Research output from the Aquaculture Microbiology Lab includes peer-reviewed publications and externally funded research projects that address fish disease from a mechanistic and systems-level perspective.
Publications and projects are closely linked, with funded research initiatives supporting research on fish health in aquaculture, marine biotechnology, and microbiology, and enabling the development of prevention-oriented approaches relevant to aquaculture systems.
Selected publications
Chalmoukis C., Droubogiannis S., Michalopoulou V.A., Triga A., Sarris P.F., & Katharios P. (2025). Development and characterization of fluorescent protein-tagged Vibrio harveyi strains as a versatile tool for studying infection dynamics and strain interactions. Pathogens, 14(3), 247.
Triga A., Issa Z.A., Smyrli M., Fenske L., & Katharios P. (2024). Virulence and pangenome analysis of Vibrio harveyi strains from Greek and Red Sea marine aquaculture. Aquaculture, 587, 740839.
Droubogiannis S., Pavlidi L., Skliros D., Flemetakis E., & Katharios P. (2023). Comprehensive characterization of a novel bacteriophage, vB_VhaS_MAG7, against a fish pathogenic strain of Vibrio harveyi and its in vivo efficacy in phage therapy trials. International Journal of Molecular Sciences, 24(9), 8200.
Smyrli M., Anka I.Z., Koutsoni O., Dotsika E., Kyriazis I.D., Pavlidis M., & Katharios P. (2022). Development of autogenous vaccines for farmed European seabass against Aeromonas veronii using zebrafish as a model for efficacy assessment. Fish & Shellfish Immunology, 123, 381–387.
Cascarano M.C., Stavrakidis-Zachou O., Mladineo I., Thompson K.D., Papandroulakis N., & Katharios P. (2021). Mediterranean aquaculture in a changing climate: temperature effects on pathogens and diseases of three farmed fish species. Pathogens, 10(9), 1205.
Skliros D., Kalatzis P.G., Kalloniati C., Komaitis F., Papathanasiou S., Kouri E.D., Udvardi M.K., Kokkari C., Katharios P., & Flemetakis E. (2021). The development of bacteriophage resistance in Vibrio alginolyticus depends on a complex metabolic adaptation strategy. Viruses, 13(4), 656.
Katharios, P., Varvarigos, P., Keklikoglou, K., Ruetten, M., Sojan, J., Akter, M., Cascarano, M.C., Tsertou, M.I. and Kokkari, C., 2020. Native parasite affecting an introduced host in aquaculture: cardiac henneguyosis in the red seabream Pagrus major Temminck & Schlegel (Perciformes: Sparidae) caused by Henneguya aegea n. sp.(Myxosporea: Myxobolidae). Parasites & vectors, 13(1), p.27.
Katharios P., Seth-Smith H.M., Fehr A., Mateos J.M., Qi W., Richter D., Nufer L., Ruetten M., Guevara Soto M., Ziegler U., & Thomson N.R. (2015). Environmental marine pathogen isolation using mesocosm culture of sharpsnout seabream: striking genomic and morphological features of novel Endozoicomonas sp. Scientific Reports, 5, 17609.
Seth-Smith H.M., Dourala N., Fehr A., Qi W., Katharios P., Ruetten M., Mateos J.M., Nufer L., Weilenmann R., Ziegler U., & Thomson N.R. (2016). Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. The ISME Journal, 10(7), 1791–1803.
A complete and continuously updated list of publications is available through the lab’s Google Scholar profile.
Research projects
Research projects in the Aquaculture Microbiology Lab are structured around interconnected thematic areas that address fundamental and applied questions in aquaculture microbiology, fish health, and sustainable disease management. These activities span from microbial ecology and genomics to translational research and policy-oriented studies at the European level.
Phage Biology and Phage Therapy in Aquaculture
Phage–bacteria interactions, biocontrol and alternative disease control strategies
A core research axis of the lab focuses on bacteriophages as biological control agents and as tools to study phage–bacteria infection networks in aquatic ecosystems. This line of research integrates environmental microbiology, experimental infection models, and applied phage therapy.
