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Animals
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Gut Microbiota in Aquatic Animals
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Gut Microbiota in Aquatic Animals

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

Deadline for manuscript submissions: 28 February 2026 | Viewed by 18118

Special Issue Editors

Dr. Gabriella do Vale Pereira

E-Mail Website
Guest Editor
SPAROS Lda, Olhao, Portugal
Interests: fish microbiome; nutrition; fish intestinal health; aquatic animals; sustainable aquaculture
Dr. Fernando Yugo Yamamoto

E-Mail Website
Guest Editor
Thad Cochran National Warmwater Aquaculture Center, Mississippi Agriculture and Forestry Experiment Station, Mississippi State University, Stoneville, MS, USA
Interests: fish nutrition; intestinal health; intestinal microbiome; fish immunology; alternative ingredients
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbiome research in aquatic animals is vital for understanding the intricate balance between hosts (aquatic animals) and their interactions with bacteria. The gut microbiome for instance, plays a crucial role in the digestion, nutrient absorption, immune function and overall health of aquatic species. By unraveling the complexities of these microbial communities, researchers can develop targeted interventions to enhance growth, disease resistance and sustainability in aquaculture systems. Understanding the microbiome allows for the optimization of feed formulations, management practices and environmental conditions, leading to improved production efficiency and reduced environmental impact. In essence, microbiome studies pave the way for innovation and advancement in the field of aquaculture.

This Special Issue of the journal Animals aims to explore the intricate relationship between nutrition, physiology, environmental and intestinal microbiota in aquatic animals’ production. The scope of this issue encompasses various aspects, including the impact of nutrition on microbiota development and the consequent host–microbe interactions. It delves into different stages of aquatic animal production, ranging from larvae, juveniles and outgrowth phase. The primary goal is to elucidate the dynamic interplay between feeding practices, physiological responses and gut microbiota composition, with a keen focus on their implications for animal health and production efficiency. The key objectives include enhancing production outcomes, optimizing feed conversion ratios and minimizing antibiotic usage through the strategic modulation of host and environmental interactions. This Special Issue will feature a blend of comprehensive reviews and original research papers, offering valuable insights into the optimization of aquatic animal production systems.

Dr. Gabriella do Vale Pereira
Dr. Fernando Yugo Yamamoto
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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

  • gut microbiota
  • aquatic animals
  • nutrition
  • physiology
  • host–microbe interaction
  • production efficiency
  • feed conversion ratio
  • antibiotics

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Published Papers (6 papers)

