Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at sea

Abstract

Factors affecting the establishment of the gut microbiota in animals living in marine environments remain largely unknown. In terrestrial animals, however, it is well established that the juvenile environment has a major impact on the gut microbiota later in life. Atlantic salmon Salmo salar is an anadromous fish important in aquaculture with a juvenile freshwater stage and an adult seawater stage. For wild salmon, there are major dietary changes with respect to availability of long-chain polyunsaturated n-3 fatty acids (LC-n-3 PUFA) with lower abundance in freshwater systems. The aim of our work was therefore to determine the effect of a juvenile freshwater diet with high LC-n-3 PUFA, as compared to a diet low in LC-n-3 PUFA (designed to increase the endogenous LC-n-3 PUFA production), on the transition to a seawater gut microbiota for Atlantic salmon. We found a juvenile freshwater microbiota high in Firmicutes for fish raised with low LC-n-3 PUFA, while the microbiota for fish given high LC-n-3 PUFA feed was high in Proteobacteria. One hundred days after transfer to a common sea cage, fish that were given low LC-n-3 PUFA diets in freshwater showed significantly higher (p = 0.02, Kruskal-Wallis) Mycoplasma content (90 ± 7%; mean ± SD) compared to fish raised on a high LC-n-3 PUFA diet in freshwater (25 ± 31% Mycoplasma). Shotgun metagenome sequencing from fish raised with a low LC-n-3 PUFA diet identified a salmon-associated Mycoplasma in sea, being distinct from currently known Mycoplasma. The genome sequence information indicated a mutualistic lifestyle of this bacterium. Mycoplasma has also previously been identified as dominant (> 70%) in sea-living adult Atlantic salmon. Taken together, our results suggest that the juvenile freshwater diet influences the establishment of the gut microbiota in marine Atlantic salmon.

Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar)

“…Core microbiota. In accordance with previous studies in Atlantic salmon (20,(33)(34)(35)(36)(37)(38), Aliivibrio, B. andersonii and Mycoplasma were identified as core microbiota in the present study. Aliivibrio is commonly found in the seawater phase Atlantic salmon intestine (35)(36)(37)(39)(40)(41)(42)(43) and has been identified as a core taxon of both wild and captive Atlantic salmon (34,36,37).…”

“…This taxon has also been found in the intestine and gill tissue of rainbow trout (Oncorhynchus Mycoplasma is widely distributed in nature and well known for its minute size and lack of cell wall. Like Aliivibrio, Mycoplasma has been frequently identified as a core taxon of both wild and captive Atlantic salmon as well (20,33,(35)(36)(37)(38). It was found to be more abundant in marine adults than in freshwater juvenile Atlantic salmon (37) and sporadically predominate intestinal microbial community in the digesta (20,36,37,41,51) and mucosa (35) reaching as high as > 90% of total read counts in extreme cases.…”

“…Like Aliivibrio, Mycoplasma has been frequently identified as a core taxon of both wild and captive Atlantic salmon as well (20,33,(35)(36)(37)(38). It was found to be more abundant in marine adults than in freshwater juvenile Atlantic salmon (37) and sporadically predominate intestinal microbial community in the digesta (20,36,37,41,51) and mucosa (35) reaching as high as > 90% of total read counts in extreme cases. Due to its small compact genome and limited biosynthesis capacities, Mycoplasma typically forms obligate parasitic or commensal relationships with its host to obtain necessary nutrients such as amino acids, fatty acids and sterols (52).…”

“…The major acids produced by Mycoplasma during fermentation are lactic acid and acetic acid (53), the latter of which was found in our recent studies to be 2-4 orders of magnitude higher than other short-chain fatty acids in the Atlantic salmon distal intestine (unpublished data). A recent study found that Atlantic salmon Mycoplasma, recovered by shotgun metagenomic sequencing, was closely related to Mycoplasma penetrans and Mycoplasma yeatsii (20). Compared to these closely related Mycoplasma species, the salmon Mycoplasma appears to carry a much lower number of unique genes that are enriched in carbohydrate uptake and low in peptidase synthesis.…”

“…Due to concerns on the economic, environmental and social sustainability of the current raw materials for Atlantic salmon farming (15), more sustainable alternative feed ingredients, such as insects (17) and yeasts (18), have been developed and used. The use of alternative feed ingredients may not only affect the nutrient utilization, fish growth, health, welfare and product quality, but also intestinal microbiota in Atlantic salmon (19)(20)(21). While studies in mammals and fish have revealed substantial differences between the digesta-and mucosa-associated intestinal microbiota (19,(22)(23)(24)(25), most studies investigating diet effects on the intestinal microbiota of fish have sampled the digesta only or a mixture of digesta and mucosa.…”