# The Role of Gut Microbiota in Fish Viral Infection: Mechanisms and Microbiota‐Targeted Interventions

**Authors:** Qiong Zhao, Jianzhong Shao, Ye Chen, Hangjun Zhang

PMC · DOI: 10.1155/anu/9336162 · Aquaculture Nutrition · 2026-02-27

## TL;DR

This review explores how gut bacteria in fish influence viral infections and how they interact with the immune system, offering insights for disease control in aquaculture.

## Contribution

The paper provides a comprehensive overview of the 'microbiota-immune-virus' interaction network in fish and its implications for green disease control strategies.

## Key findings

- Viral infections can alter the gut microbiota in fish, and vice versa.
- Gut microbiota supports antiviral defense through immune regulation and metabolite secretion.
- The review highlights the potential for microbiota-targeted interventions in aquaculture disease management.

## Abstract

Viral diseases represent one of the major threats to the global aquaculture industry. In recent years, the relationship between gut microbiota and viral infections in fish has garnered increasing attention. The gut microbiota contributes critically to fish health and is involved in antiviral defense through immune regulation, secretion of microbial metabolites, as well as enhancement of barrier function. The gut microbiota, host immunity, and viral infection form a complex and dynamic interaction network. A substantial body of 16S rRNA and metabolomics correlation studies has indicated that viral infections can alter the gut microbiota in fish, while changes in the gut microbiota can, in turn, influence viral infection. In this review, we summarize the regulatory effects of gut microbiota on fish viral infections, explore the interactions between the gut microbiota, immune system, and viral pathogenesis, and discuss future research directions and potential application prospects. By outlining the three‐dimensional interaction network of “microbiota‐immune‐virus” in fish, this review not only lays a theoretical foundation for developing targeted microecological strategies for green disease control but also provides an evolutionary perspective for understanding host–microbe coevolution in vertebrates.

