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Background  Aquaculture successfully meets global food demands for many fish species. However, aquaculture production of Atlantic cod ( Gadus morhua ) is just 2.5% of total market production. For cod farming to be a viable economic venture specific challenges on how to increase growth, health and farming productivity need to be addressed. Feed ingredients play a key role here. Macroalgae (seaweeds) have been suggested as a functional feed supplement with both health and economic benefits for terrestrial farmed animals and fish. The impact of such dietary supplements to cod gut integrity and microbiota, which contribute to overall fish robustness is unknown. The objective of this study was to supplement the diet of juvenile Atlantic cod with macroalgae and determine the impacts on fish condition and growth, gut morphology and hindgut microbiota composition (16S rRNA amplicon sequencing). Fish were fed one of three diets: control (no macroalgal inclusion), 10% inclusion of either egg wrack ( Ascophyllum nodosum ) or sea lettuce ( Ulva rigida ) macroalgae in a 12-week trial.    Results  The results demonstrated there was no significant difference in fish condition, gut morphology or hindgut microbiota between the  U. rigida  supplemented fish group and the control group at any time-point. This trend was not observed with the  A. nodosum  treatment. Fish within this group were further categorised as either ‘Normal’ or ‘Lower Growth’. ‘Lower Growth’ individuals found the diet unpalatable resulting in reduced weight and condition factor combined with an altered gut morphology and microbiome relative to the other treatments. Excluding this group, our results show that the hindgut microbiota was largely driven by temporal pressures with the microbial communities becoming more similar over time irrespective of dietary treatment. The core microbiome at the final time-point consisted of the orders  Vibrionales  ( Vibrio  and  Photobacterium ),  Bacteroidales  ( Bacteroidetes  and  Macellibacteroides ) and  Clostridiales  ( Lachnoclostridium ).    Conclusions  Our study indicates that  U. rigida  macroalgae can be supplemented at 10% inclusion levels in the diet of juvenile farmed Atlantic cod without any impact on fish condition or hindgut microbial community structure. We also conclude that 10% dietary inclusion of  A. nodosum  is not a suitable feed supplement in a farmed cod diet.    Supplementary Information  The online version contains supplementary material available at 10.1186/s42523-020-00065-1.

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae