Cargando…
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...
Autores principales: | , , , , , , , , , |
---|---|
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 |
_version_ | 1785101999008645120 |
---|---|
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. |
format | Online Article Text |
id | pubmed-10481543 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT brunoantonia aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT sandionigianna aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT panioantonella aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT rimoldisimona aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT orizioflavio aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT agostinettogiulia aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT hasanimam aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT gascolaura aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT terovagenciana aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets AT labramassimo aquacultureecosystemmicrobiomeatthewaterfishinterfacethecasestudyofrainbowtroutfedwithtenebriomolitornoveldiets |