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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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Transcriptional Regulation in Bacteria, 2nd Edition

edited by

Tomohiro Shimada

submission deadline 30 Jun 2026 | 6 articles | Viewed by 6637 | 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)

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

edited by Victoria Birlutiu

submission deadline 30 Jun 2026 | 3 articles | Viewed by 5935 | 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)

Oral Bacteria, Viruses, and Fungi: Oral Health, Disease, and Systemic Links

edited by

Maria Pia Di Palo

Federica Di Spirito

and Nicoletta Capuano

submission deadline 30 Jun 2026 | 4 articles | Viewed by 5891 | Submission Open

Keywords: oral microbiota; host– microbe interactions; antimicrobial resistance; therapeutic approaches; probiotics

(This special issue belongs to the Section Medical Microbiology)

Harnessing Microbes for Crop Protection and Fertilization

edited by

Humayun Javed

submission deadline 30 Jun 2026 | 3 articles | Viewed by 5771 | Submission Open

Keywords: microbial biocontrol; plant– microbe interactions; biofertilizers; sustainable agriculture; soil microbiome; entomopathogenic fungi; plant growth-promoting rhizobacteria (PGPR); nitrogen fixation; mycorrhizal fungi; biopesticides; microbial formulations; eco-friendly pest management; microbial secondary metabolites; soil fertility enhancement; climate-resilient farming; microbial inoculants; biological pest control; sustainable fertilization; microbial diversity; crop protection

(This special issue belongs to the Section Microbial Biotechnology)

Resource Utilization of Microorganisms: Fermentation and Biosynthesis

edited by Shoushuai Feng

submission deadline 30 Jun 2026 | 6 articles | Viewed by 5373 | Submission Open

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

(This special issue belongs to the Section Microbial Biotechnology)

Exploring the Diversity of Microbial Applications

edited by

Ihana Aguiar de Aguiar Severo

and

Anyong Hu

submission deadline 30 Jun 2026 | 2 articles | Viewed by 5129 | Submission Open

Keywords: microbial biotechnology; microbiome; environmental microbiology; microbial applications; bioremediation; industrial microbiology; microbial metabolism

(This special issue belongs to the Section Microbial Biotechnology)

Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections

edited by

Vassiliki Pitiriga

submission deadline 30 Jun 2026 | 5 articles | Viewed by 4973 | Submission Open

Keywords: infectious disease; laboratory diagnosis; epidemiology

(This special issue belongs to the Section Medical Microbiology)

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

edited by

Alex Galanis

and

Aglaia Pappa

submission deadline 30 Jun 2026 | 3 articles | Viewed by 4107 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

Evolution and Spread of Drug-Resistant Pathogens

edited by

Marcos Paulo Vieira Cunha

and

Elena Bello-López

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2914 | Submission Open

Keywords: antimicrobial resistance (AMR); food-borne pathogens; superbugs; one health; horizontal gene transfer; mobile genetic elements (MGEs); surveillance and monitoring; resistant pathogens outbreaks; resistance mechanisms

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

Meningococcal Infections

edited by

Athanasia Xirogianni

and

Georgina Tzanakaki

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2899 | Submission Open

Keywords: meningococcal infections; N. meningitidis; IMD; atypical presentations; IMD epidemiology; N. meningitidis vaccines

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

Research on Airborne Microbial Communities

edited by

Changliang Nie

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2859 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

The Host Response to Animal Virus Infection

edited by Liwei Li

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2720 | 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)

HIV Infections: Diagnosis and Drug Uses

edited by

Nompumelelo Mkhwanazi

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2686 | 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)

Interactions Between Parasites/Pathogens and Vectors, Second Edition

edited by Norman Ratcliffe and

Günter A. Schaub

submission deadline 30 Jun 2026 | 1 articles | Viewed by 2641 | Submission Open

Keywords: arboviruses; vectors; insects

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

Diversity and Applications of Yeasts: Food, Plant and Human Health

edited by

Elena Servienė

and

Juliana Lukša

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2602 | Submission Open

Keywords: yeasts; taxonomy; diversity; yeast communities; environment; biocontrol; pathogenicity; interactions; adaptation; cultivation techniques; multi-omics approach

