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Fish Microbiome, a Novel Tool to Improve Sustainable Production and Welfare in Aquaculture

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Nutrition".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 4534

Special Issue Editors

Dr. Federico Moroni

E-Mail Website
Guest Editor
Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), 12595 Ribera de Cabanes, Castellón, Spain
Interests: aquaculture; fish nutrition, physiology and nutrigenomics; stress response
Prof. Dr. Jaume Pérez-Sánchez

E-Mail Website
Guest Editor
Nutrigenomics and Fish Growth Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS, CSIC), 12595 Ribera de Cabanes, Castellón, Spain
Interests: aquaculture; fish microbiome; fish nutrition; fish physiology

Special Issue Information

Dear Colleagues,

In recent years, researchers have attempted to improve the sustainability of aquaculture production by proposing multiple solutions that are relevant in the context of climate change. Due to the high sensitivity of the fish microbiome to changes, it is essential to evaluate these strategies and to predict their short, medium, and long-term effects. Microbial populations are closely associated with aquaculture systems and farmed animals, with which they establish communities and strong functional links. The pivotal role that it plays in numerous metabolic and immune processes makes the microbiota perfect for use as a diagnostic and prognostic tool. However, our understanding of these molecular processes and the identification of bacterial biomarkers remains limited.

This Special Issue of Animals aims to enhance our understanding of the inner mechanisms that regulate the relationships between farming variables and the physiological response of animals, using the fish microbiome as the integrative foundation. The objective of this Special Issue is to reveal the full potential of the microbiota, shed light on its variability, establish robust indicators, and define their functional role within the host–microbiota system through experimental and computational approaches. This Special Issue welcomes the submission of review articles and original research papers that use the microbiome as a tool for the sustainable development of aquaculture production and the implementation of new tailored strategies for assessing fish health and welfare.

Dr. Federico Moroni
Prof. Dr. Jaume Pérez-Sánchez
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • aquaculture
  • microbiome
  • fish nutrition
  • fish welfare
  • sustainability
  • ras system
  • microbiota biomarkers
  • host-microbiota relationship

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Published Papers (3 papers)

