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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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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 622 | 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)

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 599 | 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)

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 594 | 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)

Meningococcal Infections

edited by

Athanasia Xirogianni

and

Georgina Tzanakaki

submission deadline 31 Dec 2025 | 1 articles | Viewed by 591 | 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 Interactions Between Nutrients and Microbiota

edited by

Renata Barczyńska-Felusiak

and

Agnieszka Rudzka

submission deadline 31 Dec 2025 | Viewed by 512 | Submission Open

Keywords: diet; nutrients; microbiota; human health

(This special issue belongs to the Section Food Microbiology)

HIV Infections: Diagnosis and Drug Uses

edited by

Nompumelelo Mkhwanazi

submission deadline 31 Dec 2025 | 1 articles | Viewed by 510 | 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)

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 | Viewed by 473 | 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)

Algae–Bacteria Interactions in Environment

edited by LiXiao Ni

submission deadline 31 Dec 2025 | Viewed by 457 | Submission Open

Keywords: algal– bacterial interactions; algal– bacterial symbiosis; cyanobacterial blooms; quorum sensing; biogeochemical cycling; wastewater treatment; ecological networks

(This special issue belongs to the Section Environmental 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 | Viewed by 400 | Submission Open

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

(This special issue belongs to the Section Biofilm)

Resistance of Gram-Negative Bacteria to Last-Resort Antibacterials

edited by Sophia Vourli

submission deadline 31 Dec 2025 | Viewed by 364 | 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)

Microparasites: Diversity, Phylogeny and Molecular Characterization

edited by Alena Mayo Iniguez

submission deadline 31 Dec 2025 | Viewed by 341 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Fruit Wine Fermentation and Microbial Communities

edited by

Feifei Gao

submission deadline 31 Dec 2025 | Viewed by 340 | 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)

Microbial Biofilms and Biofouling

edited by

James S. Maki

submission deadline 31 Dec 2025 | Viewed by 327 | 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)

Trichomonas vaginalis and Trichomoniasis: Biomarkers and Possible Pharmacological Alternatives

edited by

María Elizbeth Alvarez-Sánchez

Julio César Torres-Romero

and

Elisa Elvira Figueroa-Angulo

submission deadline 31 Dec 2025 | Viewed by 326 | Submission Open

Keywords: trichomoniasis in men; biomarkers; pharmaceutical alternatives

(This special issue belongs to the Section Medical Microbiology)

Microbe-Plant-Environment Interactions over Time

edited by

Phatu Mashela

submission deadline 31 Dec 2025 | Viewed by 323 | Submission Open

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

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

Rare Human Pathogens

edited by Percy Schröttner

submission deadline 31 Dec 2025 | Viewed by 296 | Submission Open

Keywords: rare; pathogen; diseases; pathogenic bacteria

(This special issue belongs to the Section Medical Microbiology)

Bloodstream Infection: Common and Uncommon Pathogens

edited by Carola Mauri

submission deadline 31 Dec 2025 | Viewed by 166 | Submission Open

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

(This special issue belongs to the Section Medical Microbiology)

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

edited by Niels Høiby and Claus Moser

submission deadline 31 Dec 2025 | Viewed by 162 | Submission Open

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

(This special issue belongs to the Section Biofilm)

Human Microbiome and Microbial Ecology of Oral Diseases

edited by

Ana Pucar

and Sanja Matić Petrović

submission deadline 31 Dec 2025 | Viewed by 157 | Submission Open

Keywords: oral microbiome; biofilms; dysbiosis; antimicrobial strategies; host– microbiota interactions

(This special issue belongs to the Section Microbiomes)

Probiotic and Postbiotic Properties of Lactobacillus, 2nd Edition

edited by

Sang-Ho Baik

submission deadline 31 Dec 2025 | Viewed by 152 | Submission Open

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

(This special issue belongs to the Section Food 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 | Viewed by 131 | 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)

Parasitic Diseases in Livestock, 2nd Edition

edited by

Aleksandra Uzelac

Luca Villa

and

Ivana Klun

submission deadline 31 Dec 2025 | Viewed by 131 | 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)

Gut Microbiota and Metabolic Disease Pathogenesis

edited by

Gerald Maarman

submission deadline 31 Dec 2025 | Viewed by 130 | 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)

Anaerobic Gut Fungi: Ecological Role and Biotechnological Potential

edited by Radwa Hanafy

submission deadline 31 Dec 2025 | Viewed by 127 | 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)

Microbiome Innovations in Food Systems for a Green Future

edited by

and

submission deadline 31 Dec 2025 | Viewed by 126 | 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 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 122 | 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)

Laboratory Diagnosis and Epidemiology of Clinical Microbial Infections

edited by

Vassiliki Pitiriga

submission deadline 31 Dec 2025 | 1 articles | Viewed by 117 | Submission Open

Keywords: infectious disease; laboratory diagnosis; epidemiology

(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 114 | 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)

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

edited by

Alex Galanis

and

Aglaia Pappa

submission deadline 31 Dec 2025 | Viewed by 112 | Submission Open

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

(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 110 | Submission Open

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

(This special issue belongs to the Section Environmental Microbiology)

Advances in Microbial Biofilm Formation (2nd Edition)

edited by

Ute Römling

submission deadline 31 Dec 2025 | Viewed by 104 | Submission Open

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

(This special issue belongs to the Section Biofilm)

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

edited by

Douglas D. Rhoads

submission deadline 31 Dec 2025 | 1 articles | Viewed by 103 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

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 101 | Submission Open

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

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

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 100 | Submission Open

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

(This special issue belongs to the Section Microbiomes)

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 97 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

Microbial Nutrient Cycling Mechanisms

edited by

Jiawen Wang

submission deadline 31 Dec 2025 | Viewed by 95 | Submission Open

Keywords: microbes; nutrient cycling; mechanism; carbon; nitrogen; phosphorus; sulfur; environmental factors; biotechnology applications

(This special issue belongs to the Section Environmental Microbiology)

Breaking Barriers: The Breakdown of Epithelial Defenses by Pathogens

edited by

Karen Bohmwald

submission deadline 31 Dec 2025 | Viewed by 92 | 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)

Unraveling the Mysteries of Gut Microbiota to Advance Sustainable Aquaculture

edited by Qunlan Zhou

submission deadline 31 Dec 2025 | Viewed by 91 | Submission Open

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

(This special issue belongs to the Section Gut Microbiota)

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

edited by

Alejandro Speck-Planche

submission deadline 31 Dec 2025 | Viewed by 83 | 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 82 | 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)

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

edited by

Dennis Cvitkovitch

submission deadline 31 Dec 2025 | Viewed by 81 | 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)

Marine Agricultural Microorganisms

edited by