FORERUNNERS – Phage–Bacteria Infection Networks in Divergent Ecosystems: A cross-continental study between Antarctica and the Cretan Sea
Hellenic Foundation for Research and Innovation (HFRI), 3rd Call · 2025 · Budget: 299,970 € · Project Coordinator
FISHPHAGE – Biological control of bacteria in fish hatcheries using phages
GSRT “EXCELLENCE” Programme · 2012 · Budget: 280,000 € · Project Coordinator
AQUAPHAGE – Network for the development of phage therapy in aquaculture
FP7 Marie Curie, IRSES-2010 · 2010 · Budget: 358,700 € · Project Coordinator
Bacterial Fish Diseases and Vibriosis
Pathogen diversity, virulence and targeted prevention
This theme addresses the microbiology and control of major bacterial diseases in aquaculture, with particular emphasis on Vibrio spp. and vibriosis.
ROBUST – Prevention of vibriosis caused by Vibrio harveyi with innovative tools
NSRF – GSRT Special Actions “Aquaculture” · 2019 · Budget: 350,463.77 € · Project Coordinator
Biocontrol of pathogens in fish hatcheries with the use of phages
NSRF – Operational Programme Fisheries and Maritime 2014–2020 · 2018 · Budget: 478,630 € · Project Coordinator
Disease Prevention and Health Management Strategies
From experimental research to policy and sector-wide needs
The lab contributes to disease prevention research at both experimental and strategic levels, supporting evidence-based health management practices and identifying future research priorities for aquaculture.
Disease prevention in farmed fish: New developments and research needs
Standing Committee on Agricultural Research (SCAR-FISH), EU · 2019 · Budget: 15,000 € · Project Coordinator
Alternative Methods for Treatment and Prophylaxis in Greek Aquaculture
GSRT – Hellenic Ministry of Education · 2010 · Budget (HCMR): 316,140 € · Work Package Leader
Vaccines, Probiotics and Microbiome-Based Approaches
Reducing antibiotic use and enhancing disease resilience
This research axis focuses on biological alternatives to antibiotics, including vaccines, probiotics, and microbiome-based strategies.
AQUATIC BIOLOGICALS – Production of autogenous vaccines for the Greek Aquaculture Industry
Open research project · 2014 · Total budget (2020): >500,000 € · Project Coordinator
PROAQUA – Reducing antibiotic use in marine larviculture by a novel combinatory probiotic strategy
Danish Strategic Research Council · 2013–2017 · Budget (HCMR): 107,000 € · Scientific Responsible for HCMR
European Research for Sustainable Aquaculture
Integrated approaches under environmental change
CURE4AQUA – Innovative solutions for sustainable aquaculture
Horizon Europe · 2022 · Budget (HCMR): 827,000 € · Scientific Responsible for HCMR
CLIMEFISH – Co-creating a decision support framework for sustainable fish production under climate change
Horizon 2020 · 2015 · Total budget: 5,000,000 € · Participating Researcher
Diversification of Aquaculture Species and Production Systems
New species, reproduction and production biology
DIVERSIFY – Exploring the biological and socio-economic potential of new and emerging candidate fish species
FP7-KBBE · 2013–2018 · Total budget: 11.8 million € · Work Package Leader
KRANIOS – Development of reproduction and rearing methods for meagre (Argyrosomus regius)
GSRT · 2010 · Budget (HCMR): 86,200 € · Work Package Leader
Marine Biotechnology and Foundational Research
Biotechnological resources and emerging research directions
BIOEXPLORE – Biotechnology for the exploitation of microalgae
GSRT – Hellenic Ministry of Education · 2010 · Total budget: 1,499,400 € · Budget (HCMR): 288,000 € · Project Coordinator
MOUNT – MOdern UNifying Trends in marine biology
Operational Programme Competitiveness, Entrepreneurship and Innovation · 2018 · Participating Researcher