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Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets

BACKGROUND: Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made t...

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Autores principales: Bruno, Antonia, Sandionigi, Anna, Panio, Antonella, Rimoldi, Simona, Orizio, Flavio, Agostinetto, Giulia, Hasan, Imam, Gasco, Laura, Terova, Genciana, Labra, Massimo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10481543/
https://www.ncbi.nlm.nih.gov/pubmed/37674159
http://dx.doi.org/10.1186/s12866-023-02990-y
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author Bruno, Antonia
Sandionigi, Anna
Panio, Antonella
Rimoldi, Simona
Orizio, Flavio
Agostinetto, Giulia
Hasan, Imam
Gasco, Laura
Terova, Genciana
Labra, Massimo
author_facet Bruno, Antonia
Sandionigi, Anna
Panio, Antonella
Rimoldi, Simona
Orizio, Flavio
Agostinetto, Giulia
Hasan, Imam
Gasco, Laura
Terova, Genciana
Labra, Massimo
author_sort Bruno, Antonia
collection PubMed
description BACKGROUND: Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples. RESULTS: Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group. CONCLUSIONS: Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02990-y.
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spelling pubmed-104815432023-09-07 Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets Bruno, Antonia Sandionigi, Anna Panio, Antonella Rimoldi, Simona Orizio, Flavio Agostinetto, Giulia Hasan, Imam Gasco, Laura Terova, Genciana Labra, Massimo BMC Microbiol Research BACKGROUND: Sustainable aquaculture relies on multiple factors, including water quality, fish diets, and farmed fish. Replacing fishmeal (FM) with alternative protein sources is key for improving sustainability in aquaculture and promoting fish health. Indeed, great research efforts have been made to evaluate novel feed formulations, focusing especially on the effects on the fish gut microbiome. Few studies have explored host-environment interactions. In the present study, we evaluated the influence of novel insect-based (Tenebrio molitor) fish diets on the microbiome at the water-fish interface in an engineered rainbow trout (Oncorhynchus mykiss) farming ecosystem. Using 16S rRNA gene metabarcoding, we comprehensively analyzed the microbiomes of water, tank biofilm, fish intestinal mucus, fish cutis, and feed samples. RESULTS: Core microbiome analysis revealed the presence of a highly reduced core shared by all sample sources, constituted by Aeromonas spp., in both the control and novel feed test groups. Network analysis showed that samples were clustered based on the sample source, with no significant differences related to the feed formulation tested. Thus, the different diets did not seem to affect the environment (water and tank biofilm) and fish (cutis and intestinal mucus) microbiomes. To disentangle the contribution of feed at a finer scale, we performed a differential abundance analysis and observed differential enrichment/impoverishment in specific taxa, comparing the samples belonging to the control diet group and the insect-based diet group. CONCLUSIONS: Omic exploration of the water-fish interface exposes patterns that are otherwise undetected. These data demonstrate a link between the environment and fish and show that subtle but significant differences are caused by feed composition. Thus, the research presented here is a step towards positively influencing the aquaculture environment and its microbiome. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-023-02990-y. BioMed Central 2023-09-06 /pmc/articles/PMC10481543/ /pubmed/37674159 http://dx.doi.org/10.1186/s12866-023-02990-y Text en © The Author(s) 2023, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Bruno, Antonia
Sandionigi, Anna
Panio, Antonella
Rimoldi, Simona
Orizio, Flavio
Agostinetto, Giulia
Hasan, Imam
Gasco, Laura
Terova, Genciana
Labra, Massimo
Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title_full Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title_fullStr Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title_full_unstemmed Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title_short Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets
title_sort aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with tenebrio molitor novel diets
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10481543/
https://www.ncbi.nlm.nih.gov/pubmed/37674159
http://dx.doi.org/10.1186/s12866-023-02990-y
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