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Research

Jump to: Review

17 pages, 6183 KB  
Article
Intestinal Development Patterns and Gut Microbiota Colonization Dynamics in Sichuan Bream (Sinibrama taeniatus)
by Shixia Huang, Qiang Zhao, Chao Deng, Yuexin Sun, Xiao Yang, Shilin Li, Tianzhi Jin, Zhe Zhao, Kaixuan Liu, Qilin Feng, Hailong Ge, Zhijian Wang and Fang Li
Animals 2025, 15(23), 3431; https://doi.org/10.3390/ani15233431 - 28 Nov 2025
Viewed by 494
Abstract
Sichuan bream (Sinibrama taeniatu), an endemic small economic fish in the upper Yangtze River, has achieved captive breeding breakthroughs. To advance standardized and large-scale aquaculture, this study investigated intestinal development, enzyme activities, gut microbiota, and its interactions with rearing water microbiota [...] Read more.
Sichuan bream (Sinibrama taeniatu), an endemic small economic fish in the upper Yangtze River, has achieved captive breeding breakthroughs. To advance standardized and large-scale aquaculture, this study investigated intestinal development, enzyme activities, gut microbiota, and its interactions with rearing water microbiota across six developmental stages (G1–G6) from hatching to sexual maturity of Sichuan bream. Results showed its progressive refinement of external morphology and intestinal developing into multiple flexures. Histology examination revealed four foregut layers with continuously increasing villus height. Digestive enzyme analysis revealed significantly higher activity of trypsin compared to that of amylase and lipase (p < 0.05). 16S rRNA sequencing identified Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Fusobacteria as the dominant phyla in both gut and rearing water microbiota. Gut communities shifted from Proteobacteria-dominance (C1–C5) to Firmicutes-dominance (C6). The microbial source tracking analysis indicated water contributed to gut microbiota of Sichuan bream, particularly during G3. This study clarified the intestinal development patterns and gut microbiota colonization dynamics of Sichuan bream. The findings provide reference materials for the research on the growth patterns and host–microbe interaction of Sichuan bream. They lay a theoretical foundation for the protection and utilization of Sichuan bream resources, ultimately aiding in their proliferation and release. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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28 pages, 5330 KB  
Article
In Vitro and In Vivo Evaluation of Autochthonous Probiotics and Their Effects on the Mucosal Health of Nile Tilapia (Oreochromis niloticus)
by Sherilyn T. Abarra, Sahya Maulu, Sheu G. Odu-Onikosi, Taofik A. Momoh, Benjamin Eynon, Matthew Emery, Mark Rawling and Daniel L. Merrifield
Animals 2025, 15(22), 3296; https://doi.org/10.3390/ani15223296 - 15 Nov 2025
Viewed by 2907
Abstract
The host microbiome is a promising source of probiotics for aquaculture species including Nile tilapia. In this study, the probiotic potential of autochthonous bacterial isolates from Nile tilapia and carp mid-intestines were screened in vitro. Two isolates (C61 and T70), closely related [...] Read more.
The host microbiome is a promising source of probiotics for aquaculture species including Nile tilapia. In this study, the probiotic potential of autochthonous bacterial isolates from Nile tilapia and carp mid-intestines were screened in vitro. Two isolates (C61 and T70), closely related to Bacillus subtilis, exhibited antagonistic activity against multiple pathogen species and demonstrated multiple digestive enzyme activities. Their antagonistic activity in Aeromonas hydrophila assays remained even under simulated intestinal juice (SIJ) exposure. Subsequently, C61 (PT1) and T70 (PT2) were added to experimental diets at log 7 CFU/g of diet, and fed to Nile tilapia (5.32 ± 0.12 g) for 40 days. There were no significant differences observed in the growth performance across treatments. Despite limited Bacillus intestinal recovery levels, 16S rRNA gene metabarcoding revealed subtle shifts in the intestinal microbial community composition of the probiotic-fed groups. In addition, the PT1 group showed significantly longer mucosal fold length, elevated intestinal and skin goblet cell levels, and higher skin goblet cell coverage compared to the control. These results indicate the potential benefits of the isolates as functional feed additives for enhancing the mucosal health of Nile tilapia, but their benefits were likely achieved through transient activity given the low level of Bacillus recovery in the intestine. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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22 pages, 3331 KB  
Article
One Function, Many Faces: Functional Convergence in the Gut Microbiomes of European Marine and Freshwater Fish Unveiled by Bayesian Network Meta-Analysis
by Federico Moroni, Fernando Naya-Català, Genciana Terova, Ricardo Domingo-Bretón, Josep Àlvar Calduch-Giner and Jaume Pérez-Sánchez
Animals 2025, 15(19), 2885; https://doi.org/10.3390/ani15192885 - 2 Oct 2025
Cited by 2 | Viewed by 1030
Abstract
Intestinal microbiota populations are constantly shaped by both intrinsic and extrinsic factors, including diet, environment, and host genetics. As a result, understanding how to assess, monitor, and exploit microbiome–host interplay remains an active area of investigation, especially in aquaculture. In this study, we [...] Read more.
