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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 5011

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Dr. Yongjun Chen

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College of Fisheries, Southwest University, Chongqing, China
Interests: carbohydrate utilization; glycolipid metabolism; liver health; feed additives; fish species
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Dr. Gang Yang

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Department of Fisheries Science, School of Life Science, Nanchang University, Nanchang 330031, China
Interests: aquaculture nutrition; feed additives; intestinal microbiota; immunology; fish physiology
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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

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Keywords

fish species
gut microbiome
dietary modification
water environment
immunity

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Published Papers (10 papers)

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Research

23 pages, 4569 KiB

Open AccessArticle

Multi-Omics Analysis Provides New Insights into the Interplay Between Gut Microbiota, Fatty Acid Metabolism, and Immune Response in Cultured and Wild Coilia nasus from the Yangtze River Area in China

by Chang Yang, Kai Liu, Yanmin Deng, Qianhui Wang, Shiqian Cao and Qunlan Zhou

Microorganisms 2025, 13(7), 1711; https://doi.org/10.3390/microorganisms13071711 - 21 Jul 2025

Abstract

To elucidate the interactions among fatty acid metabolism, immune status, and gut microbiota, both cultured and wild Coilia nasus from the Yangtze River were examined in China. The results demonstrated that wild C. nasus exhibited markedly higher lipid and docosahexaenoic acid (DHA) contents, a greater ratio of total ω-3 PUFAs to total ω-6 PUFAs, and more active antioxidant enzymes compared to cultured C. nasus. However, the shear force, water-holding capacity, and total n-6 PUFA content were lower in wild C. nasus. Transcriptome analysis revealed distinct gene expression patterns: wild C. nasus upregulated immune-related genes, while cultured C. nasus downregulated genes related to fatty acid metabolism. Significant differences were observed in alpha and beta diversity between cultured and wild groups. LEfSe analysis identified Clostridium_T, Escherichia, and Glutamicibacter as biomarkers for cultured C. nasus, while eight genera, including Pseudomonas_E and Sphingomonas_L, were predominant in wild C. nasus. Modular analysis identified five modules linked to immune functions and fatty acid metabolism. Clostridium_T, Sphingomonas_L, and Pseudomonas_E were dominant in the first two modules, with Pseudomonas_E and Clostridium_T as key regulators of fatty acid metabolism and immune processes. These differences, likely due to gut microbiota variations, provide insights for C. nasus nutritional studies. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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14 pages, 1998 KiB

Open AccessArticle

Effects of Dietary Yeast Culture Supplementation on Growth Performance, Digestive Function, and Intestinal Health of Largemouth Bass Micropterus salmoides

by Zheng Huang, Dingrui Mo, Xifeng Liu, Yuanfa He, Li Luo, Shimei Lin and Yongjun Chen

Microorganisms 2025, 13(7), 1671; https://doi.org/10.3390/microorganisms13071671 - 16 Jul 2025

Viewed by 156

Abstract

This study was performed to investigate the effects of dietary yeast culture (YC) supplementation on growth performance, digestive function, intestinal inflammatory response, and microbiota composition of largemouth bass Micropterus salmoides (LMB). Six diets were formulated with graded levels of YC (0, 5, 10, 15, 20, and 30 g/kg), referred to as CON, YC5, YC10, YC15, YC20, and YC30, respectively. Each diet was assigned to four replicate tanks of LMB juveniles (initial body weight 8.11 ± 0.05 g) with twenty fish per tank. After an 8-week feeding trial, final body weight and specific growth rate showed an increasing trend with 5~20 g/kg YC and reached a maximum at 15 g/kg YC. Feeding ratio decreased, but feed efficiency ratio (FER) improved in response to dietary YC inclusion, and FER was higher in the YC10 fish than in the YC5, YC20, and YC30 fish. Proximate composition (moisture, protein, and lipid) of the whole fish was not affected by dietary YC levels. The activities of intestinal lipase and trypsin were higher in the YC10 fish, while the relative expression of interleukin-8 (il-8) and il-1β was downregulated in the hindgut of the YC15 fish compared with the CON fish. Histological examination showed that the villus height of the midgut, together with goblet cell density of the foregut and midgut, was higher in the YC10 and YC30 fish than in the CON fish. 16S rRNA sequencing showed that Proteobacteria, Fusobacteria, and Firmicutes dominated the intestinal microbiota in LMB. The decrease in harmful Mycoplasma accounted for the dramatic change in Firmicutes abundance, while the increase in Cetobacterium (specifically C. somerae) accounted for the change in Fusobacteria abundance in the gut of the YC10 and YC30 fish compared with the CON fish. The increase in the beneficial Endozoicomonas was the main reason for the change in Proteobacteria abundance in the intestine of the YC30 fish as compared with the CON fish. Taken together, the alteration of intestinal microbiota composition contributed to the improved digestive function and feed utilization in LMB fed YC-supplemented diets. Based on growth performance, the optimal YC level in the diet for LMB was 15 g/kg. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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18 pages, 2892 KiB

