Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.

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Evidence for a core gut microbiota in the zebrafish

It is well known that healthy gut microbiota is essential to promote host health and well-being. The intestinal microbiota of endothermic animals as well as fish are classified as autochthonous or indigenous, when they are able to colonize the host's epithelial surface or are associated with the microvilli, or as allochthonous or transient (associated with digesta or are present in the lumen). Furthermore, the gut microbiota of aquatic animals is more fluidic than that of terrestrial vertebrates and is highly sensitive to dietary changes. In fish, it is demonstrated that [a] dietary form (live feeds or pelleted diets), [b] dietary lipid (lipid levels, lipid sources and polyunsaturated fatty acids), [c] protein sources (soybean meal, krill meal and other meal products), [d] functional glycomic ingredients (chitin and cellulose), [e] nutraceuticals (probiotics, prebiotics, synbiotics and immunostimulants), [f] antibiotics, [g] dietary iron and [h] chromic oxide affect the gut microbiota. Furthermore, some information is available on bacterial colonization of the gut enterocyte surface as a result of dietary manipulation which indicates that changes in indigenous microbial populations may have repercussion on secondary host–microbe interactions. The effect of dietary components on the gut microbiota is important to investigate, as the gastrointestinal tract has been suggested as one of the major routes of infection in fish. Possible interactions between dietary components and the protective microbiota colonizing the digestive tract are discussed.

https://biblio.ugent.be/publication/8517580/file/8525700.pdf

Effect of dietary components on the gut microbiota of aquatic animals. A never‐ending story?

EFFECTS OF PLANT-BASED DIETS ON THE DISTAL GUT MICROBIOME OF RAINBOW TROUT (Oncorhynchus mykiss).

Environmental and physiological factors shape the gut microbiota of Atlantic salmon parr (Salmo salar L.).

https://backend.orbit.dtu.dk/ws/files/83296245/prod11389623155607.Ingerslev_et_al_2014_.pdf

The development of the gut microbiota in rainbow trout (Oncorhynchus mykiss) is affected by first feeding and diet type

Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss)

P.N. was supported by a scholarship from the Dr Stekel
fellowship from INTA-Nestl´e. P.M. received a scholarship
from CONICYT-Chile. This investigation was supported by
a grant (FONDECYT no. 1080480) from CONICYT-Chile
and ECOS-CONICYT C07B04.

Macarena Riveros

Papers

Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss)

Molecularanalysis of intestinalmicrobiota of rainbowtrout (Oncorhynchusmykiss)