Microbial Communities and Host Immunity for Resilient and Sustainable Aquaculture

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

Deadline for manuscript submissions: 31 October 2026 | Viewed by 1109

Editor


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Guest Editor
National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathum Thani, Thailand
Interests: shrimp gut microbiome; host–microbial interactions; multi-omics plat-forms; immunostimulants

Special Issue Information

Dear Colleagues,

As global demand for aquatic food products increases, the aquaculture industry faces a critical challenge. The sector must sustain intensive production outputs while simultaneously navigating the pressures of a changing climate and emerging disease threats. Achieving food security requires understanding of the microorganisms underpinning the health of fish, shellfish, and other aquatic invertebrates.

This Special Issue explores the role of microbial communities in aquaculture. We invite original research, reviews, and short communications ranging from foundational microbiome profiling to mechanistic studies on immunomodulation. We aim to understand how these communities establish, evolve, and can be leveraged to optimize disease resistance and production.

Topics of interest include, but are not limited to, the following:

  • Microbial diversity: Baseline characterization and comparative analysis across developmental stages and environment.
  • Microbiome modulation: The application of probiotics, prebiotics, synbiotics, and postbiotics in functional aquafeeds.
  • Host–microbe interactions: Mechanisms of immunomodulation and mucosal health across the gut, skin, and gills.
  • Environmental resilience: Microbial adaptation strategies in response to climate change, thermal stress, and water quality fluctuations.
  • Disease control: Novel alternatives to antibiotics, including phage therapy and quorum sensing inhibition.
  • Sustainable systems: Microbial ecology within Recirculating Aquaculture Systems (RASs), biofloc technologies, and open-water systems.

Dr. Wanilada Rungrassamee
Guest Editor

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Keywords

  • aquaculture
  • microbiome
  • probiotics
  • functional feeds
  • host immunity
  • disease
  • shrimp
  • fish
  • shellfish

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Published Papers (2 papers)

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Research

17 pages, 5230 KB  
Article
Host-Associated and Environmental Microbiota of Hatchery-Reared Sichuan Taimen (Hucho bleekeri): Community Structure and Functional Profiling
by Qinyao Wei, Yeyu Chen, Huanchao Yang, Jun Du, Hua Li and Zhaobin Song
Animals 2026, 16(13), 2089; https://doi.org/10.3390/ani16132089 - 6 Jul 2026
Viewed by 360
Abstract
The diversity and complexity of symbiotic microbiota in fish may significantly influence the host’s physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the [...] Read more.
The diversity and complexity of symbiotic microbiota in fish may significantly influence the host’s physiological, metabolic and immunological functions. In order to understand the microbial assembly in Sichuan taimen (Hucho bleekeri), an endangered fish species in the upper reaches of the Yangtze River, the microbiota of the skin, oral cavity and feces of artificially reared individuals and the microbiota of the rearing water were characterized through metagenomic sequencing. The results demonstrated that Pseudomonadota were shared across the skin, oral cavity, feces and rearing water, suggesting that they may constitute a shared microbial group connecting the aquatic environment and host mucosal surfaces. Based on functional prediction analyses, these taxa were potentially associated with organic matter degradation, nutrient cycling, and microbial and immune homeostasis. Likewise, Actinomycetota and Bacillota were consistently detected across multiple mucosal tissues and were predicted to be associated with nutrient transformation, antimicrobial defense, and the maintenance of mucosal microbial stability. Fusobacteriota were detected solely in feces, suggesting a strong tissue-specific colonization capacity. The alpha diversity of the microbiota did not differ significantly among tissues, and the beta diversity revealed strong clustering of host-associated samples and clear separation from water samples. Functional annotation further revealed that the water microbiota exhibited broader yet more dispersed functional potential, whereas host-associated microbiota showed stronger functional specialization closely aligned with host physiological demands. Collectively, the findings are better presented as baseline information for future comparative and hypothesis-driven studies in Sichuan taimen. Full article
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14 pages, 5956 KB  
Article
Setup of a Simple and Cost-Effective pH-Sensitive Assay to Evaluate Phagocytosis in Rainbow Trout (Oncorhynchus mykiss) Peripheral Blood Leukocytes
by Teresina De Iorio, Maria Carmela Scatà, Arianna Martini, Marco Martinoli, Riccardo Napolitano, Nicolò Tonachella, Domitilla Pulcini and Fabrizio Capoccioni
Animals 2026, 16(12), 1760; https://doi.org/10.3390/ani16121760 - 6 Jun 2026
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Abstract
Phagocytosis in vitro assays are widely used to assess the health status of fish, since it may be affected by diseases and environmental factors. To date, studies have evaluated phagocytosis in fish by observing fluorescent beads or bacteria engulfed by phagocytes. However, particles [...] Read more.
Phagocytosis in vitro assays are widely used to assess the health status of fish, since it may be affected by diseases and environmental factors. To date, studies have evaluated phagocytosis in fish by observing fluorescent beads or bacteria engulfed by phagocytes. However, particles adhering to the external surface of the phagocyte membrane cannot be easily distinguished from those that are truly internalized. This work aimed to: (1) test whether a pHrodo™ (pHR)-based method improves the accuracy of phagocytosis detection compared to traditional assays; (2) evaluate the influence of opsonization, incubation time, and temperature on the phagocytosis ability of rainbow trout (Oncorhynchus mykiss) peripheral blood leukocytes (PBLs). Opsonization increased the PBLs’ phagocytic activity. To evaluate the effects of incubation time and temperature on PBL phagocytosis ability, 30% autologous plasma was used. Leukocytes incubated at 16 °C for 2 h showed a significantly higher (p < 0.05; H = 45.43) percentage of phagocytic cells. This incubation setting also resulted in increased pHR-related fluorescence intensity (p < 0.05; F = 58.39), directly proportional to the number of phagocytosed particles. These findings indicate that opsonization enhances phagocytic ability and capacity, and that a 2 h incubation at 16 °C may be recommended for future large-scale studies aimed at evaluating innate immune function in rainbow trout. Full article
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