Open AccessArticle

Risk of Secondary Bacterial Infections Revealed by Changes in Trachinotus ovatus Skin and Gill Microbiota During a Cryptocaryon irritans Infection Cycle

by Naiqi Liang, Li Zhu, Shifeng Wang, Weihao Zhang, Xinlei Lin, Yongcan Zhou, Haizhu Ke, Shanheng Yuan, Meijing Li and Yan Cai

Microorganisms 2025, 13(7), 1660; https://doi.org/10.3390/microorganisms13071660 - 14 Jul 2025

Viewed by 238

Abstract

This study aims to investigate the response of surface bacterial communities in Trachinotus ovatus to Cryptocaryon irritans infection at different stages of a single infection cycle (0~168 h). These samples were analyzed using high-throughput 16S rRNA sequencing. Alpha diversity analysis showed a reduction in the richness and diversity of skin microbiota during infection, with partial recovery post-detachment. Beta diversity analysis revealed distinct structural shifts in skin microbiota at early (24 h) and post-detachment (168 h) stages compared to other phases, while gill microbiota remained stable except during detachment. At the phylum level, Proteobacteria, Actinobacteriota, Bacteroidetes, and Firmicutes were dominant on the skin at different stages, whereas the gill microbiota was predominantly Proteobacteria (>90%). At the genus level, opportunistic pathogens, such as Vibrio and Nautella, increased in relative abundance on the skin with the infection progression, while gill microbiota composition barely changed. The hepatic bacterial load continued to increase with infection duration. These findings indicate that C. irritans alters microbiota composition on skin, facilitating pathogen invasion, thereby elevating the risk of secondary bacterial infections in T. ovatus. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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18 pages, 3287 KiB

Open AccessArticle

Evaluation of the Application Effects of Siniperca chuatsi in Biofloc Systems: A Comparative Study on the Use of Bamboo Flour and Rice Straw as Carbon Sources

by Huiling Zhang, Zhaojie Deng, Shijun Chen, Xi Xiong, Wenhui Zeng, Fang Chen, Huanjiao Tan, Xuran Chen, Canmin Yang, Yuhui He, Dizhi Xie and Lian Gan

Microorganisms 2025, 13(7), 1631; https://doi.org/10.3390/microorganisms13071631 - 10 Jul 2025

Viewed by 267

Abstract

A 56-day trial was conducted to assess the effects of rice straw (RS) and bamboo flour (BF) on growth performance, water quality, gill histology, and the bacterial community of water and the intestine of mandarin fish (Siniperca chuatsi) in biofloc technology systems. The results showed that mandarin fish in the RS and BF groups had comparable survival rates of 100.00 ± 0.00 and 93.33 ± 3.85%; feed conversion ratios of 1.13 ± 0.02 and 1.40 ± 0.15; and weight gain rates of 112.21 ± 1.56 and 100.92 ± 6.45%, respectively. From days 11 to 56 of the farming period, the BF group was more effective than the RS group in removing total ammonia nitrogen (TAN) and NO₂⁻-N, maintaining TAN levels below 0.24 ± 0.05 mg/L. During the early stage of the experiment, the TAN level in the RS group was higher; however, with the supplementation of a carbon source, it gradually decreased and eventually stabilized at 0.13 ± 0.03 mg/L later in the farming period. The secondary gill lamella in the RS group was curved and showed hyperplasia, and the basal gill lamellae showed an increase in the volume of interlamellar cell mass in the BF group. Genes related to denitrification (narG, napA, nirS, nirK, and nosZ) and anammox showed higher expression levels in the BF group than in the RS group, although the differences were not statistically significant (p > 0.05). The results of 16S rRNA sequencing research showed that both treatment groups’ intestinal and water bacterial communities had comparable levels of richness and diversity. Pseudomonas mosselii was the dominant bacterial species in the water. In the BF group, the dominant intestinal species were Bacillus halodurans and Caldalkalibacillus thermarum, while in the RS group, the dominant species was Plesiomonas shigelloides. In conclusion, rice straw and bamboo flour are applicable in BFT systems for mandarin fish culture, with good growth performance and water quality. The BF group showed higher nitrogen removal efficiency and denitrification gene expression than the RS group. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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19 pages, 18888 KiB

