. 2023 Jun 1;14:1186645. doi: 10.3389/fphys.2023.1186645

TABLE 1.

Summary of gut microbiota modulation in cardiovascular, neural, and immune system in zebrafish.

Model of zebrafish	Effector	Method of administration	Effects	References
Cardiovascular
Larval zebrafish	High fat diet	Direct administration with feed in rearing water	Gene ontology enrichment analysis showed that genes associated with liver development, blood coagulation, triglyceride homeostasis and response to oxidative stress were altered, increased expression of genes associated with hyperlipidemia such as cyp 51, acox1, hmox1a, and fads2 as well as increase in the activity of signaling pathways associated with metabolic regulation in zebrafish on high fat diet.	Ka et al. (2020)
Germ free larvae	Fecal microbiota transplant (FMT) from mouse on high fat diet	Immersion in sterile E3 embryo media	Larvae that received FMT was more susceptible to hyperlipidemia, which was driven by Stenotrophomonas maltophilia and Enterococcus faecalis, evidenced by the increase in lipid droplet accumulation, while inoculation of E. faecalis in zebrafish larvae with myd88 knockdown showed significantly less lipid droplet accumulation.	Manuneedhi Cholan et al. (2022)
Germ free larvae	Enterococcus faecalis	Immersion in sterile E3 embryo media		Manuneedhi Cholan et al. (2022)
Larval zebrafish	Lactobacillus rhamnosus	Direct inoculation in rearing water	Administration of L. rhamnosus increased the abundance of Firmicutes and reduced abundance of Actinobacteria, modulated lipid metabolism by decreasing expression of fit2, agpat4, dgat2, mgll, hnf4α, scap, and cck which is involved in metabolism of cholesterol and triglyceride, increased absorptive surface area, and improved the growth of the larvae compared to the control group.	Falcinelli et al. (2015)
Larval zebrafish	Lactobacillus rhamnosus	Direct inoculation in rearing water	Administration of L. rhamnosus increased the abundance of Firmicutes, reduced abundance of Actinobacteria, increased expression of nucb2a, glp-1, insulin, goat, leptin, decreased expression of mc4r, cb1 and npy, which decreased glucose levels and appetite and smaller lipid droplets, higher levels of SCFA accumulated in the intestine and gallbladder compared to control group.	Falcinelli et al. (2016)
Germ free larvae	-	-	Decreased pro-angiogenic factors in the intestine and genes associated with regulation of leukocyte migration, cell proliferation and sprouting angiogenesis.	Willms et al. (2022)
Adult zebrafish	Overfeeding regime	Direct exposure in rearing water	Decrease in abundance of Fusobacteria, and Tenericutes and increase in Proteobacteria.	Buerger et al. (2020)
Adult zebrafish	Diethylhexyl phthalate	Direct exposure in rearing water		Buerger et al. (2020)
Neural
Adult zebrafish	Lyophilized L. rhamnosus IMC 501	Direct inoculation in rearing water	Increase in shoaling and explorative behavior, change in abundance of Fusobacteria, Proteobacteria, Firmicutes, Cyanobacteria at phylum level in treatment group, increase in expression of bdnf, tph1a, tph1b, tph2, htr1aa, slc6a4a, and mao in the brain, and decrease in expression of tph1b, htr1aa in the gut.	Borrelli et al. (2016)
Adult zebrafish	Enrofloxacin	Direct inoculation in rearing water	Increase in anxiety like behavior, increase in Bacteroidetes, decrease in Firmicutes/Bacteroidetes ratio, increase in intestinal levels of IL-6, TNF-α, 5-HT, and decrease in corticotropin-releasing hormone, BDNF, and neuropeptide Y in the brain.	Tian et al. (2023)