Phloem Localized Insect Transmitted Bacteria Associated with Plant Diseases (2nd Edition)

edited by

Assunta Bertaccini

submission deadline 30 Jun 2026 | Viewed by 2393 | Submission Open

Keywords: phytopathogenic bacteria; ‘ Candidatus Phytoplasma’ species; ‘ Candidatus Liberibacter’ species and subspecies; plant disease; prevention; management; detection; identification; insect vectors

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

The Pathogenesis, Epidemiology and Diagnosis of Infectious Diseases in Livestock Animals, 2nd Edition

edited by

Selwyn Arlington Headley

submission deadline 30 Jun 2026 | 2 articles | Viewed by 2338 | Submission Open

Keywords: pathogenesis; epidemiology; diagnosis; livestock animals; infectious diseases

(This special issue belongs to the Section Veterinary Microbiology)

Gut Microbiota and Metabolic Disease Pathogenesis

edited by

Gerald Maarman

submission deadline 30 Jun 2026 | 1 articles | Viewed by 2302 | 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)

Exploring Foliar Plant–Bacterial Pathogen Interactions and Innovative Control Approaches

edited by

Yasuhiro Ishiga

and

Nanami Sakata

submission deadline 30 Jun 2026 | 1 articles | Viewed by 2137 | 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)

Genomics of Microorganisms from Traditional Fermented Products

edited by

Cristian Mauricio Barreto Pinilla

and Frank Guzman

submission deadline 30 Jun 2026 | 2 articles | Viewed by 1772 | Submission Open

Keywords: fermented foods; microbial genomics; metabolic pathways; probiotics; food safety; biotechnology; metagenomics; flavor development; traditional foods; microbial ecology

(This special issue belongs to the Section Food Microbiology)

Infectious Diseases in Companion Animals

edited by

Olga Szalus̈-Jordanow

submission deadline 30 Jun 2026 | 2 articles | Viewed by 1702 | Submission Open

Keywords: companion animals; veterinary medicine; infectious diseases

(This special issue belongs to the Section Veterinary Microbiology)

Detection Techniques and Assay Development for Bacterial Susceptibility and Resistance

edited by Pavel Ivanoff Reyes

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1618 | Submission Open

Keywords: antimicrobial treatments; chemical assays; susceptibility; resistance

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

Food- and Waterborne Pathogens: Epidemiology, Genomics, Virulence, and Resistance Profiles, 2nd Edition

edited by

Angela Pista

and

Rita Batista

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1589 | Submission Open

Keywords: antimicrobial resistance; mobile genetic elements; persistence and biofilms; whole-genome sequencing; public health and epidemiology; trends of microbial pathogens; influence of environmental changes in gene expression; animal health; food safety; water quality; prevention and control of food- and waterborne pathogens

(This special issue belongs to the Section Environmental Microbiology)

Microbial Enzymes—Tools for Biotechnological Processes

edited by

Rita de Cássia Garcia Simão

and

Rosane Marina Peralta

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1574 | Submission Open

Keywords: molecular tools; biotechnological applications; enzyme engineering; industrial microbial enzymes; sustainability and circular economy

(This special issue belongs to the Section Microbial Biotechnology)

Fruit Wine Fermentation and Microbial Communities

edited by

Feifei Gao

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1512 | 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)

Microparasites: Diversity, Phylogeny and Molecular Characterization

edited by Alena Mayo Iniguez

submission deadline 30 Jun 2026 | 2 articles | Viewed by 1497 | Submission Open

Keywords: parasitology; diversity; molecular biology; phylogeny; genomics; paleogenetics; taxonomy

