Aquaculture 574 (2023) 739672 Available online 13 May 2023 0044-8486/© 2023 Elsevier B.V. All rights reserved. Mucosal bacteriomes of rainbow trout (Oncorhynchus mykiss) intestines are modifed in response to dietary phytase Süheyla Karatas ¸ a, * , Emre Turgay a , Mustafa Yıldız a , Victor E. Kaiza c, d , Remziye Eda Yardımcı a , Terje Marken Steinum b a Dept. of Aquaculture and Fish Diseases, Faculty of Aquatic Sciences, Istanbul University, Istanbul, Turkiye b Dept. of Molecular Biology and Genetics, Faculty of Life Sciences, Istanbul University, Istanbul, Turkiye c Istanbul University, Institute of Graduate Studies in Science and Technology, Dept. of Aquaculture and Fish Diseases, Istanbul, Turkiye d Fisheries Education and Training Agency (FETA), Tanzania A R T I C L E INFO Keywords: Bacterial 6-phytase Functional feed Intestinal mucosa Monocalcium phosphate Mycoplasma Optiphos ABSTRACT Global aquaculture has seen an unprecedented expansion in recent years partly due to “functional feeds” that is known to improve feed utilization, fsh growth performance and resilience to infectious disease. Nevertheless, a knowledge gap exists about how dietary phytase might infuence intestinal bacteriomes of farmed fsh. We therefore performed 16S rRNA gene-based community profling. The remarkably uniform mucosal bacteriomes of rainbow trout (median Bray-Curtis similarity index 0.76 ± 0.09) fed the control diet were dominated by lactic acid bacteria (LAB) from putative phytase producing genera Lactococcus and Leuconostoc that likely originated from plant-based feed ingredients. Mucosal bacteriomes developed into uniform communities instead dominated by Mycoplasma-bacteria (median Bray-Curtis similarity index 0.55 ± 0.13) in response to the optimal amount of dietary phytase (0.15 g/kg feed). Both community types had a similar median species richness with 933 ± 301 and 1005 ± 678 bacterial taxa, respectively. A functional genomics analysis revealed that especially genes for amino acid and carbohydrate metabolism/transport were enriched in the LAB-dominated mucosal bacteriomes supporting their role as providers of otherwise inaccessible nutrients from for example dietary fbres. In contrast, only genes for energy production and conversion were marginally enriched in Mycoplasma-dominated commu- nities. It is plausible that a combination of nutrient and mucosal space/attachment site competition is behind the observed shift in mucosal communities. Our results confrm previous reports that dietary phytase improve signifcantly both fsh growth performance and feed utilization (p < 0.05). Moreover, dietary phytase is rec- ommended for use in aquaculture as the enzyme apparently can facilitate the establishment of benefcial My- coplasma-dominated bacteriomes in the intestinal mucosa of farmed rainbow trout. 1. Introduction In recent years, aquaculture has arguably seen the fastest growth in global food production. But fsh in aquaculture systems remain suscep- tible to infectious agents as they are kept in densely populated and often physically restricted environments. Another limiting factor is the availability of marine raw materials, like fsh oil and meal, to meet the ever-growing demand for high quality fsh feed. A milestone was the partial replacement of fsh meal with plant-based ingredients or later other alternative protein sources (Arag˜ ao et al., 2022) that contributes towards true sustainability in aquaculture. However, unforeseen risks include increased occurrence of chronic intestinal infammation and rare cases of intestinal tumours (Dale et al., 2009) as carnivore cultured salmonids are not adapted to partially plant-based diets. A second advance in fsh feed formulation has been the inclusion of various sup- plements to improve fsh growth performance, feed utilization or resil- ience to infectious disease. Such “functional feeds” for rainbow trout include either pre/probiotics (Gonçalves and Gallardo-Esc´ arate, 2017), inorganic feed supplements (Mili´ an-Sorribes et al., 2021) or microbial enzymes like phytases (Lee et al., 2020). Plant-based ingredients in fsh feed and in livestock/poultry diets are high in phytate. However, phytate (phytic acid) is indigestible for non- ruminant animals and stores phosphorus in a stable form that binds micro/macro-nutrients including minerals, proteins, sugars and lipids * Corresponding author. E-mail address: skaratas@istanbul.edu.tr (S. Karatas ¸). Contents lists available at ScienceDirect Aquaculture journal homepage: www.elsevier.com/locate/aquaculture https://doi.org/10.1016/j.aquaculture.2023.739672 Received 25 January 2023; Received in revised form 13 April 2023; Accepted 10 May 2023