Open AccessArticle

Effects of Lactobacillus plantarum-Fermented Feed on Growth and Intestinal Health in Haliotis discus hannai

by Ling Ke, Chenyu Huang, Song Peng, Mengshi Zhao, Fengqiang Lin and Zhaolong Li

Microorganisms 2025, 13(7), 1603; https://doi.org/10.3390/microorganisms13071603 - 8 Jul 2025

Viewed by 332

Abstract

This study multidimensionally investigates the comprehensive effects of Lactobacillus plantarum (LP)-fermented feed on growth performance, intestinal health, and metabolic regulation in Pacific abalone (Haliotis discus hannai). The results demonstrate that LP fermentation significantly alters feed’s physical properties and nutritional profile, softening texture, increasing viscosity, and emitting an acidic aroma. Notably, it enhanced contents of cis-9-palmitoleic acid, α-linolenic acid (ALA), and functional amino acids (GABA, L-histidine, and L-asparagine), indicating that fermentation optimized ω-3 fatty acid accumulation and amino acid profiles through the modulation of fatty acid metabolic pathways, thereby improving feed biofunctionality and stress-resistant potential. Further analyses revealed that fermented feed markedly improved intestinal morphology in abalone, promoting villus integrity and upregulating tight junction proteins (ZO-1, Claudin) to reinforce intestinal barrier function. Concurrently, it downregulated inflammatory cytokines (TNF-α, NF-κB, IL-16) while upregulating anti-inflammatory factors (TLR4) and antioxidant-related genes (NRF2/KEAP1 pathway), synergistically mitigating intestinal inflammation and enhancing antioxidant capacity. Sequencing and untargeted metabolomics unveiled that fermented feed substantially remodeled gut microbiota structure, increasing Firmicutes abundance while reducing Bacteroidetes, with the notable enrichment of beneficial genera such as Mycoplasma. Metabolite profiling highlighted the significant activation of lipid metabolism, tryptophan pathway, and coenzyme A biosynthesis. A Spearman correlation analysis identified microbiota–metabolite interactions (such as Halomonas’ association with isethionic acid) potentially driving growth performance via metabolic microenvironment regulation. In conclusion, LP-fermented feed enhances abalone growth, immune response, and aquaculture efficiency through multi-dimensional synergistic mechanisms (nutritional optimization, intestinal homeostasis regulation, microbiota–metabolome crosstalk), providing critical theoretical foundations for aquafeed development and probiotic applications in aquaculture. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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22 pages, 3591 KiB

Open AccessArticle

Dietary Supplementation with Encapsulated or Non-Encapsulated Sodium Butyrate Enhances Growth, Antioxidant Defense, Immunity, and Gut Health in Largemouth Bass (Micropterus salmoides)

by Minghui He, Zhiwei Zou, Wanjia Zhu, Haipeng Li, Ting Liang, Liwei Liu and Jianmei Su

Microorganisms 2025, 13(7), 1594; https://doi.org/10.3390/microorganisms13071594 - 6 Jul 2025

