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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MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Sequencing technologies – the next generation
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066
Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness
Gotelli, N., & Colwell, R. K. (2001) · Ecology Letters · doi:10.1046/j.1461-0248.2001.00230.x · Cited by 6,529
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747
Next-Generation DNA Sequencing Methods
Mardis, E. R. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164359 · Cited by 2,469
Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology
Muyzer, G., & Smalla, K. (1998) · Antonie van Leeuwenhoek · doi:10.1023/a:1000669317571 · Cited by 2,065
Removing Noise From Pyrosequenced Amplicons
Quince, C., Lanzén, A., Davenport, R. J., & Turnbaugh, P. J. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-38 · Cited by 1,634
Comparison of Next-Generation Sequencing Systems
Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., Lin, D., Lü, L., & Law, M. (2012) · BioMed Research International · doi:10.1155/2012/251364 · Cited by 1,605
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
Větrovský, T., & Baldrián, P. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057923 · Cited by 1,201

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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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