(This special issue belongs to the Section Environmental Microbiology)

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

edited by

Teresa Semedo-Lemsaddek

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1479 | 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)

Advances in Microbial Infections and Rheumatic Diseases

edited by

Rossella Talotta

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1409 | Submission Open

Keywords: rheumatic diseases; microorganisms; host– pathogen interaction; dysbiosis; antibiotics; prebiotics; probiotics; vaccines; biomarkers; drug– drug interaction

(This special issue belongs to the Section Medical Microbiology)

Feature Papers on Respiratory Virus Infections

edited by

Hirokazu Kimura

and Fuminori Mizukoshi

submission deadline 30 Jun 2026 | 2 articles | Viewed by 1406 | Submission Open

Keywords: respiratory viruses; next-generation sequencing; molecular epidemiology; viral evolution; host– pathogen interactions; transmission dynamics; vaccine development; antiviral strategies; genomic surveillance; phylogenetics

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

Emerging Trends in Next-Generation Vaccines to Combat Infectious Diseases

edited by

Ravendra P. Chauhan

submission deadline 30 Jun 2026 | Viewed by 1400 | Submission Open

Keywords: mRNA vaccine; recombinant vaccine; antigen presentation; antigen delivery; infectious diseases; emerging viruses

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

New Advances in Sporothrix and Sporotrichosis

edited by

Sandro Pereira

and

Damiana Téllez-Martínez

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1319 | Submission Open

Keywords: Sporothrix; sporotrichosis; fungus– environment interactions; zoonotic transmission; molecular diagnosis; antifungal therapy; omics approaches; host– pathogen interactions; immunotherapeutic strategies; immune response

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

Poultry Pathogens and Poultry Diseases, 3rd Edition

edited by

Renfu Yin

and

Aleksandar Dodovski

submission deadline 30 Jun 2026 | 2 articles | Viewed by 1260 | Submission Open

Keywords: poultry pathogens; poultry diseases; avian viruses and diseases

(This special issue belongs to the Section Veterinary Microbiology)

Advancement in Enterotoxigenic Escherichia coli (ETEC) Vaccines

edited by Ann-Mari Svennerholm

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1138 | Submission Open

Keywords: ETEC vaccine candidates; protective antigens; adjuvants; clinical trial phase 1-2b; ETEC epidemiology; travellers; children in LMIC; ETEC in animals

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

Klebsiella pneumoniae: Resistance, Virulence, and Epidemiology in Healthcare and Community Settings

edited by

Branka Bedenic

submission deadline 30 Jun 2026 | 1 articles | Viewed by 1054 | Submission Open

Keywords: Klebsiella pneumoniae; hypervirulent CRKP (hv-CRKP); carbapenemase-producing Klebsiella pneumoniae (CRKP); community-acquired infections; immune evasion; biofilm formation; global dissemination

(This special issue belongs to the Section Medical Microbiology)

Molecular Mechanisms of Algal and Microbial Adaptation to Extreme Temperature Conditions

edited by

Senjie Lin

and

Tangcheng Li

submission deadline 30 Jun 2026 | 1 articles | Viewed by 969 | Submission Open

Keywords: algae; molecular mechanisms; genomic; adaptation; plasticity; extremophiles; thermophilic; psychrophilic; temperature effects; global warming

(This special issue belongs to the Section Environmental Microbiology)

Microbiome Innovations in Food Systems for a Green Future

edited by

and

submission deadline 30 Jun 2026 | 2 articles | Viewed by 926 | 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)

The Molecular Epidemiology of Infectious Diseases, 2nd Edition

edited by Jonathan Hon-kwan Chen

submission deadline 30 Jun 2026 | 1 articles | Viewed by 919 | Submission Open

Keywords: molecular epidemiology; infectious diseases; outbreak investigations; transmission; genotyping; disease control