Larval zebrafish	Vibrio	Inoculation in flask	Zebrafish lacking sox10 gene lacks a functional ENS resulted in intestinal bacterial overgrowth with increase in pro-inflammatory bacteria (Vibrio) and decrease in anti-inflammatory bacteria (Escherichia) as well as increased intestinal inflammation as evidenced by increase in intestinal neutrophils and increased epithelial cell proliferation which was dependent on TNF signaling. Colonization of mutant larvae with Escherichia and Shewanella as well as transplant of ENS precursors from wild-type donor rescued the inflammatory effects.	Rolig et al. (2017)
	Shewanella
	Escherichia
Larval zebrafish	Edwardsiella tarda	Immersion	Administration of E. tarda activated EEC via transient receptor potential ankyrin A1 (Trpa1), increased intestinal motility and activation of EECs stimulated the vagal sensory ganglia and cholinergic enteric neurons in the gut by releasing serotonin.	Ye et al. (2021)
Germ free larvae	Lactobacillus plantarum	Direct inoculation in rearing water	Germ free larvae showed increase in locomotor activity and in anxiety related behavior. Supplementation with Lactobacillus plantarum decreased anxiety like behavior. Change in relative abundance at phylum level with lower abundance of Bacteroidetes, Cyanobacteria and higher abundance of Proteobacteria in CV compared to CR larvae.	Davis et al. (2016a)
Conventionalized (CV) and conventionally raised (CR) larvae	Lactobacillus plantarum	Direct inoculation in rearing water		Davis et al. (2016a)
Adult zebrafish	Lactobacillus plantarum	Direct inoculation in rearing water	Decrease in anxiety like behavior, increase in gabra1 and slc6a4a in the brain.	Davis et al. (2016b)
Adult zebrafish	Lactobacillus delbrueckii	Direct inoculation in rearing water	Decrease in anxiety like behavior and increase in expression of gad1 in brain and gut.	Olorocisimo et al. (2023)
Adult zebrafish	Paraburkholderia sabiae	Direct inoculation in rearing water	Decrease in anxiety like behavior, increase in exploratory behavior, increase in levels of taurine in brain and gut, increase in expression of oxti, bdnf, and tph2 in brain, no change in expression levels of GABAergic genes and decrease in abundance of Actinobacteria and Chloroflexi in treatment group.	Ichikawa et al. (2023)
Adult zebrafish	Melatonin	Direct inoculation in rearing water	Alteration in levels of γ-GABA, dopamine and serotonin, and alteration in intestinal microbiota where microbiota community structure in melatonin and probiotic treatment group was comparable to control group, change in intestinal metabolism as well as increase in acetic and propionic acid following melatonin treatment in a neurotransmitter secretion disorder model.	Zhang et al. (2021b)
Adult zebrafish	Lactobacillus plantarum HNU082	Direct inoculation in rearing water		Zhang et al. (2021b)
Adult zebrafish	Amoxicillin	Direct administration in rearing water	Decrease in diversity of microbial community in the intestine, altered behavior showing anxiety like behavior, and increase in corticotrophin releasing hormone.	Deprey (2016)
Adult zebrafish	Amoxicillin	Direct administration in rearing water	Exposure to high dose (100 mg/L) of Amoxicillin decreased social interaction behavior, locomotor activity, catalase activity and increase in superoxide dismutase activity in the brain tissue.	Gonçalves et al. (2020)
Larval zebrafish	Aeromonas veronii	Immersion	Increase in locomotor activity in germ free larvae and colonization with Aeromonas veronii or Vibrio cholerae blocked the hyperactive locomotion and distinct microbial communities among germ free, germ free colonized and conventionally colonized larval zebrafish.	Phelps et al. (2017)
Larval zebrafish	Vibrio cholerae	Immersion		Phelps et al. (2017)
Larval zebrafish	Metabolites from zebrafish intestine	Immersion	Delay in expression of notch1b, ngn1, ascl1a, decrease in expression of fgf8 and phox2bb which is involved in neurodevelopmental in germ free compared to conventionally raised and treatment with zebrafish metabolites in germ free larvae rescued the expression of the neural development genes.	Rea et al. (2022)