Intestinal microbiota populations are constantly shaped by both intrinsic and extrinsic factors, including diet, environment, and host genetics. As a result, understanding how to assess, monitor, and exploit microbiome–host interplay remains an active area of investigation, especially in aquaculture. In this study, we analyzed the taxonomic structure and functional potential of the intestinal microbiota of European sea bass and rainbow trout, incorporating gilthead sea bream as a final reference. The results showed that the identified core microbiota (40 taxa for sea bass and 20 for trout) held a central role in community organization, despite taxonomic variability, and exhibited a predominant number of positive connections (>60% for both species) with the rest of the microbial community in a Bayesian network. From a functional perspective, core-associated bacterial clusters (75% for sea bass and 81% for sea bream) accounted for the majority of predicted metabolic pathways (core contribution: >75% in sea bass and >87% in trout), particularly those involved in carbohydrate, amino acid, and vitamin metabolism. Comparative analysis across ecological phenotypes highlighted distinct microbial biomarkers, with genera such as Vibrio, Pseudoalteromonas, and Paracoccus enriched in saltwater species (Dicentrarchus labrax and Sparus aurata) and Mycoplasma and Clostridium in freshwater (Oncorhynchus mykiss). Overall, this study underscores the value of integrating taxonomic, functional, and network-based approaches as practical tools to monitor intestinal health status, assess welfare, and guide the development of more sustainable production strategies in aquaculture. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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15 pages, 8313 KB  
Article
Seasonal and Regional Dynamics of the Intestinal Microbiota in Schizothorax nukiangensis from the Nujiang River
by Fengyue Zhu, Jie Ma, Mingyang Xue, Weitong Xu, Wenzhi Liu, Yong Zhou, Mingdian Liu and Yuding Fan
Animals 2025, 15(7), 961; https://doi.org/10.3390/ani15070961 - 27 Mar 2025
Cited by 1 | Viewed by 878
Abstract
The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected [...] Read more.
The dynamic alterations in intestinal microbiota can provide insights into the adaptive relationships between these microorganisms and their hosts in response to environmental changes. Schizothorax nukiangensis is widely distributed throughout the Nujiang River and exhibits numerous unique adaptations. In this study, we collected samples of S. nukiangensis across different seasons and regions within the Nujiang River to comprehensively elucidate the diversity and composition of its intestinal microbiota using metagenomic technology. The results indicated that Firmicutes and Proteobacteria predominated at the phylum level, while Priestia, Bacillus, and Aeromonas were the most abundant genera identified. Notably, the relative abundance of these microorganisms varied significantly across different seasons and regions. From autumn through spring and into summer, the predominant microorganisms shifted from Firmicutes to Proteobacteria. Biomarker analysis revealed that Firmicutes (including the class bacilli and the genera Priestia and Bacillus) exhibited a higher relative abundance within the upstream group, where categories related to amino acid metabolism and carbohydrate metabolism were significantly enriched. Conversely, Proteobacteria (including several potential pathogens, such as Saezia, Pantoea, Lelliotia, and Aeromonas genera) showed an increased relative abundance within downstream groups, where disease-related categories exhibited significant enrichment. Our findings significantly enhance our understanding of how S. nukiangensis adapts to its environment, providing valuable data support for the conservation of S. nukiangensis and for ecological security assessment of the Nujiang River. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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26 pages, 4136 KB  
Article
Impact of Autolysed Brewer’s Yeast and Soluble Dried Yeast Extract on Growth Performance and Mucosal Health of Atlantic Salmon (Salmo salar) Parr
by Sheu G. Odu-Onikosi, Taofik A. Momoh, Sherilyn T. Abarra, Noah E. Wood, Folasade D. Amulejoye, Matthew Emery, Glenn M. Harper, Benjamin Eynon, Victor Kuri, Holger Kühlwein and Daniel L. Merrifield
Animals 2025, 15(3), 323; https://doi.org/10.3390/ani15030323 - 23 Jan 2025
Cited by 2 | Viewed by 3054
Abstract
Yeast-based feed additives have emerged as promising functional feed additives (FFAs) to promote sustainable aquaculture development through enhanced gut health and immune modulation in fish. The present study evaluated the impact of autolysed brewer’s yeast (ABY) and soluble dried yeast extract (SDYE) in [...] Read more.
Yeast-based feed additives have emerged as promising functional feed additives (FFAs) to promote sustainable aquaculture development through enhanced gut health and immune modulation in fish. The present study evaluated the impact of autolysed brewer’s yeast (ABY) and soluble dried yeast extract (SDYE) in improving the intestinal and skin histology, immune response, and intestinal microbiome of Atlantic salmon parr (Salmo salar) over a 9-week feeding trial. Three experimental diets were produced: a control diet, a diet supplemented with ABY at 2.5 g/kg, and a diet supplemented with SDYE at 2.5 g/kg. These diets were administered to triplicate tanks of Atlantic salmon. The yeast-supplemented diets, especially ABY, improved intestinal mucosal fold length, lamina propria width, microvilli density, and intestinal goblet cell counts, as well as skin goblet cell counts. The yeast additives had no detrimental effects on the fish haematology, with no significant differences in haemoglobin concentration, red blood cell counts, and white blood cell counts among the treatment groups. Gene expression analysis revealed upregulation of il-1β and muc-2 in fish fed the ABY diet, indicating enhanced immune function and potentially mucosal protection. Intestinal microbiota analysis revealed Firmicutes as the most dominant phylum in all groups, followed by Actinobacteriota. Distinct bacterial community shifts were observed between the treatment groups, with a significant increase in the relative abundance of taxa such as Staphylococcus in yeast-supplemented diets and a significant decrease in Streptococcus and Weissella. Collectively, these findings suggest that the yeast additives, especially ABY, enhance gut health and immune function without compromising growth performance. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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Review

