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Microorganisms
Special Issues
Microbiome in Fish and Their Living Environment, Second Edition
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Microbiome in Fish and Their Living Environment, Second Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1259

Special Issue Editors

Dr. Yongjun Chen

E-Mail Website
Guest Editor
College of Fisheries, Southwest University, Chongqing, China
Interests: carbohydrate utilization; glycolipid metabolism; liver health; feed additives; fish species
Special Issues, Collections and Topics in MDPI journals
Dr. Gang Yang

E-Mail Website
Guest Editor
Department of Fisheries Science, School of Life Science, Nanchang University, Nanchang 330031, China
Interests: aquaculture nutrition; feed additives; intestinal microbiota; immunology; fish physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our 2025 Special Issue “Microbiome in Fish and Their Living Environment”.

Over the past few decades, aquaculture has emerged as one of the fastest-growing food-producing sectors, playing a crucial role in providing high-quality protein for humans. Globally, total aquaculture production reached 130.9 million tons in 2022, with fish accounting for 53% of this total. Thus, fish farming plays a vital role in the global aquaculture industry. Fish are the most diverse group of vertebrates, and there are huge quantities of microorganisms in the gut of fish. Fish immunity can shape the intestinal microbiota and maintain intestinal homeostasis. Additionally, the intestinal microbiome can control the proliferation of pathogenic microorganisms and regulate fish immunity. Dietary composition (nutrient balance and the inclusion of probiotics, prebiotics, postbiotics, and other feed additives) has a significant impact on the microbiomes in fish gut and their living environment, thereby regulating intestinal health and disease resistance. In this collection, we particularly welcome papers that provide insights into the effects of dietary input on the gut microbiome of fish, interactions between gut microbiomes and fish immunity, and interactions between the gut microbiomes of fish and their living environment.

Dr. Yongjun Chen
Dr. Gang Yang
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. Microorganisms is an international peer-reviewed open access monthly 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

  • fish species
  • gut microbiome
  • dietary modification
  • water environment
  • immunity

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

16 pages, 3889 KB  
Article
Diet-Induced Modulation of Gut Microbiota Affects Meat Quality in Grass Carp (Ctenopharyngodon idellus)
by Weiting Chen, Yuqin Fan, Yazhi Huang, Junbao He and Xiongjun Liu
Microorganisms 2026, 14(2), 504; https://doi.org/10.3390/microorganisms14020504 - 20 Feb 2026
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Abstract
Understanding meat quality and gut microbiota hold great potential for promoting healthy and sustainable fish production, while also contributing to fisheries management and conservation. However, differences in meat quality and the diversity, structure, and function of gut microbiota among fish across different feeding [...] Read more.
Understanding meat quality and gut microbiota hold great potential for promoting healthy and sustainable fish production, while also contributing to fisheries management and conservation. However, differences in meat quality and the diversity, structure, and function of gut microbiota among fish across different feeding regimes remain poorly understood. This study compared meat quality and gut microbiota between grass carp (gc) and crisped grass carp (cgc) to support sustainable aquaculture and provide more tasted fish meat. Cgc exhibited higher levels of free amino acids, fatty acids, and collagen, whereas gc had greater concentrations of hydrolyzed amino acids, nucleotides, and antioxidant indices. Fatty acid composition differed significantly between the two. Gut microbiota diversity was higher in cgc, with Proteobacteria, Fusobacteriota, and Firmicutes being dominant, while gc was dominated by Proteobacteria, Bacteroidota, and Firmicutes. The microbial community structures differed significantly. Functional predictions showed 1612 COG and 2032 KEGG pathways varied between groups. Significant correlations were found between microbial abundance and meat quality traits, including fatty acids, hydrolyzed amino acids, and collagen. These findings offered valuable insights for enhancing fish nutrition, optimizing feed formulations, and improving aquaculture practices. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment, Second Edition)
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19 pages, 8166 KB  
Article
TMAO Supplementation to High-Carbohydrate Diet Reprogrammed Hepatic Metabolism and Intestinal Microbiota to Improve Liver Health and Disease Resistance of Micropterus salmoides
by Weijun Tang, Yan Lei, Linyuan Jiang, Huijuan Ren, Shambel Boki, Xinyue Du, Kexin Xiong, Shihao Liu, Yaoqiang Yue and Qingchao Wang
Microorganisms 2026, 14(2), 284; https://doi.org/10.3390/microorganisms14020284 - 26 Jan 2026
Viewed by 516
Abstract
This study aimed to evaluate the effects of trimethylamine oxide (TMAO) supplementation (0.5% and 1%) to a high-carbohydrate diet on the growth performance, liver health, hepatic metabolome, intestinal microbiota and disease resistance of largemouth bass (Micropterus salmoides). After an eight-week feeding [...] Read more.
This study aimed to evaluate the effects of trimethylamine oxide (TMAO) supplementation (0.5% and 1%) to a high-carbohydrate diet on the growth performance, liver health, hepatic metabolome, intestinal microbiota and disease resistance of largemouth bass (Micropterus salmoides). After an eight-week feeding trial with three replicates, fish fed with TMAO-supplemented diets showed growth-promoting potential with increased difference with a prolonged rearing period. Importantly, TMAO supplementation significantly improved liver structure and function, with reduced intrahepatic glycogen accumulation due to reprogrammed glycogen metabolism, including down-regulated gys2 and ugp2b but up-regulated pygl expression levels. Targeted liver metabolomics analysis indicated the enhanced synthesis of long-chain fatty acid and amino acid in the 1% TMAO group, accompanied by decreased cortisol, indicating the attenuation of the stress response. Furthermore, TMAO supplementation changed the structure of the intestinal microbiota and particularly the intestinal content of Romboutsia, an important probiotic that can effectively utilize different kinds of dietary carbohydrate, showed an increasing trend with the increased TMAO supplementation levels. Finally, after sampling, all remaining fish were challenged with Nocardia seriolae. TMAO supplementation significantly enhanced the immune clearance function of largemouth bass against invading N. seriolae, with alleviated granulomatous nodules within liver but enhanced hepatic expression levels of nlrp3, caspase1, il-1β and il-18. These results collectively underscore the finding that TMAO may promote intestinal Romboutsia growth and reprogram hepatic metabolism to improve liver health, giving TMAO potential as a feed additive for growth and health promotion in largemouth bass. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment, Second Edition)
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