Adult zebrafish	Morphine	Direct administration with feed in rearing water	Administration of Sinomenine inhibited the dependence on morphine in zebrafish, diminished the changes in bacterial community in gut, restored the reduced expression levels of occludin a and b in the brain and inhibited expression of il1b in brain and intestine in morphine treatment group.	Chen et al. (2020)
Adult zebrafish	Sinomenine	Direct administration with feed in rearing water		Chen et al. (2020)
Immune
Germ free larvae	Aeromonas	Immersion	Colonization of germ-free zebrafish with zebrafish derived bacterial isolates, Vibrio showed significant increase in the number of neutrophils response while Aeromonas showed no clear relationship between neutrophil response and bacterial abundance when compared to germ free showing that immunostimulatory effects varies among bacterial species.	Rolig et al. (2015)
	Vibrio
	Shewanella
	Variovorax
	Delftia
	Acinetobacter
	Aeromonas sp. 2
	Pseudomonas
	Pleisomonas
	Enterobacter
Embryos	Lipopolysaccharide (LPS)	Immersion	Embryos exposed to LPS induced activation of pro-inflammatory cytokines such as TNF-α and IL-1β.	Watzke et al. (2007)
Germ free larvae	Aeromonas veronii biovar sobria	Immersion	Mono-colonization of germ-free larvae with gram negative bacteria (Aeromonas and Pseudomonas species) induced intestinal alkaline phosphatase (AP) activity comparable to conventionalized larvae while mono-colonization with gram positive bacteria isolates (Streptococcus and Staphylococcus species) showed no induction of intestinal AP activity. Exposure to LPS showed reduced expression of TNF-α and TNF-β in myd88-MO compared to wild-type. Authors also showed that germ free larvae had no neutrophils in the intestine compared to wild type.	Bates et al. (2007)
	Pseudomonas fluorescens
	Streptococcus
	Staphylococcus
	LPS
Adult zebrafish	Adherent-invasive Escherichia coli (AIEC)	Bath inoculation	Infection with AIEC upregulated intestinal expression of pro-inflammatory cytokines such as TNF-α, IL-1β, IFNγ and S100A-10b (like human calprotectin). Treatment with probiotic EcN rescued the pro-inflammatory response, tissue damage and decreased AIEC colonization.	Nag et al. (2022)
Adult zebrafish	E. coli Nissle 1917 (EcN)	Bath inoculation		Nag et al. (2022)
Immune—Dietary Factors
Larval zebrafish	Butyrate	Immersion	Exposure to butyrate, but not acetate or propionate decreased recruitment of neutrophils following a tail wound injury comparable to levels seen with dexamethasone treatment. Butyrate also reduced macrophage and TNF-α recruitment at the wound site while propionate increased macrophage recruitment.	Cholan et al. (2020)
	Acetate
	Propionate
	Dexamethasone
Larval zebrafish	Acetic acid	Immersion	Treatment with TNBS induced colitis with increased tissue damage, inflammation, gut dysbiosis as seen with increase in Betaproteobacteria and Actinobacteria, decreased goblet cells and endocytic function. Treatment with acetic, propionic, and butyric acid (SCFAs) reduced expression of inflammatory cytokines (il1b and il6), recruitment of neutrophils in the intestinal, maintained bacterial population level in gut comparable to control, but did not restore tissue damage in intestinal wall or number of goblet cells.	Morales Fénero et al. (2021)
	Propionic acid
	Butyric acid
	2,4,6-trinitrobenzene sulfonic acid (TNBS)
Larval zebrafish	High fat diet (control diet with 10% w/w of cocoa butter)	Direct administration with feed in rearing water	Administration of high fat diet for 25 days in larval zebrafish induced microbial dysbiosis with increase in the abundance of Bacteroidetes, upregulation in the expression of inflammatory cytokines (IL22, IL1B, TNF, MYD88, NFκB), receptors involved in host-microbiome interaction (TLR2, TLR5, NOD1), antimicrobial peptides (IAP, MPO, MMP9, DEF1), damaged intestinal barrier and increased goblet cell production in comparison to control group on a normal diet.	Arias-Jayo et al. (2018b)