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31 pages, 432 KB  
Review
Promising Probiotic Candidates for Sustainable Aquaculture: An Updated Review
by Seyed Hossein Hoseinifar, Mehwish Faheem, Iram Liaqat, Hien Van Doan, Koushik Ghosh and Einar Ringø
Animals 2024, 14(24), 3644; https://doi.org/10.3390/ani14243644 - 17 Dec 2024
Cited by 11 | Viewed by 8527
Abstract
With the intensification of aquaculture to meet the rising demands of fish and shellfish, disease outbreaks during the larval and adult stages are a major challenge faced by aqua culturists. As the prophylactic use of vaccines and antibiotics has several limitations, research is [...] Read more.
With the intensification of aquaculture to meet the rising demands of fish and shellfish, disease outbreaks during the larval and adult stages are a major challenge faced by aqua culturists. As the prophylactic use of vaccines and antibiotics has several limitations, research is now focused on sustainable alternatives to vaccines and antibiotics, e.g., medicinal plants, probiotics, postbiotics, prebiotics, and synbiotics, as promising candidates to strengthen the immune response of fish and shellfish and to control disease outbreaks. With respect to probiotics, numerous studies are available revealing their health-promoting and beneficial impacts in aquaculture. However, most studies focus on Bacillus and Lactobacillus species. Keeping in view the positive effects of probiotic lactic acid bacteria in aquaculture, researchers are now looking for other probiotic bacteria that can be used in aquaculture. Recently, many non-lactic acid bacteria (non-LAB), which are mainly host-associated, have been reported to reveal beneficial effects in fish and shellfish aquaculture. The main non-LAB probiotic genera are Bifidobacterium, Clostridium, Microbacterium, Micrococcus, Paenibacillus, Acinetobacter, Alcaligenes, Enterobacter, Phaeobacter Pseudoalteromonas, Pseudomonas, Pseudomonas, and Vibrio. Despite the promising effects of non-LAB probiotics, comparably, there is limited available information in this context. This review focuses only on probiotic strains that are non-LAB, mostly isolated from the host digestive tract or rearing water, and discusses their beneficial effects in fish and shellfish aquaculture. This review will provide detailed information on the use of various non-LAB bacteria and provide a roadmap to future studies on new probiotics for sustainable aquaculture. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals)
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