Table 1.

List of some recent studies concerning fish gut microbiome. In all cases, the targeted region used for amplicon sequencing is the hypervariable region(s) of bacterial 16S rRNA gene sequence which is denoted by its standard code(s). AU and AL, here, stand for autochthonous and allochthonous microbiomes respectively

Host	NGS platform	Amplicon/shotgun Sequencing	Microbiome	Study design	Problem addressed	Dominant phyla	Important inferences	References
Silurus meridionalis	Illumina Hiseq	Amplicon: V4–V5	AU and AL	Gut microbiome of lab-reared fish over developmental stages	Effect of host age and—associated factors on gut microbiome	Tenericutes, Fusobacteria, Proteobacteria, and Bacteroidetes	Microbial diversity increases with host age; is significantly Abundance of Tenericutes decrease while Fusobacteria, Proteobacteria and increase with host age	[107]
Silurus meridionalis	Illumina HiSeq	Amplicon: V4–V5	AL	Gut microbiome of stomach and intestine at different time intervals after feeding	Spatial and temporal microbial dynamics within gut	Fusobacteria, Firmicutes, Proteobacteria, and Bacteroidetes	Distinguishable communities between stomach and intestine; higher diversity in stomach. Firmicutes increase and Fusobacteria decrease after feeding	[108]
Danio rerio	Illumina Miseq	Amplicon: V4	Not defined	Microbiome of formulated diet fed group compared with that of control	Effect of gluten formulated diet (GFD) on gut microbiome	Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes dominated control samples. Planctomycetes, Fusobacteria, and Verrucomicrobia dominated GFD samples	Legionellales, Rhizobiaceae, and Rhodobacter abundant in GFD fed group. Cobalamin synthesizing Bacteroides and Lactobacillus present in control group and absent in experimental group	[109]
Siganus fuscescens	Illumina Miseq	Amplicon: V4	AU and AL	Microbiome of different regions in GI tract	Differences at the level of individuals, gut locations and sample types	Proteobacteria, Cyanobacteria and Firmicutes	Midgut communities highly diverse for both adherent and non-adherent microbiome; Greater diversity of adherent microbiome accounting for its active selection by host	[110]
Gambusia affinis	Illumina HiSeq	Amplicon: V4	AU and AL	Effect of broad range antibiotic rifampicin on gut microbiome	Microbiome composition and its response towards antibiotic stress	Proteobacteria, Planctomycetaceae; Myroides genus of Flavobacteria dominated during treatment	Antibiotic treatment lowers the diversity and unstably alters the composition to become antibiotic resistant during treatment while the microbiome takes long to recover	[111]
Oncorhynchus mykiss	Illumina Miseq	Amplicon: V6–V8	AU and AL	Juvenile fish fed with plant- and animal-derived dietary proteins	Role of dietary nutrients source in microbiome composition	Proteobacteria, Firmicutes, Bacteroidetes, Fusobacteria and Actinobacteria	Gut microbial diversity decreases as the source of nutrient derivation in diet is restricted	[72]
Carassius auratus	Illumina Miseq	Amplicon: V4–V5	AU and AL	‘Red-operculum’ disease affected individuals compared with healthy individuals	Differences in healthy and diseased gut microbiome	Fusobacteria, Proteobacteria and Bacteriodetes	Distinct differences in microbiome composition in two groups; potential of some species as disease-specific bacterial signatures	[112]
Ctenopharyngodon idellus, Megalobrama amblycephala, Carassius auratus, Hypophthalmichthys molitrix and H. nobilis,	Pyrosequencing	Amplicon: V4	AL	Species with three different feeding habits raised under identical husbandry conditions	Relationship among host evolutionary distance, gut microbiota and metabolic profiles	Fusobacteria, Proteobacteria, Bacteroidetes and Firmicutes	Gut microbiome composition as well as metabolite profiles are significantly altered by host species and feeding behaviour	[71]
Danio rerio	Illumina Hiseq	Amplicon: V4	Not defined	Adaptive immune compromised individuals compared with wild-type individuals	Ecological filtering of microbiome composition by adaptive immunity of the host	Proteobacteria, Fusobacteria and Actinobacteria	Functional adaptive immunity affects the neutral assembly processes; Adaptive immunity specifies the microbiome composition in each host which otherwise seems to be much similar; Co-housing individuals of different genotypes increases the microbiome diversity	[113]
Salmo salar L.	Illumina Miseq	Amplicon: V3 and V4	AL	Lab reared and commercial freshwater fish farm	Effect of habitat on microbiome composition	Firmicutes, Proteobacteria, Tenericutes	Presence of core gut microbial flora regardless of the habitat type indicating operational host selective forces	[61]
Salmo salar	Ion Torrent	Amplicon: V1 and V2	AU and AL	Reference and experimental groups fed with alternative protein sources	Effect of alternative diets on microbiome structure and function	Firmicutes, Proteobacteria, Fusobacteria, Bacteroidetes, Actinobacteria	Significantly different adherent and non-adherent communities; Non-adherent microbiome much diverse and diet-dependent than adherent microbiome	[114]
Oreochromis niloticus	Illumina MiSeq	Amplicon: V4–V5	AL	Cadmium(Cd)-exposed, Cd-exposed and probiotic fed, only probiotic fed and control groups	Toxic effects of pollutants on microbiome and application of probiotics for treatment	Fusobacteria, Proteobacteria, Bacteroidetes and Firmicutes	Probiotic supplementation improved the gut health status in Cd-exposed fish to prevent death	[115]
