Table 1.

Biological function of gut microbiota in zebrafish

Biological function	Intestinal bacteria	Molecular mechanism	Reference
Development	Aeromonas veronii biovar sobria, Pseudomonas fluorescens	Promoting intestinal epithelial maturation through distinct host recognition pathways	Bates et al. 2006
	Gut microbiota	Determining the fate of intestinal epithelial secretory cells through Myd88-dependent inhibition of Notch signaling	Troll et al. 2018
	Aeromonas veronii HM21	Enhancing the stability of β-catenin in intestinal epithelial cells and promoting cell proliferation in the development of vertebrate intestine	Cheesman et al. 2011
	Aeromonas veronii HM21, Shewanella	Releasing BefA protein that causes the multiplication of pancreatic β cells	Hill et al. 2016
	Aeromonas veronii: dTomato HM21, Vibrio cholerae:GFP ZWU0020	Being required for normal neurobehavioral development in early life of zebrafish	Phelps et al. 2017
	Vibrio	Excessive growth of Vibrio species inhibit the development of adaptive immunity in larval zebrafish	Brugman et al. 2014
Reproduction	Lactobacillus rhamnosus IMC 501	Promoting gonadal differentiation through the regulation of GnRH and IGF signalings	Avella et al. 2012; Carnevali et al. 2013
	Lactobacillus rhamnosus IMC 501	Regulating ovary physiology by inhibiting follicular apoptosis and increasing follicular survival	Gioacchini et al. 2013)
	Lactobacillus rhamnosus IMC 501	Promoting follicle maturation and fecundity by modulating the gene expression of neuropeptide hormones and metabolic signals	Gioacchini et al. 2010; Gioacchini et al. 2011, 2013
	Pediococcus acidilactici	As a probiotic supplement in male zebrafish diet for the improvement of molecular parameters in testicular cells	Valcarce et al. 1887
	The commercial probiotic mixture SLAb51	Counteracting the adverse effects of BPA on zebrafish reproduction by interacting with gametogenesis-related genes	Giommi et al. 2021
Immunity	Aeromonas veronii biovar sobria, Pseudomonas fluorescens, Streptococcus, and Staphylococcus	Influencing host immunity through the regulation of Myd88 and TNF receptor	Bates et al. 2007
	Exiguobacterium ZWU0009, Chryseobacterium ZOR0023	Inducing changes in intestinal leukocyte subsets and Myd88-dependent gene expression of host	Koch et al. 2018
	Gut microbiota	Induces expressions of proinflammatory and antiviral factors, which results in the increased resistance of larvae to viral infection	Galindo-Villegas et al. 2012
	Gut microbiota	Suppressing systemic neutrophil activation by microbiota-induced Serum amyloid A	Murdoch et al. 2019
	Pseudomonas aeruginosa PAK	Regulating dynamic temporal and spatial transcription activation of NF-кB and subsequent up-regulation of target genes in intestine	Kanther et al. 2011
	Lactobacillus	Adhesive probiotic Lactobacillus has anti-infective in protecting zebrafish against pathogenic infections, which is correlated with their spatial distribution in the intestine	He et al. 2017
	Chryseobacterium massiliae	Protecting zebrafish from intestinal damage upon Flavobacterium columnare infection	Stressmann et al. 2021
Metabolism	Aeromonas hydrophila (ATCC 35654), Pseudomonas aeruginosa PA01	Modulating cholesterol metabolism and trafficking through the regulation of ApoB and Fdps	Rawls et al. 2004
	Gut microbiota	Promoting the uptake of macromolecular proteins in the distal intestine	Bates et al. 2006
	Exiguobacterium sp. ZWU0009, Chryseobacterium sp. ZOR0023, Pseudomonas sp.ZWU0006	Stimulating fatty acids uptake and lipid droplet accumulation in intestinal epithelia and liver	Semova et al. 2012
	Gut microbiota	Regulating expression of intestinal Angptl4 and storage of peripheral fat by suppressing the intestine-specific transcriptional enhancer	Camp et al. 2012
	Gut microbiota	Increasing lipid accumulation in intestinal epithelia by regulating gene expression related to lipid metabolism	Sheng et al. 2018
	Stenotrophomonas maltophilia, Enterococcus faecalis	The mouse high fat-diet-associated microbiota accelerate hyperlipidaemic phenotype in zebrafish embryos	Manuneedhi Cholan et al. 2022
	SCFAs	SCFAs produced by zebrafish microbiota reduces liver phosphoenolpyruvate carboxykinase 1 expression and overall glucose level	Han 2018
Behavior	Aeromonas veronii: dTomato HM21, Vibrio cholerae:GFP ZWU0020	Being necessary for locomotor activity of zebrafish larvae	Phelps et al. 2017
	Lactobacillus plantarum	Modulating communication with CNS via microbiome-gut-brain axis	Davis et al. 2016a, b; Borrelli et al. 2016