Table 1.

Key published literature describing system parameter effects on animal microbiomes and production outcomes.

Species	Microbiomes (s)	System (s)	Factor	Description	References
Atlantic salmon (Salmo salar)	Gut and water	RAS	Membrane filtration	Salmon parr in RAS with membrane ultrafiltration (mRAS) compared against conventional RAS (cRAS) in periods of high and low organic loading. With high organic loading in cRAS, opportunistic bacteria colonized the gut microbiome. Ultrafiltration in mRAS stabilized the water microbiota, preventing growth of and colonization by opportunists.	Bugten et al. (2022)
Nile tilapia (Oreochromis niloticus)	Gut	RAS and FTS	Hatchery type	Tilapia embryos reared to fry in FTS, RAS or RAS with probiotic feed (RASB). Lower survival in fish reared in FTS compared to RAS and RASB. Gut microbiota composition differed in fish from different hatchery types and showed correlation with survival rate and size at harvest.	Deng et al. (2022)
Tilapia (Coptodon rendalli and Oreochromis shiranus)	Skin and water	Pond	Location	Tilapia reared in seven earthen ponds in two pond systems in distinct geographic regions. 92% of taxa shared by skin and water, but enriched and core taxa differed. Strong site-specific clustering of water samples, but not skin, highlighting some independence of skin microbiome from that of the environment.	McMurtrie et al. (2022)
Common carp (Cyprinus carpio)	Gut, sediment and water	Pond	Water quality	Carp reared in pond and sampled on 10 occasions across five months. The impact of water quality on water microbiota was stronger than the influence of gut or sediment microbiota. Gut microbiota dynamics were most closely associated with sediment microbiota.	Jing et al. (2021)
European lobster (Homarus Gammarus)	Larvae, biofilm and water	RAS and FTS	UV disinfection	Lobster larvae reared in RAS, RAS with UV disinfection or FTS in two separate experiments. Significantly different larval and water microbiomes were identified in each system. Survival was consistently highest in RAS without disinfection in replicate tanks and experiments.	Attramadal et al. (2021)
Eastern oyster (Crassostrea virginica)	Larvae and water	RAS and FTS	Hatchery type	Compared microbiomes of larvae originating from 4 different hatcheries for two consecutive spawning events. Larval microbiota were distinct from water and between hatcheries and spawning events. Hatchery had the strongest effect. Core OTUs (n = 25) identified across larval microbiomes.	Arfken et al. (2021)
Nile tilapia (Oreochromis niloticus)	Gut, biofloc, water and feed	RAS	Biofloc	Tilapia reared in RAS, RAS with in situ biofloc or fed a diet containing live or dead ex situ biofloc. In situ biofloc increased microbiome diversity in the gut with an increase in abundance of potentially beneficial taxa. Growth was also increased in fish from the in situ biofloc treatment.	Deng et al. (2021)
Pacific whiteleg shrimp (Litopenaeus vannamei)	Gut and biofloc	Static tank	Biofloc	Shrimp reared in indoor tanks with no water exchange, with or without biofloc. Microbiota composition similar with or without biofloc, but individual taxa enriched. Expression of immune-related genes and immune status enhanced in shrimp reared with biofloc.	Tepaamorndech et al. (2020)

RAS, recirculating aquaculture system; FTS, flow-through system.