Cited by 670Aquaculture disease management and microbiotaAquaculture Nutrition and GrowthGut microbiota and health

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A new view of the fish gut microbiome: Advances from next-generation sequencing

Ghanbari, Mahdi, Kneifel, Wolfgang, Domig, Konrad J.·2015·Aquaculture

DOI 10.1016/j.aquaculture.2015.06.033

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Abstract

The fish gut microbiota contributes to digestion and can affect the nutrition, growth, reproduction, overall population dynamics and vulnerability of the host fish to disease; therefore, this microbial community is highly relevant for aquaculture practice. Recent advances in DNA sequencing technologies and bioinformatic analysis have allowed us to develop a broader understanding of the complex microbial communities associated with various habitats, including the fish gut microbiota. These recent advances have substantially improved our knowledge of bacterial community profiles in the fish intestinal microbiota in response to a variety of factors affecting the host, including variations in temperature, salinity, developmental stage, digestive physiology and feeding strategy. The goal of this review is to highlight the potential of next-generation sequencing platforms for analysing fish gut microbiota. Recent and promising results in this field are presented along with a focus on new perspectives and future research directions of fish gut microbial ecology.

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Additional file 2 of Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream
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Additional file 5 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages
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Additional file 4 of Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history
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Additional file 1 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages
Tawfik, M. M., Lorgen-Ritchie, M., Król, E., McMillan, S., Norambuena, F., Bolnick, D. I., Douglas, A., Tocher, D. R., Betancor, M. B., & Martin, S. A. M. (2024) · Figshare · doi:10.6084/m9.figshare.26143740
Additional file 10 of Circadian dynamics of the teleost skin immune-microbiome interface
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Additional file 3 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages
Tawfik, M. M., Lorgen-Ritchie, M., Król, E., McMillan, S., Norambuena, F., Bolnick, D. I., Douglas, A., Tocher, D. R., Betancor, M. B., & Martin, S. A. M. (2024) · Figshare · doi:10.6084/m9.figshare.26741126
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Additional file 4 of Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats
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Additional file 4 of Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream
Piazzon, M. C., Naya-Català, F., Perera, E., Palenzuela, O. R., Sitjà‐Bobadilla, A., & Pérez-Sánchez, J. (2020) · Figshare · doi:10.6084/m9.figshare.13278407
Additional file 1 of Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats
Wu, B., Huang, L., Chen, J., Zhang, Y., Wang, J., & He, J. (2021) · Figshare · doi:10.6084/m9.figshare.14576612
Additional file 2 of Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history
Scheelings, T. F., Moore, R. J., Van, T. T. H., Klaassen, M., & Reina, R. D. (2020) · Figshare · doi:10.6084/m9.figshare.12270401
Additional file 2 of Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats
Wu, B., Huang, L., Chen, J., Zhang, Y., Wang, J., & He, J. (2021) · Figshare · doi:10.6084/m9.figshare.14576615
Additional file 3 of Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream
Piazzon, M. C., Naya-Català, F., Perera, E., Palenzuela, O. R., Sitjà‐Bobadilla, A., & Pérez-Sánchez, J. (2020) · Figshare · doi:10.6084/m9.figshare.13278404
Additional file 7 of Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream
Piazzon, M. C., Naya-Català, F., Perera, E., Palenzuela, O. R., Sitjà‐Bobadilla, A., & Pérez-Sánchez, J. (2020) · Figshare · doi:10.6084/m9.figshare.13278416
Additional file 2 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages
Tawfik, M. M., Lorgen-Ritchie, M., Król, E., McMillan, S., Norambuena, F., Bolnick, D. I., Douglas, A., Tocher, D. R., Betancor, M. B., & Martin, S. A. M. (2024) · Figshare · doi:10.6084/m9.figshare.26143787
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Additional file 5 of Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages
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Additional file 3 of Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats
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Additional file 4 of Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages
Tawfik, M. M., Lorgen-Ritchie, M., Król, E., McMillan, S., Norambuena, F., Bolnick, D. I., Douglas, A., Tocher, D. R., Betancor, M. B., & Martin, S. A. M. (2024) · Figshare · doi:10.6084/m9.figshare.26741129
Additional file 4 of Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages
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Wu, X., Liu, J., He, J., Liu, Z., Yuan, F., Li, D., & 黄伟卿 (2026) · Veterinary Sciences · doi:10.3390/vetsci13111156

Authors: Ghanbari, M., Kneifel, W., & Domig, K. J.
Affiliations: Zabol University (IR)
BOKU University (AT)
Corresponding author: Ghanbari, Mahdi
ORCID: Ghanbari, Mahdi
Kneifel, Wolfgang
Domig, Konrad J.
Venue: Aquaculture
Publisher: Elsevier BV
Published: 2015-11
Volume: 448
Pages: 464-475
ISSN: 0044-8486 (ISSN-L)
DOI: 10.1016/j.aquaculture.2015.06.033
OpenAlex: W1004644096
Cited by: 669
References: 90
Citations by year: 2026: 45 · 2025: 69 · 2024: 82 · 2023: 88 · 2022: 88 · 2021: 93 · 2020: 68 · 2019: 52 · 2018: 37 · 2017: 24 · 2016: 19 · 2015: 2
FWCI: 13.45
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Aquaculture (publishedVersion)
Topics: Life Sciences › Immunology and Microbiology › Immunology › Aquaculture disease management and microbiota
Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Aquaculture Nutrition and Growth
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords: fish gut microbiota, gut microbiota, microbial ecology, host factors, temperature, salinity, developmental stages, digestive physiology, feeding strategies

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A new view of the fish gut microbiome: Advances from next-generation sequencing

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