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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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Microbial Fermentation in Food Processing

edited by

Wenchao Cai

and Qin Zhang

submission deadline 31 Dec 2025 | 3 articles | Viewed by 4157 | 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)

Pathogenic Microbes in the Environment and Infectious Disease Control

edited by

Panagiotis Karanis

submission deadline 31 Dec 2025 | 2 articles | Viewed by 3762 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Microorganisms: Climate Change and Terrestrial Ecosystems

edited by

Tengxiang Lian

and Xin Sui

submission deadline 31 Dec 2025 | 4 articles | Viewed by 3761 | Submission Open

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

(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 3705 | Submission Open

Keywords: medical bacteria; diagnosis; treatment; prevention

(This special issue belongs to the Section Medical Microbiology)

Transcriptional Regulation in Bacteria, 2nd Edition

edited by

Tomohiro Shimada

submission deadline 31 Dec 2025 | 4 articles | Viewed by 3565 | 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)

Marine Microbes, Biocontamination and Bioremediation

edited by

Hideyuki Kanematsu

submission deadline 31 Dec 2025 | 2 articles | Viewed by 3363 | Submission Open

Keywords: biofouling; biofilm; marine bacteria; marine structures

(This special issue belongs to the Section Environmental 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 3291 | 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 3267 | 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)

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 3252 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Accelerated Topics in Public Health Microbiology and Microbial Food Safety

edited by

Aliyar Fouladkhah

submission deadline 31 Dec 2025 | 2 articles | Viewed by 2960 | 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)

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

edited by

Annamaria Bevivino

Alessia Fiore

and

Silvia Tabacchioni

submission deadline 31 Dec 2025 | 3 articles | Viewed by 2892 | Submission Open

Keywords: soil microbiome; plant holobiont; one health; 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 | 3 articles | Viewed by 2777 | 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)

Applied Gut Molecular Microbiology Technology

edited by

Donglei Sun

and

Yi-Zhou Gao

submission deadline 31 Dec 2025 | 1 articles | Viewed by 2726 | Submission Open

Keywords: gut microorganisms; applied microbiology; probiotics

(This special issue belongs to the Section Microbial Biotechnology)

Advances in Novel Antibacterial Agents, 2nd Edition

edited by Mariateresa Vitiello

submission deadline 31 Dec 2025 | 1 articles | Viewed by 2217 | Submission Open

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

(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 | 1 articles | Viewed by 2187 | 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)

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

edited by

Ian Connerton

and Adam Lee

submission deadline 31 Dec 2025 | 1 articles | Viewed by 2132 | 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)

Resource Utilization of Microorganisms: Fermentation and Biosynthesis

edited by Shoushuai Feng

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1939 | Submission Open

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

(This special issue belongs to the Section Microbial Biotechnology)

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

edited by

Douglas D. Rhoads

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1885 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

Interplays Between Gut Microbiome and Animal Health, Disease and Production Performance

edited by Shi-Yi Chen

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1638 | Submission Open

Keywords: gut microbiota; host health and disease; production traits; domestic animals; microbiability; microbial heritability

(This special issue belongs to the Section Veterinary Microbiology)

Novel Antimicrobial Approaches in Biofilm Control in the Food Industry: Future Perspectives

edited by

Ružica Tomičić

and

Meta Sterniša

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1604 | Submission Open

Keywords: microbial growth; biofilm formation; antimicrobial strategies; food industry; combined treatments

(This special issue belongs to the Section Biofilm)

From Sewers to Solutions: Wastewater Surveillance in the Fight Against Antimicrobial Resistance

edited by Mohamed M. H. Abdelbary,

Guido Werner

and Kazunari Sei

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1543 | Submission Open

Keywords: AMR pathogens in wastewater; carbapenem-resistant enterobacterales; wastewater resistome; culture-based detection; molecular methodologies for pathogens detection; digital PCR; hospital and urban Wastewater; wastewater microbiome; mobile genetic elements; AMR plasmids

