

Feature Paper in Plant–Microbe Interactions in Asia

edited by

Congyan Wang

submission deadline 31 Dec 2025 | 4 articles | Viewed by 4091 | Submission Open

Keywords: plant; microbe; interactions; community structure; growth performance; metabolic activity

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

Viral Infection on Swine: Pathogenesis, Diagnosis and Control

edited by Liwei Li

submission deadline 31 Dec 2025 | 4 articles | Viewed by 3974 | Submission Open

Keywords: swine virus infection; variability; virulence; monoclonal antibody; diagnosis; surveillance; epidemiology; therapy; vaccine

(This special issue belongs to the Section Veterinary Microbiology)

Phytoplasmas and Phytoplasma Diseases

edited by

Carmine Marcone

and

Assunta Bertaccini

submission deadline 31 Dec 2025 | 3 articles | Viewed by 3934 | Submission Open

Keywords: yellows and decline diseases; ‘ Candidatus Phytoplasma’ species; 16Sr group/subgroups; Phytoplasma taxonomy; symptomatology; epidemiology; fruit trees; forest trees; shrubs; herbaceous crops; flower crops; weeds

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

Selected Papers from the 3rd International Electronic Conference on Microbiology (ECM 2025)

edited by

Nico Jehmlich

Theodoros Varzakas

and

Ute Römling

submission deadline 31 Dec 2025 | 3 articles | Viewed by 3890 | Submission Open

Keywords: gut microbiota; foodborne pathogens and food safety; antimicrobial agents and resistance; emerging infectious diseases; microbiome and soil science; microbial characterization and bioprocess; microbe-plant interactions

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 | 2 articles | Viewed by 3768 | 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)

The Microbial Pathogenesis

edited by

Tingting Wang

and Canfeng Hua

submission deadline 31 Dec 2025 | 3 articles | Viewed by 3519 | 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)

Pathogenic Microbes in the Environment and Infectious Disease Control

edited by

Panagiotis Karanis

submission deadline 31 Dec 2025 | 2 articles | Viewed by 3482 | Submission Open

Keywords: pathogens; bacteria; viruses; fungi; parasites; environment; epidemiology; control

(This special issue belongs to the Section Environmental Microbiology)

Microbial Fermentation in Food Processing

edited by

Wenchao Cai

and Qin Zhang

submission deadline 31 Dec 2025 | 3 articles | Viewed by 3392 | Submission Open

Keywords: microbial fermentation; food processing; flavor development; fermentation kinetics; microbial communities; metabolic pathways; food safety; sensory attributes; nutritional enhancement; food science and technology

(This special issue belongs to the Section Microbial Biotechnology)

Microorganisms: Climate Change and Terrestrial Ecosystems

edited by

Tengxiang Lian

and Xin Sui

submission deadline 31 Dec 2025 | 4 articles | Viewed by 3155 | Submission Open

Keywords: global change biology; nitrogen depostion; soil microbial divesity

(This special issue belongs to the Section Environmental Microbiology)

The Notion of Microorganisms-Based Bio-Refinery: Transitioning from Wastewater Treatment to By-Products Recovery

edited by Giovanni Antonio Lutzu

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2969 | Submission Open

Keywords: microalgae; mixotrophy; heterotrophy; bio-products; wastewater treatment; nutraceuticals; pharmaceuticals; biostimulants; bioplastics; biodiesel

(This special issue belongs to the Section Environmental Microbiology)

Marine Microbes, Biocontamination and Bioremediation

edited by

Hideyuki Kanematsu

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2954 | Submission Open

Keywords: biofouling; biofilm; marine bacteria; marine structures

(This special issue belongs to the Section Environmental 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 | 3 articles | Viewed by 2896 | Submission Open

Keywords: medical bacteria; diagnosis; treatment; prevention

(This special issue belongs to the Section Medical Microbiology)

Insights into Microbial Infections, Co-Infections, and Comorbidities

edited by

Zilungile Mkhize-Kwitshana

and

Veron Ramsuran

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2892 | Submission Open

Keywords: antimicrobial resistance; cancer; cardiovascular diseases; co-infections; comorbidities; complex disease profiles; diabetes; infection pathogenesis; immune modulation; microbiome and co-infections; noncommunicable diseases; pathogen interactions; pneumonia; pulmonary infections; sepsis; stress tolerance; therapeutics; vaccine development

(This special issue belongs to the Section Medical Microbiology)

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

edited by

Dilfuza Egamberdieva

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2872 | 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)

Accelerated Topics in Public Health Microbiology and Microbial Food Safety

edited by

Aliyar Fouladkhah

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2678 | 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)

Transcriptional Regulation in Bacteria, 2nd Edition

edited by

Tomohiro Shimada

submission deadline 31 Dec 2025 | 3 articles | Viewed by 2519 | Submission Open

Keywords: transcription; gene regulation; genome regulation; regulatory network; RNA polymerase; sigma factor; transcription factor; nucleoid

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

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