## Full-text entities

- **Genes:** irak4 (interleukin-1 receptor-associated kinase 4) [NCBI Gene 393132] {aka zgc:55553}, DDX41 [NCBI Gene 394020], tlr3 (toll-like receptor 3) [NCBI Gene 403126] {aka zgc:123006}, mavs (mitochondrial antiviral signaling protein) [NCBI Gene 562867] {aka wu:fj20d04, zgc:158392}, traf3 (TNF receptor-associated factor 3) [NCBI Gene 445119] {aka zgc:92367}, HLA-C (major histocompatibility complex, class I, C) [NCBI Gene 3107] {aka D6S204, HLA-JY3, HLAC, HLC-C, MHC, PSORS1}, TLR8 [NCBI Gene 100334317], tlr2 (toll-like receptor 2) [NCBI Gene 403125], irf7 (interferon regulatory factor 7) [NCBI Gene 393650] {aka wu:fl24c03, zgc:66043, zgc:77947}, tlr21 (toll-like receptor 21) [NCBI Gene 402884] {aka TLR21.1}, RIGI (RNA sensor RIG-I) [NCBI Gene 23586] {aka DDX58, RIG-I, RIG1, RLR-1, SGMRT2}, rigi (RNA sensor RIG-I) [NCBI Gene 100333797] {aka RIG-I, RIG-Ia, RIG-Ib, RIG-Ic, RIG-Id, ddx58}, ticam1 (TIR domain containing adaptor molecule 1) [NCBI Gene 403147] {aka trif}, espl1 (extra spindle pole bodies like 1, separase) [NCBI Gene 797406] {aka espl1,, fl55e11, mp:zf637-3-001691, wu:fl55e11}, hsp90aa1.1 (heat shock protein 90, alpha (cytosolic), class A member 1, tandem duplicate 1) [NCBI Gene 30591] {aka fb17b01, hsp90, hsp90a, hsp90a.1, hsp90alpha, wu:fb17b01}, tbk1 (TANK-binding kinase 1) [NCBI Gene 692289] {aka wu:fk70c05, zgc:136548}, sting1 (stimulator of interferon response cGAMP interactor 1) [NCBI Gene 101243556] {aka tmem173}, myd88 (MYD88 innate immune signal transduction adaptor) [NCBI Gene 403145] {aka zgc:103541}, stat3 (signal transducer and activator of transcription 3 (acute-phase response factor)) [NCBI Gene 30767] {aka STAT3b1, STAT3b2, wu:fc15d02, wu:fl59g06, z-Stat3}, tlr9 (toll-like receptor 9) [NCBI Gene 403128] {aka sb:eu392}, tlr22 (toll-like receptor 22) [NCBI Gene 403135] {aka TLR21.2}, irf3 (interferon regulatory factor 3) [NCBI Gene 564854], tlr7 (toll-like receptor 7) [NCBI Gene 100534776] {aka TLR7A}, traf6 (TNF receptor-associated factor 6) [NCBI Gene 554561] {aka fi15f02, wu:fi15f02, zgc:63704}, ifnphi1 (interferon phi 1) [NCBI Gene 360134] {aka ifn, ifn1, ifnab}, trmt5 (tRNA methyltransferase 5) [NCBI Gene 564078] {aka wu:fi28b08}, ighm (immunoglobulin heavy constant mu) [NCBI Gene 378762] {aka ighm1, wu:fj14a08, zgc:101769}, il6 (interleukin 6 (interferon, beta 2)) [NCBI Gene 100885851]
- **Diseases:** exophthalmos (MESH:D005094), VHS (MESH:D031941), GCHD (MESH:D006470), SVC (MESH:D014766), Dysbiosis of Gut (MESH:D064806), CEVD (MESH:D004487), degenerative (MESH:D019636), disease (MESH:D004194), inflammation (MESH:D007249), Fish Virus Infection (MESH:D005393), necrosis (MESH:D009336), IHN (MESH:D003141), tissue damage (MESH:D017695), inflammatory bowel disease (MESH:D015212), bacterial infections (MESH:D001424), infection (MESH:D007239), lethargy (MESH:D053609), ascites (MESH:D001201), Fish Viral Disease (MESH:D014777), gut microbiota disorder (MESH:C536735)
- **Chemicals:** vitamin C (MESH:D001205), inulin (MESH:D007444), galactose (MESH:D005690), poly I:C (MESH:D011070), vitamin E (MESH:D014810), polysaccharides (MESH:D011134), mannose (MESH:D008358), DCA (MESH:D003840), palmatine (MESH:C005413), Aflatoxin B1 (MESH:D016604), CLA (MESH:D017291), oxygen (MESH:D010100), zinc (MESH:D015032), DG (MESH:D004075), SCFAs (MESH:D005232), beta-glucan (MESH:D047071), glucose (MESH:D005947), PHB (MESH:C003182), Prebiotics (MESH:D056692), fructose (MESH:D005632), lipid (MESH:D008055), Butyrate (MESH:D002087), bile acid (MESH:D001647), SMX (MESH:D013420), EPS (-), alpha-Gal (MESH:C055075), oligosaccharides (MESH:D009844)
- **Species:** Rubroshorea almon (species) [taxon 292004], Oncorhynchus tshawytscha (Chinook salmon, species) [taxon 74940], Bacillus sp. (in: firmicutes) (species) [taxon 1409], Cetobacterium somerae (species) [taxon 188913], Cyprinid herpesvirus 3 (no rank) [taxon 180230], Viral hemorrhagic septicemia virus (no rank) [taxon 11287], Lymphocystis disease virus 1 (no rank) [taxon 36363], Salmonidae (salmonids, family) [taxon 8015], Parabacteroides distasonis (species) [taxon 823], Grass carp reovirus (no rank) [taxon 128987], Flavobacterium (genus) [taxon 237], Paralichthys olivaceus (bastard halibut, species) [taxon 8255], Largemouth bass virus (no rank) [taxon 176656], Scophthalmus maximus (turbot, species) [taxon 52904], Ctenopharyngodon idella (grass carp, species) [taxon 7959], Nannocystis (genus) [taxon 53], Novirhabdovirus hirame (species) [taxon 1980915], Carassius gibelio (gibel carp, species) [taxon 101364], Infectious spleen and kidney necrosis virus (no rank) [taxon 180170], Vibrio (genus) [taxon 662], Lacticaseibacillus casei str. Zhang (strain) [taxon 498216], Vibrio sp. (species) [taxon 678], Actinopterygii (fishes, superclass) [taxon 7898], Salmo trutta (river trout, species) [taxon 8032], Cyprinid herpesvirus 2 (no rank) [taxon 317878], Lactiplantibacillus plantarum (species) [taxon 1590], Oncorhynchus nerka (sockeye salmon, species) [taxon 8023], Infectious hematopoietic necrosis virus (no rank) [taxon 11290], Micropterus salmoides rhabdovirus (no rank) [taxon 2527734], Tilapia lake virus (no rank) [taxon 1549864], Multiple sclerosis associated retrovirus (no rank) [taxon 62805], Bacteroides (genus) [taxon 816], Aeromonas sp. (species) [taxon 647], Bacteria Latreille et al. 1825 (Bacteria stick insect, genus) [taxon 629395], Infectious pancreatic necrosis virus (no rank) [taxon 11002], Oncorhynchus mykiss (rainbow trout, species) [taxon 8022], Cyprinus carpio (carp, species) [taxon 7962], Homo sapiens (human, species) [taxon 9606], Mycobacterium (genus) [taxon 1763], Salmo salar (Atlantic salmon, species) [taxon 8030], Micropterus salmoides (largemouth bass, species) [taxon 27706], Danio rerio (leopard danio, species) [taxon 7955], Lacticaseibacillus casei (species) [taxon 1582]

## Full text

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## Figures

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## References

120 references — full list in the complete paper: https://tomesphere.com/paper/PMC12948727/full.md

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Source: https://tomesphere.com/paper/PMC12948727