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Microorganisms
Special Issues
Microbiome in Fish and Their Living Environment
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Microbiome in Fish and Their Living Environment

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 2922

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,

Over the past few decades, aquaculture has emerged as one of the fastest-growing food-producing sectors, playing a crucial role in providing quality protein for human beings. Globally, the total aquaculture production reached 130.9 million tons in 2022, and fish species account for 53% of this amount. 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. The immunity of fish can shape the intestinal microbiota and maintain intestinal homeostasis. Additionally, the intestinal microbiomes can control the abundant proliferation of pathogenic microorganisms and regulate the immunity of fish. Dietary composition (nutrient balance and the inclusion of probiotics, prebiotics, postbiotics and other feed additives) has huge impacts on microbiomes in fish gut and their living environment, thus regulating intestinal health and disease resistance. In this collection, we particularly welcome papers that provide insights on 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 100 words) can be sent to the Editorial Office for announcement on this website.

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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Published Papers (3 papers)

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Research

17 pages, 5545 KiB  
Article
A Comprehensive Investigation of Potential Bacterial Pathogens in Largemouth Bass (Micropterus salmoides)
by Yun-Yao Tu, Qun Lu, Na Zhang, Jie Leng, Qin Yang, Jie Yu, Cheng-Ke Zhu, Tao He, Jian-Yong Hu, Ming-Ji Lv and Song Zhu
Microorganisms 2025, 13(6), 1413; https://doi.org/10.3390/microorganisms13061413 - 17 Jun 2025
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Abstract
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers [...] Read more.
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers on body surface, and petechial hemorrhages in liver. Following isolation and identification, a total of 21 potential bacterial pathogens (numbered strain 1 to 21, respectively) were identified. The genus Aeromonas had the highest proportion (67.14%), among which the frequency of Aeromonas veronii was 24.60%. TEM analysis revealed that the bacterial strains exhibited three predominant shapes (rod-shaped, spherical, and curved) with length ranging from 0.5 to 3 μm. Flagellar structures were observed in strains 1–4, 6–8, 11–17, and 19–21, with variations in number and growth sites. Three isolates (strains 9, 10, 18) demonstrated Gram-positive characteristic, and strains 5, 11, and 18 have capsule structures. Strains 5, 9, 10, and 18 were non-motile, and strains 1–4, 6, 7, 9–11, 16–18, and 21 exhibited β-hemolysis. Physiological and biochemical characteristics of the 21 bacterial isolates were comprehensively analyzed. Antibiotic sensitivity testing revealed that florfenicol and enrofloxacin exhibited excellent antibacterial effects. These data will enrich the potential bacterial diseases information and promote the healthy development of the largemouth bass industry. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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19 pages, 4427 KiB  
Article
Effects of Dietary Clostridium butyricum on Growth and Intestinal Mucosal Barrier Functions of Juvenile Channel Catfish (Ictalurus punctatus)
by Zihe Guo, Ye Qian, Xiao Peng, Chanxia Qin, Huige Ren, Jingyi Du, Chengrui Huang, Mingzhu Pan and Weihao Ou
Microorganisms 2025, 13(5), 1061; https://doi.org/10.3390/microorganisms13051061 - 2 May 2025
Viewed by 486
Abstract
An 8-week feeding trial was conducted to investigate the effects of dietary Clostridium butyricum on the growth and intestinal mucosal barrier functions of juvenile channel catfish (Ictalurus punctatus). The diets included the control group feed (CD group) and the treatment group [...] Read more.
An 8-week feeding trial was conducted to investigate the effects of dietary Clostridium butyricum on the growth and intestinal mucosal barrier functions of juvenile channel catfish (Ictalurus punctatus). The diets included the control group feed (CD group) and the treatment group feed (containing 1 × 108 CFU/g C. butyricum; CB group). The CB group showed a rising trend in the growth performance. The CB group had significantly higher digestive and antioxidant enzyme activities, and significantly lower malondialdehyde and superoxide anion contents of the intestine. In terms of intestinal mechanical barrier, the CB group showed significantly higher gene expression of intestinal tight junction proteins. With regard to intestinal immune barrier, the CB group displayed significantly lower gene expression of pro-inflammatory factors. Regarding intestinal chemical barrier, the CB group had significantly higher gene expression of mucin-4, β-galactoside-binding lectin, lysozyme-c, and NK-lysin type 1. Dietary C. butyricum significantly increased the abundance of some beneficial bacteria and increased the levels of some beneficial metabolites in the intestine. Collectively, dietary C. butyricum could increase growth, enhance intestinal digestion and antioxidant capacity, strengthen intestinal mucosal barrier, and improve the intestinal metabolism of juvenile channel catfish. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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15 pages, 9278 KiB  
Article
Effects of Seawater from Different Sea Areas on Abalone Gastrointestinal Microorganisms and Metabolites
by Zhaolong Li, Ling Ke, Chenyu Huang, Song Peng, Mengshi Zhao, Huini Wu and Fengqiang Lin
Microorganisms 2025, 13(4), 915; https://doi.org/10.3390/microorganisms13040915 - 16 Apr 2025
Viewed by 456
Abstract
Significant regional variations in seawater characteristics (temperature, salinity, pH, nutrients) exist across marine environments, yet their impacts on abalone gastrointestinal microbiota and metabolites remain underexplored. This study investigated seawater nutrient and pH interactions on abalone gut ecosystems through comparative analysis of three marine [...] Read more.
Significant regional variations in seawater characteristics (temperature, salinity, pH, nutrients) exist across marine environments, yet their impacts on abalone gastrointestinal microbiota and metabolites remain underexplored. This study investigated seawater nutrient and pH interactions on abalone gut ecosystems through comparative analysis of three marine regions (Pingtan (PT), Xiapu (XP), Lianjiang (LJ)). Seawater characteristics revealed distinct patterns: LJ exhibited the lowest total phosphorus (TP: 0.12 mg/L), total nitrogen (TN: 2.8 mg/L), NH3-N (0.05 mg/L) but the highest salinity (32.1‰) and lowest pH (7.82), while PT/XP showed elevated nutrients (TP: 0.24–0.28 mg/L; TN: 4.2–4.5 mg/L). Microbial diversity peaked in LJ samples (Shannon index: 5.8) with dominant genera Psychrilyobacter (12.4%) and Bradyrhizobium (9.1%), contrasting with PT’s Mycoplasma-enriched communities (18.7%) and XP’s Vibrio-dominant profiles (14.3%). Metabolomic analysis identified 127 differential metabolites (VIP > 1.5, p < 0.05), predominantly lipids (38%) and organic acids (27%), with pathway enrichment in sulfur relay (q = 4.2 × 10−5) and tryptophan metabolism (q = 1.8 × 10−4). Stomach-specific metabolites correlated with fatty acid degradation (e.g., inosine diphosphate, r = −0.82 with vibrionimonas) and glutathione metabolism (methionine vs. mycoplasma, r = −0.79). Critically, pH showed negative correlations with beneficial Psychrilyobacter (oleamide: r = −0.68) and positive associations with pathogenic Vibrio (trigonelline: r = 0.72). Elevated NH3-N (>0.15 mg/L) and TP (>0.25 mg/L) promoted Mycoplasma proliferation (R2 = 0.89) alongside cytotoxic metabolite accumulation. These findings demonstrate that higher pH (>8.0) and nutrient overload disrupt microbial symbiosis, favoring pathogens over beneficial taxa. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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