Larval zebrafish	Soybean-meal based diet	Direct administration with feed in rearing water	Soybean meal diet induced a Th17 response in zebrafish compared to control diet. Administration of soybean-based meal diet in a Rag1 deficient larvae produced no inflammation response showing a T-cell dependent inflammatory response.	Coronado et al. (2019)
Adult zebrafish	Sea buckthorn polysaccharide	Direct administration with feed in rearing water	Supplementation of sea buckthorn polysaccharide with high fat diet improved the survival rate significantly with a decrease in levels of triglycerides, total cholesterol, aspartate aminotransferase, alanine transaminase in the serum, lipid accumulation in the liver, increased expression of Nrf2, Cu/Zn-SOD, and TGF-β1 in the intestine and liver. Dietary supplementation of sea buckthorn also corrected the dysbiosis in microbial community by promoting proliferation of beneficial intestinal bacteria (e.g.,: Cetobacterium) compared to zebrafish on high fat diet alone.	Lan et al. (2022)
Adult zebrafish	High fat diet	Direct administration with feed in rearing water	Supplementation of a probiotic like protein (AM-ZHY1) with Amuc-100 anchored to surface of Lactobacillus lactis ZHY1 with high fat diet showed a significant decrease in hepatic steatosis, decreased expression of PPARy, SREBP-1c, FAS, ACC1, CD36, FABP6, TNF-α, and IL6 in the liver, increased expression of intestinal tight junction proteins and reduced abundance of Proteobacteria and Fusobacteria compared to high fat diet alone.	Zhang et al. (2021a)
	Amuc_1100,
	Lactobacillus lactis ZHY1
Adult zebrafish	Exopolysaccharide (EPS) from Lactobacillus rhamnosus GG (LGG) and L. casei (BL23)	Direct administration with feed in rearing water	Administration of EPS derived from LGG promoted microbial homeostasis, activates HIF1α in the intestine which increases expression of antimicrobial peptides and has decreased expression of pro-inflammatory cytokines in the liver while EPS derived from BL23 induced liver inflammation with an increase in ALT, AST levels in the serum, increased expression of TNF-α, IL-6, IL-10 and gut microbial dysbiosis. EPS from both strains reduced hepatic steatosis in zebrafish on high fat diet and increased levels of intestinal acetate and propionate compared with high fat diet.	Zhang et al. (2019b)
Adult zebrafish	Lactobacillus rhamnosus GCC-3 EPS	Direct administration with feed in rearing water	Supplementation of diet with EPS from GCC-3 improved the survival rate of zebrafish infected with spring viremia of carp virus compared to control. There was also an increased expression of type I interferon and improved the gut microbiota homeostasis. In-vitro studies with fibroblast cells from zebrafish showed that culture of supernatant of GCC-3 EPS associated microbiota inhibited replication of the spring viremia of carp virus compared to culture supernatants on control diet.	Xie et al. (2022)
Larval zebrafish	High fat diet (emulsion of chicken egg yolk)	Direct administration in egg water	High fat diet inhibited nutrient sensing, decreased EECs signaling activity, altered the microbial composition in the gut and changed morphology of the EECs to a more “close type” that lacks apical extension increased abundance of Acinetobacter bacteria compared to control group.	Ye et al. (2019)
