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Gut Microbiota in Aquatic Animals Nutrition, Immunity, and Host–Microbe Interactions
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Gut Microbiota in Aquatic Animals Nutrition, Immunity, and Host–Microbe Interactions

A special issue of Biology (ISSN 2079-7737). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: 15 February 2026 | Viewed by 1763

Special Issue Editor

Prof. Dr. Qunlan Zhou

E-Mail Website
Guest Editor
1. Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi 214081, China
2. Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081 China
Interests: fish immunology; virus; AMPs; toxicology; cell lines; vaccines; aquaculture; biotechnology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Intestinal microbiota play a crucial role in aquatic animals' physiological processes, acting as a "second genome" that regulates nutrition, immunity, and overall health. By participating in energy metabolism, vitamin synthesis, and pathogen defense, gut microbes significantly influence host fitness and adaptation. Advances in high-throughput sequencing and metabolomics have deepened our understanding of host–microbiota relationships, yet key challenges remain—particularly in unraveling mechanistic pathways and developing effective microbial management strategies.

This Special Issue explores the interdisciplinary frontier of gut microbiota in aquatic animals, emphasizing the following:

  • Nutrient utilization mechanisms shaped by microbial communities, enhancing metabolic efficiency;
  • Microbial–immune system crosstalk, offering insights into disease resistance and probiotic applications;
  • Resilience of gut ecosystems under environmental stressors, informing conservation and husbandry practices. 

We welcome original research on topics such as host–microbe coevolution, functional probiotic screening, and multi-omics approaches to decode microbiota dynamics. Contributions may span wild or captive aquatic species, from invertebrates to vertebrates, providing a holistic perspective on microbial roles in aquatic ecosystems.

Prof. Dr. Qunlan Zhou
Guest Editor

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 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 animal health
  • host–microbe interactions
  • functional probiotics
  • immunomodulation
  • nutrient metabolism
  • multi-omics integration
  • microbial ecology
  • environmental adaptation

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Published Papers (2 papers)

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Review

21 pages, 608 KB  
Review
Crosstalk Between Intestinal Microbiota and Host Defense Peptides in Fish
by Xiao-Zheng Yu, Yang Yu and Zi-Yan Liu
Biology 2025, 14(9), 1243; https://doi.org/10.3390/biology14091243 - 11 Sep 2025
Viewed by 628
Abstract
The intricate crosstalk between intestinal microbiota and host defense peptides (HDPs) in aquaculture has emerged as a cornerstone for advancing sustainable disease management and reducing reliance on antibiotics. This review synthesizes current insights into the bidirectional interactions shaping aquatic animal health, where HDPs, [...] Read more.
The intricate crosstalk between intestinal microbiota and host defense peptides (HDPs) in aquaculture has emerged as a cornerstone for advancing sustainable disease management and reducing reliance on antibiotics. This review synthesizes current insights into the bidirectional interactions shaping aquatic animal health, where HDPs, multifunctional immune molecules, directly neutralize pathogens while selectively modulating intestinal microbial communities to favor beneficial taxa (including Lactobacillus, Bacillus, Cetobacterium, Lactococcus, and so on) and suppress harmful species. Conversely, intestinal microbiota regulate HDP expression through microbial-derived signals, such as lipopolysaccharides and metabolites, which activate host immune pathways like Toll-like receptors (TLRs) to amplify innate defenses. This dynamic interplay underpins critical physiological functions, including nutrient absorption, intestinal barrier integrity, and systemic immune homeostasis, offering a dual mechanism to enhance disease resistance and growth performance. Practical applications, such as HDP-enriched feeds and probiotic–HDP synergies, have demonstrated efficacy in reducing mortality and improving productivity across species like shrimp, salmon, and carp. However, challenges such as HDP instability, species-specific variability in peptide efficacy, and the complexity of microbiota–HDP networks hinder broad implementation. Future research must prioritize innovative strategies, including engineered microbial systems for scalable HDP production, multi-omics approaches to unravel interaction mechanisms, and eco-friendly combinatorial therapies integrating HDPs, probiotics, and plant-derived compounds. By bridging immunology, microbiology, and aquaculture science, this field can transition toward antibiotic-free practices, ensuring ecological sustainability and global food security in the face of rising aquatic disease threats and environmental pressures. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals Nutrition, Immunity, and Host–Microbe Interactions)
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30 pages, 723 KB  
Review
Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications
by Tsireledzo Goodwill Makwarela, Nimmi Seoraj-Pillai and Tshifhiwa Constance Nangammbi
Biology 2025, 14(8), 1086; https://doi.org/10.3390/biology14081086 - 20 Aug 2025
Cited by 1 | Viewed by 892
Abstract
Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an [...] Read more.
Mollusks are among the most ecologically and economically significant invertebrates; yet, their associated microbiomes remain understudied relative to those of other metazoans. This scoping review synthesizes the current literature on the diversity, composition, functional roles, and ecological implications of molluscan microbiomes, with an emphasis on three major groups: gastropods, bivalves, and cephalopods. Drawing on studies from terrestrial, freshwater, and marine systems, we identified the dominant bacterial phyla, including Proteobacteria, Bacteroidetes, and Firmicutes, and explored how microbiota vary across different habitats, diets, tissue types, and host taxonomies. We examined the contribution of molluscan microbiomes to host functions, including digestion, immune modulation, stress responses, and nutrient cycling. Particular attention was given to the role of microbiota in shell formation, pollutant degradation, and adaptation to environmental stressors. The review also evaluated microbial interactions at different developmental stages and under aquaculture conditions. Factors influencing microbiome assembly, such as the host’s genetics, life history traits, and environmental exposure, were mapped using conceptual and graphical tools. Applications of molluscan microbiome research in aquaculture, conservation biology, and environmental biomonitoring are highlighted. However, inconsistencies in the sampling methods, taxonomic focus, and functional annotations limit the generalizability across taxa. We identify key knowledge gaps and propose future directions, including the use of meta-omics, standardized protocols, and experimental validation to deepen insights. By synthesizing emerging findings, this review contributes to a growing framework for understanding mollusk–microbiome interactions and their relevance to host fitness and ecosystem health. It further establishes the importance of mollusks as model systems for advancing microbiome science. Full article
(This article belongs to the Special Issue Gut Microbiota in Aquatic Animals Nutrition, Immunity, and Host–Microbe Interactions)
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