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Research

14 pages, 1893 KB  
Article
Gut Microbiota Response in Meagre (Argyrosomus regius) Subjected to a Plant-Based Nutritional Challenge
by Joana Oliveira, Marisa Barata, Rafaela Santos, Cláudia Serra, Florbela Soares, Pedro Pousão-Ferreira, Aires Oliva-Teles and Ana Couto
Animals 2026, 16(3), 407; https://doi.org/10.3390/ani16030407 - 28 Jan 2026
Viewed by 462
Abstract
The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of [...] Read more.
The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of juvenile meagre (Argyrosomus regius) (initial weight 4.6 ± 0.4 g) fed for seven weeks on diets in which fishmeal (FM) and fish oil (FO) were replaced by increased proportions of plant-based ingredients, with the aim of identifying microbial profiles associated with nutritional challenge. Fish were fed a FM/FO control diet (CTRL; 55.1% FM, 11.3% FO), a low FM/FO diet (CD; 15% FM, 7% FO), or a very low FM/FO diet (ED; 5% FM, 5% FO). Next-generation sequencing analysis of gut mucosa and digesta revealed no significant differences in alpha or beta diversity among different dietary groups. Firmicutes dominated all samples, particularly Bacilli, Mycoplasmatales, Mycoplasmataceae, and Mycoplasma. Significant differences were only observed in low-abundance taxa (<1%), with higher abundance of Thermoactinomycetales (p = 7.71 × 10−4), Thermoactinomycetaceae (p = 7.71 × 10−4), Kroppenstedtia (p = 1.70 × 10−3), and Pseudogracilibacillus (p = 0.039) in challenged groups. This study highlights the potential of low-abundance microbial groups as targets to establish gut health biomarkers in fish. Full article
(This article belongs to the Special Issue Fish Microbiome, a Novel Tool to Improve Sustainable Production and Welfare in Aquaculture)
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23 pages, 3309 KB  
Article
Autochthonous and Allochthonous Gut Microbes May Work Together: Functional Insights from Farmed Gilthead Sea Bream (Sparus aurata)
by Alvaro Belenguer, Federico Moroni, Fernando Naya-Català, Paul George Holhorea, Ricardo Domingo-Bretón, Josep Àlvar Calduch-Giner and Jaume Pérez-Sánchez
Animals 2026, 16(3), 360; https://doi.org/10.3390/ani16030360 - 23 Jan 2026
Viewed by 928
Abstract
In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the [...] Read more.
In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the anterior and posterior intestine of farmed gilthead sea bream and evaluated the resident microbiome at 24 and 48 h post-feeding. Microbial DNA was sequenced using the Oxford Nanopore Technology platform. Data were analyzed through statistical and discriminant approaches, as well as a Bayesian network framework to assess bacterial interactions. Transient communities showed higher richness and diversity, regardless of intestinal section, suggesting a more specialized and stable microbial environment in the mucus layer. The two communities differed markedly in structure and composition. Variations associated with intestinal region were less pronounced, particularly for autochthonous bacteria, and post-feeding fluctuations in the resident microbiome were minimal. Functionally, results indicated relevant synergies between communities. Protein metabolism pathways were enriched in autochthonous bacteria, whereas allochthonous microorganisms contributed mainly to bile acid and carbohydrate metabolism. Overall, resident and transient bacteria constitute distinct communities in the gut of gilthead sea bream, with numerous genera present in both but most being differentially represented and interconnected. Full article
(This article belongs to the Special Issue Fish Microbiome, a Novel Tool to Improve Sustainable Production and Welfare in Aquaculture)
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21 pages, 1838 KB  
Article
Effects of Short-Term Feeding with Diets Containing Insect Meal on the Gut Microbiota of African Catfish Hybrids
by Balázs Libisch, Zsuzsanna J. Sándor, Tibor Keresztény, Chioma Lilian Ozoaduche, Péter P. Papp, Katalin Posta, Janka Biró, Viktor Stojkov, Vojislav Banjac, Nóra Adányi, Mária Berki, Éva Lengyel-Kónya, Rita Tömösközi-Farkas and Ferenc Olasz
Animals 2025, 15(9), 1338; https://doi.org/10.3390/ani15091338 - 6 May 2025
Cited by 4 | Viewed by 2298
Abstract
The impact of short-term feeding of three distinct diets containing insect meals on the intestinal microbiota of African catfish hybrid (Clarias gariepinus × Heterobranchus longifilis) juveniles was examined. The animals received experimental diets containing 30% insect meals derived from black soldier-fly [...] Read more.
The impact of short-term feeding of three distinct diets containing insect meals on the intestinal microbiota of African catfish hybrid (Clarias gariepinus × Heterobranchus longifilis) juveniles was examined. The animals received experimental diets containing 30% insect meals derived from black soldier-fly larvae (BSL) (Hermetia illucens), yellow mealworm (Tenebrio molitor) or blue bottle-fly larvae (Calliphora vicina) for 18 days. The relative abundance of the Bacillaceae, the Planococcaceae and other bacteria significantly increased (p < 0.05) in the intestinal microbiota of the BSL group and also in the pooled group of the three catfish groups that received insect meals. Several strains of the Bacillales cultured from BSL feed had higher (p < 0.05) abundance in the intestinal microbiota of the BSL group compared to those of the control group. Among these Bacillales strains, a single fosB antibiotic resistance gene was identified. In the gut resistomes of both the BSL and the control catfish groups, the tetA(P), tetB(P) and lnu(C) antibiotic-resistance determinants were detected, while fosB was detected only in the BSL group. Overall, the study showed that a short-term shift to diets containing insect meals can induce significant (q < 0.05) changes in the gut microbiota of the African catfish without the development of reduced α-diversity and without the overgrowth of bacteria pathogenic to fish. Full article
(This article belongs to the Special Issue Fish Microbiome, a Novel Tool to Improve Sustainable Production and Welfare in Aquaculture)
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