Carassius auratus gibelio	Illumina Miseq	Amplicon: V4	AL	Development of microbiota in a bacteria-free fish gut ecosystem over a year	Factors governing colonization of germ- free gut	Proteobacteria, Fusobacteria and Firmicutes	Gut microbial diversity increases as the fish develop and is less affected by surrounding environment than by host diet and development	[62]
Oncorhynchus mykiss	Illumina MiSeq	Amplicon: V4	AL	Fish from different sources i.e. reared in farm and in aquarium	Complexity of microbiome composition in differently sourced individuals of a species	Tenericutes, Firmicutes, Proteobacteria, Spirochaetae Bacteroidetes	Similar gut microbiota regardless of source; shaped by host factors; Differences in composition highlight the habitat specific taxa	[116]
Antarctic Fish spp.: Trematomus bernacchii, Chionodraco hamatus, Gymnodraco acuticeps and Pagothenia borchgrevinki	Illumina Miseq	Amplicon: V4–V5	AL	Analysis of gut microbiota	Complexity of microbiome composition in different species	Proteobacteria, Actinobacteria, Firmicutes,Thermi,Bacteriodetes and Tenericutes	Gut microbial communities in different species are not exactly same but also not different altogether	[117]
Ictalurus punctatus	Illumina MiSeq	Amplicon: V4	AU and AL	Microbiome at different life stages with different diet formulations to study gut microbiota across developmental ontogeny	Influence of age as well as the dynamic dietary and environmental factors on gut microbiome	Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria	Age has a significant influence on the intestinal microbiota; Water microbiota strongly influence gut microbiota at early life stages	[118]
Oreochromis niloticus	Illumina HiSeq	Amplicon: V4	AU and AL	Gut microbiome of cultured fish in axenic, probiotic-supplemented and later active life phases	Effect of short-term probiotic administration on gut microbiome	Firmicutes, Actinobacteria and Proteobacteria (control groups)	Probiotic administration for a short period significantly affects the gut microbiota composition at later stages of life	[119]
Dicentrarchus labrax	Pyrosequencing	Amplicon: V3–V4	AU	Gut microbiome of two different nutritionally stressed groups and effect on host’s growth or resistance to hypoxia	Correlation between gut microbiota composition, dietary stress and host’s health	Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes	Gut microbiome is dependent upon the host life history or genetic background; Different nutritional stresses affect host microbiome and health differently	[120]
Ctenopharyngodon idellus, Siniperca chuatsi, Silurus meridionalis, Carnis megalobramae, Carassius auratus Cyprinus carpio and Canna micropeltes	Illumina Miseq	Amplicon: V4	AL	Assembly of gut microbiota in larval and adult fish	Effect of ecological processes on gut microbiota assemby	Proteobacteria, Firmicutes and Bacteroidetes	Gut environment and other host development processes shape the microbiome	[44]
Danio rerio	Illumnina Hiseq	Amplicon: V4	AU and AL	Survey of intestinal bacteria at key developmental time points	Microbiome composition across developmental stages	Proteobacteria, Firmicutes, Fusobacteria, Actinobacteria and Bacteroidetes	Environmental factors more strongly influence microbiome at early life stages	[121]
Salmo salar	Illumina HiSeq	Amplicon: V6	AU and AL	Influence of alternative diet on microbiome, recirculating waters and biofilters	Effect of alternative feeds on microbiome in fish cultured in recirculating water systems	Proteobacteria and others	Gut microbiome differs by diet treatment but communities in biofilters remain stable independent of diet; Gut communities less diverse than those of water and biofilters	[122]
Megalobrama amblycephala, Ctenopharyngodon idellus, Siniperca chuatsi, Culter alburnus, Cyprinus carpio, Carassius auratus, Hypophthalmichthys molitrix, H. nobilis	Illumina MiSeq	Amplicon: V4	AL	Influence of trophic level on the gut microbiome	Differences in gut microbiota in herbivorous, carnivorous, omnivorous and filter feeding species	Proteobacteria, Firmicutes, Fusobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia and Cyanobacteria	Trophic level strongly influence the microbiome composition of fish from same habitats; Evidence of a large core gut microbiota in multiple species	[19]
Salmo salar L.	Pyrosequencing	Amplicon: V3 to V6	AL	Effect of diet on the gut microbiome	Diet as a factor controlling microbiome composition	Bacteroidetes, Firmicutes and Proteobacteria	Diet, time of sampling and host specific factors influence the microbes	[123]
Oreochromis niloticus	Pyrosequencing	Amplicon: V1–V2	AU and AL	Gut microbiome development in larvae	Impact of rearing environment on microbiota assembly in early life stages	Proteobacteria and Actinobacteria	Water microbial communities strongly shape those in the gut; Correlation between water and gut microbial community dynamics	[63]
Salmo salar	Illumina MiSeq	Amplicon: V4	AL	Gut microbiomes of freshwater and marine specimens	Effect of geographical distance on microbiome	Proteobacteria, Firmicutes, Bacteriodetes and Actinobacteria	Geographical distance has less impact on gut microbiome; Diversity and identity of microbial communities is more strongly determined by life-cycle stage	[124]
Pimephales promelas	Illumina MiSeq	Amplicon: V3–V4	AU and AL	Gut microbiome of triclosan exposed fish	Effect of antimicrobial compounds on gut microbiome	Proteobacteria, Bacteroidetes and Fusobacteria	Microbiome is significantly altered even at low level of environmental changes but has strong resilience power	[125]