Viewed by 345

Abstract

This study aimed to evaluate the effects of dietary supplementation with sodium butyrate (SB) in different forms on the growth performance, antioxidant capacity, immune response, and intestinal health of largemouth bass (Micropterus salmoides). Five diets were formulated: a basal diet (SB0), diets with 1000 (ESB1), 1500 (ESB2), and 2000 mg/kg encapsulated SB (ESB3), and a diet with 2000 mg/kg raw powder sodium butyrate (RSB, non-encapsulated). After 49 days of feeding trials, the ESB2 group exhibited significantly higher weight gain and specific growth rates and a lower feed coefficient than those of the SB0 group (p < 0.05). Compared with the SB0 group, proximal intestinal villus length and width were significantly increased in the ESB1, ESB2, and ESB3 groups (p < 0.05). The expressions of tight junction genes zo-1, claudin-1, and claudin-4 were up-regulated in these SB-supplemented groups and most pronounced in the ESB2 group (p < 0.05). Compared with the SB0 group, antioxidant enzyme activities (catalase and superoxide dismutase) and their gene expressions increased in the ESB1, ESB2, and RSB groups (p < 0.05). Immune-related genes il-10 and tgf-β1 were up-regulated in the ESB1 and ESB2 groups, while their il-8, il-1β, and tnf-α were down-regulated (p < 0.05). The ESB2 group had higher intestinal abundance of Firmicutes and Lactobacillus. In conclusion, dietary supplementation with 1500 mg/kg encapsulated SB (ESB2) improved growth, antioxidant capacity, immunity, and gut health in largemouth bass. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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16 pages, 2462 KiB

Open AccessArticle

Potential of LP as a Biocontrol Agent for Vibriosis in Abalone Farming

by Ling Ke, Chenyu Huang, Song Peng, Mengshi Zhao, Fengqiang Lin and Zhaolong Li

Microorganisms 2025, 13(7), 1554; https://doi.org/10.3390/microorganisms13071554 - 2 Jul 2025

Viewed by 242

Abstract

Vibrio species are among the primary pathogenic bacteria affecting abalone aquaculture, posing significant threats to farming practices. Current clinical control predominantly relies on antibiotics, which can result in antibiotic residues in both abalone and the surrounding marine environments. Lactobacillus plantarum (LP) has been shown to release bioactive antagonistic substances and exhibits potent inhibitory effects against marine pathogenic bacteria. This study aimed to screen and characterize the probiotic properties of LP strains isolated from rice wine lees to develop a novel biocontrol strategy against Vibriosis in abalone. The methods employed included selective media cultivation, streak plate isolation, and single-colony purification for strain screening, followed by Gram staining, 16S rDNA sequencing, and phylogenetic tree construction using MEGA11 for identification. The resilience, antimicrobial activity, and in vivo antagonistic efficacy of the strains were evaluated through stress tolerance assays, agar diffusion tests, and animal experiments. The results demonstrated the successful isolation and purification of four LP strains (NDMJ-1 to NDMJ-4). Phylogenetic analysis revealed closer genetic relationships between NDMJ-3 and NDMJ-4, while NDMJ-1 and NDMJ-2 were found to be more distantly related. All strains exhibited γ-hemolytic activity, bile salt tolerance (0.3–3.0%), and resistance to both acid (pH 2.5) and alkali (pH 8.5), although they were temperature sensitive (inactivated above 45 °C). The strains showed susceptibility to most of the 20 tested antibiotics, with marked variations in hydrophobicity (1.91–93.15%) and auto-aggregation (13.29–60.63%). In vitro antibacterial assays revealed that cell-free supernatants of the strains significantly inhibited Vibrio parahaemolyticus, V. alginolyticus, and V. natriegens, with NDMJ-4 displaying the strongest inhibitory activity. In vivo experiments confirmed that NDMJ-4 significantly reduced mortality in abalone infected with V. parahaemolyticus. In conclusion, the LP strains isolated from rice wine lees (NDMJ-1 to NDMJ-4) possess robust stress resistance, adhesion capabilities, and broad antibiotic susceptibility. Their metabolites exhibit significant inhibition against abalone-pathogenic Vibrios, particularly NDMJ-4, which demonstrates exceptional potential as a candidate strain for developing eco-friendly biocontrol agents against Vibriosis in abalone aquaculture. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)

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17 pages, 5545 KiB

Open AccessArticle

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

Viewed by 451

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 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

Open AccessArticle

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

Cited by 1 | Viewed by 555

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 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

Open AccessArticle

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 512

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 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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