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Biology
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Intestinal Health of Aquatic Animals
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Intestinal Health of Aquatic Animals

A Special Issue of Biology (ISSN 2079-7737) belonging to the section "Marine and Freshwater Biology".

Deadline for manuscript submissions: 31 July 2027 | Viewed by 1372

Editor

Dr. Yafei Duan

E-Mail Website
Guest Editor
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: environmental stress; aquatic toxicology; pollutants; intestine microbiota; nutritional immunity; multiomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The intestine is the core organ for digestion, absorption, and immune defense in aquatic animals, hailed as the “first line of health defense”. The maintenance of intestinal health relies on an intact mucosal barrier, a stable microbial community, and normal local immune function, which collectively ensure efficient nutrient conversion in the intestine and disease resistance of the host. However, stressors such as fluctuations in the aquaculture environment, pathogenic infections, and adverse feed components are prone to damaging the intestinal barrier and disrupting the microbial community balance. Once intestinal health is impaired, it can induce enteritis, dysbiosis, and decreased barrier function in the host, thereby reducing growth performance and weakening stress resistance. Therefore, deciphering the mechanisms underlying the effects of stressors on the intestinal health of aquatic animals and developing precise nutritional strategies for intestinal health regulation are of great significance for improving the stress resistance of aquatic animals and aquaculture benefits.

This Special Issue sincerely welcomes original research and review articles, with a particular focus on the following areas:

  1. Effects of harmful factors on the intestinal health of aquatic animals;
  2. Regulatory strategies for intestinal health in aquatic animals;
  3. Resource exploration and application of intestinal microbial and metabolites in aquatic animals.

Dr. Yafei Duan
Guest Editor

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-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biology 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 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

  • aquatic animals
  • intestinal health
  • mucosal barrier
  • intestinal microbial
  • microbiota balance
  • host-microbe interaction
  • immune defense
  • metabolites
  • nutritional regulation
  • omics

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Published Papers (2 papers)

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Research

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24 pages, 25089 KB  
Article
Regional Variation in Gut Microbial Community Structure and Predicted Phenotypic Characteristics of Farmed Large Yellow Croaker (Larimichthys crocea)
by Ling Lin, Wangyang Jin, Huijuan Wang, Xiaojun Yan, Lihua Jiang and Shun Chen
Biology 2026, 15(17), 1463; https://doi.org/10.3390/biology15171463 - 27 Aug 2026
Viewed by 290
Abstract
Large yellow croaker (Larimichthys crocea) is an economically important marine fish species in China, yet regional variation in its gut microbial community structure and functional characteristics remains insufficiently understood. This study aimed to characterize and compare the gut microbiota of farmed large [...] Read more.
Large yellow croaker (Larimichthys crocea) is an economically important marine fish species in China, yet regional variation in its gut microbial community structure and functional characteristics remains insufficiently understood. This study aimed to characterize and compare the gut microbiota of farmed large yellow croaker across five representative aquaculture regions. Intestinal microbial communities were characterized using 16S rRNA gene sequencing, followed by analyses of microbial diversity, taxonomic composition, predicted bacterial phenotypes, co-occurrence networks, and environmental associations. The five cultured populations shared a broadly similar microbial community structure dominated by Proteobacteria, Bacteroidota, and Firmicutes, whereas the relative abundance of several dominant taxa varied among regions. Alpha-diversity differences were mainly associated with community evenness and dominance rather than estimated richness. Although regional samples partially overlapped in ordination analyses, the aquaculture region explained 41.4% of the variation in gut microbial composition, indicating significant region-associated differentiation. Predicted microbial characteristics were comparatively similar among cultured populations, despite variation in taxonomic composition, while microbial network organization also differed across regions. Environmental variables showed clearer associations with water microbiota than with gut microbiota, and local aquaculture water represented a detectable but limited potential source of intestinal microorganisms. Overall, farmed large yellow croaker maintained a shared gut microbial community structure but exhibited region-associated variation in community composition and predicted bacterial phenotypes. These findings provide a regional baseline for understanding gut microbial variation in farmed large yellow croaker under different aquaculture conditions. Full article
(This article belongs to the Special Issue Intestinal Health of Aquatic Animals)
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Review

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43 pages, 15802 KB  
Review
Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk
by Zhongquan Jiang, Jiale Chen, Yuanhao Ren, Tingting Lin, Siping Li, Fengyuan Shen, Bo Qin, Lei Li, Changjian Li, Na Ying and Hanfeng Zheng
Biology 2026, 15(13), 1066; https://doi.org/10.3390/biology15131066 - 3 Jul 2026
Viewed by 798
Abstract
The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based [...] Read more.
The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome–mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater–seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG–MGE associations. Risk assessment should therefore move beyond ARG abundance toward host–ARG–MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons. Full article
(This article belongs to the Special Issue Intestinal Health of Aquatic Animals)
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