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

Engineering of Microbial Factories for the Production of Useful Compounds

edited by

Yun-Peng Chao

and

Chung-Jen Chiang

submission deadline 30 Jun 2026 | 1 articles | Viewed by 847 | Submission Open

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

(This special issue belongs to the Section Microbial Biotechnology)

Microbial Communities Responding to Emerging Contaminants in Wastewater Treatment

edited by Yiqi Cao, Jiajie Xu and

Qian Chen

submission deadline 30 Jun 2026 | 1 articles | Viewed by 840 | Submission Open

Keywords: biological wastewater treatment; emerging contaminants; environmental conditions; microbial community; community stability; resource recovery; sustainable development

(This special issue belongs to the Section Environmental Microbiology)

Pediatric Osteoarticular Infections: Diagnosis, Management, and Emerging Challenges

edited by

Ceroni Dimitri

submission deadline 30 Jun 2026 | 1 articles | Viewed by 803 | Submission Open

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

(This special issue belongs to the Section Medical Microbiology)

Ecology and Genetics of Medically Important Fungi

edited by

Caroline Maria Marcos

Liliana Scorzoni

and

Haroldo de Oliveira

submission deadline 30 Jun 2026 | 1 articles | Viewed by 790 | Submission Open

Keywords: medical mycology; fungal ecology; molecular genetics of pathogenic fungi; antifungal resistance; fungal omics; host– pathogen interaction; environmental adaptation; fungal virulence

(This special issue belongs to the Section Medical Microbiology)

Advances in Aspergillus and Aspergillosis

edited by

Raquel Sabino

submission deadline 30 Jun 2026 | 1 articles | Viewed by 771 | Submission Open

Keywords: Aspergillus; Aspergillosis; integrating genomics; immunology; diagnosis; therapeutics; environmental science; antifungal resistance

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

Emerging Technologies for Pathogen Detection in Agriculture, Medicine, and Food Safety

edited by

Adriana Calderaro

and

Fangchi Shao

submission deadline 30 Jun 2026 | 1 articles | Viewed by 740 | Submission Open

Keywords: pathogen detection; biosensors; microfluidics; molecular diagnostics; antimicrobial resistance; point-of-care testing; food safety; artificial Intelligence

Environmental Microbes in Antimicrobial Resistance and Soil Pollution Mitigation

edited by Yan Wang

submission deadline 30 Jun 2026 | 1 articles | Viewed by 716 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Recent Advances in Diagnostic Microbiology

edited by Hin Fung Tsang

submission deadline 30 Jun 2026 | 1 articles | Viewed by 706 | Submission Open

Keywords: innovations; diagnostic microbiology; infectious diseases; patient management; artificial intelligence; machine learning; next-generation sequencing; antimicrobial resistance

(This special issue belongs to the Section Medical Microbiology)

Detection and Analysis of Clinical Microbial Infections, Third Edition

edited by

Stefano Ravaioli

submission deadline 30 Jun 2026 | 1 articles | Viewed by 693 | Submission Open

Keywords: microorganisms’ detection and analysis; clinical microbiology; identification technologies; new identification methods; heterogeneous dissemination; unculturable pathogens; mixed microbial populations; new emerging pathogens; genomics; transcriptomics; proteomics; metabolomics; standardization of testing; sample data centralization

(This special issue belongs to the Section Medical Microbiology)

Foodborne Pathogens in Complex Food Systems: Ecology, Surface Interactions, and Sustainable Control Strategies

edited by

Wilson Jose Fernandes Lemos Junior

submission deadline 30 Jun 2026 | 1 articles | Viewed by 684 | Submission Open

Keywords: foodborne pathogens; microbial ecology; predictive models; packaging– pathogen interactions; plastics; metals; food-contact surfaces; ozone; ohmic heating; sustainable interventions; biofilms; food safety monitoring

(This special issue belongs to the Section Food Microbiology)

Lactic Acid Bacteria and Dairy Food Production

edited by