Juvenile zebrafish	Butyrate	Direct administration with feed in rearing water	Butyrate and saponin supplemented feed increased expression of pro-inflammatory genes and activity of oxidoreductase, decreased expression genes involved in histone modification, mitotic process, GPCR activity, and increased relative abundance of Rhodobacter, Flavobacterium and Bacteroides, which are associated with inflammation in juvenile zebrafish gut, increased eosinophils, rodlet cells and reduced mucus producing cells in the gut compared to control diet.	López Nadal et al. (2023)
Juvenile zebrafish	Saponin	Direct administration with feed in rearing water		López Nadal et al. (2023)
Immune—Environmental Factors
Adult zebrafish	Perfluoroalkyl phosphonic acids	Direct exposure in rearing water	Exposure to perfluoroalkyl phosphonic acids induced anxiety like behavior, increased abundance of gram-negative bacteria leading to increased levels of LPS in the brain, serum, and gut, increased expression of iL-1B and decreased expression of iL-10 in the brain, compared to control. Increased levels of LPS in the brain also altered permeability of the blood-brain barrier as seen by a decrease in the expression of tight junction proteins, leading to brain injury as seen by damaged myelin sheath fibers, increase in ROS production and apoptotic cells in the brain. Co-exposure of perfluoroalkyl phosphonic acid with CH (AhR inhibitor) decreased expression of ARNT1, CYP1A1 and iL-1B and increased expression of iL-10 in the brain while also decreasing anxiety like behavior relative to treatment of perfluoroalkyl itself.	Zhang et al. (2023)
	Antibiotics
	AhR inhibitor
Adult zebrafish	Triclosan,	Triclosan was directly administered in rearing water	Supplementation with Lactobacillus plantarum diminished toxic effects due to triclosan exposure, restored levels of triglycerides and total cholesterol, decreased number of CD4 T cells in the lamina propria of duodenal mucosa, and decrease in expression of intestinal pro-inflammatory cytokines (NF-κB, and lysozyme). Supplementation with Lactobacillus plantarum also decreased anxiety like behavior and improved learning/memory following chronic Triclosan exposure.	Zang et al. (2019)
Adult zebrafish	Lactobacillus plantarum ST-III	Lyophilized bacteria supplemented in feed		Zang et al. (2019)
Adult zebrafish	Microcystin-LR (MC-LR)	Direct exposure in rearing water	Exposure to MC-LR or/and GLY decreased expression of claudin-5, occludin, zonula occludens-1, increased intestinal permeability, increased levels of intestinal IL-1β and IL-8, p53, bax, bcl-2, caspase-3, caspase-9, activated activity of superoxide dismutase, increased relative abundance of Fusobacteria and Proteobacteria. PCRUSt analysis showed alteration in pathways involving lipid metabolism, circulatory metabolism, energy metabolism, metabolism of cofactors, vitamins, replication and repair, and translation.	Ding et al. (2021)
Adult zebrafish	Glyphosate (GLY)	Direct exposure in rearing water		Ding et al. (2021)
Adult zebrafish	Polystyrene microplastics	Direct exposure in rearing water	Exposure to 100nm and 200 µm of polystyrene microplastics caused an increased in levels of TNF-a and TLR 2 in the intestine, increased abundance of pathogenic bacteria while the lowest concentration (100 nm) also induced increased expression of genes related to ROS production and increased production of mucus secreting cells. Exposure to the polystyrene microplastics also increased the abundance of pathogenic bacteria such as Actinobacillus, Mycoplasma (100 nm), Staphylococcus (5 µm), Vibrio, Acinetobacter, Porphyromonas, Haemophilus, Neisseria, Lactococcus (200 µm) in the intestine of zebrafish.	Gu et al. (2020)
Adult zebrafish	Microcystis aeruginosa	Direct inoculation in rearing water	Exposure to M. aeruginosa increased number of intestinal goblet cells, inflammation, and relative abundance of Cyanobacteria, Actinobacteria at the phylum level and abundance of Vibrio, Lactobacillus, Shewanella, Methylobacterium, Pseudomonas and Halomonas at the genus level.	Qian et al. (2019)