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

Fungi and Health

edited by

Jialing Bao

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1529 | Submission Open

Keywords: fungi; human health; human pathogenic fungi; Aspergillus fumigatus; Cryptococcus neoformans and gattii; Candida albicans spp.; Coccidioides spp.; Microsporidia phylum; diagnostic methods; clinical data

(This special issue belongs to the Section Medical Microbiology)

Research on Airborne Microbial Communities

edited by

Changliang Nie

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1475 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

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

edited by

Alex Galanis

and

Aglaia Pappa

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1470 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

The Host Response to Animal Virus Infection

edited by Liwei Li

submission deadline 31 Dec 2025 | 2 articles | Viewed by 1461 | 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 31 Dec 2025 | 1 articles | Viewed by 1313 | 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)

Meningococcal Infections

edited by

Athanasia Xirogianni

and

Georgina Tzanakaki

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1264 | 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)

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

edited by

Selwyn Arlington Headley

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1251 | Submission Open

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

(This special issue belongs to the Section Veterinary Microbiology)

Microbiological Approaches to Water Pollution Control and Water Ecological Restoration

edited by

Haiya Zhang

Weigao Zhao

and

Xiaoou Wang

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1207 | 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)

Beneficial Microbes: Food, Mood and Beyond—Third Edition

edited by

Mohamed Zommiti

and

Marc G. J. Feuilloley

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1164 | Submission Open

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

Novel Sequencing Technologies for the Characterization of Multidrug-Resistant Bacteria

edited by

Costas C. Papagiannitsis

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1155 | 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)

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

edited by

Angela Pista

and

Rita Batista

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1091 | 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)

The Interactions Between Nutrients and Microbiota

edited by

Renata Barczyńska-Felusiak

and

Agnieszka Rudzka

submission deadline 31 Dec 2025 | 1 articles | Viewed by 1010 | Submission Open

Keywords: diet; nutrients; microbiota; human health

(This special issue belongs to the Section Food Microbiology)

Fruit Wine Fermentation and Microbial Communities

edited by

Feifei Gao

submission deadline 31 Dec 2025 | 1 articles | Viewed by 960 | 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)

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

edited by Moussa Diarra and

Wen Chen

submission deadline 31 Dec 2025 | 1 articles | Viewed by 950 | Submission Open

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

Current Updates on Multidrug-Resistant Gram-Negative Bacterial Infections

edited by

Maria Balasoiu

and Andreea-Loredana Golli

submission deadline 31 Dec 2025 | 1 articles | Viewed by 848 | Submission Open

Keywords: antimicrobial resistance; gram-negative bacterial infections; pathogens; Acinetobacter baumannii; hospital-acquired infections

(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 | 1 articles | Viewed by 821 | Submission Open

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

(This special issue belongs to the Section Biofilm)

Microparasites: Diversity, Phylogeny and Molecular Characterization

edited by Alena Mayo Iniguez

submission deadline 31 Dec 2025 | 1 articles | Viewed by 753 | Submission Open

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

(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 | 1 articles | Viewed by 685 | 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)

Microbial Biofilms and Biofouling

edited by

James S. Maki

submission deadline 31 Dec 2025 | 1 articles | Viewed by 663 | Submission Open

Keywords: microbial attachment; biofilm formation; microbial extracellular production of cues; interactions between all microbes in a natural biofilm community; sessile invertebrate larvae; algal zoospores

(This special issue belongs to the Section Environmental 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 624 | 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)

Resistance of Gram-Negative Bacteria to Last-Resort Antibacterials

edited by Sophia Vourli

submission deadline 31 Dec 2025 | Viewed by 415 | Submission Open

Keywords: last-resort antimicrobials; mechanisms of resistance to new antimicrobials; PK/PD of new and old antimicrobials; combination therapy; resistance genomics

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

Trichomonas vaginalis and Trichomoniasis: Biomarkers and Possible Pharmacological Alternatives

edited by