Microbiome diversity and dysbiosis in aquaculture

Sandra Infante‐Villamil; Roger Huerlimann; Dean R. Jerry

doi:10.1111/raq.12513

journal article Oct 27, 2020

Microbiome diversity and dysbiosis in aquaculture

Sandra Infante‐Villamil

Roger Huerlimann Dean R. Jerry

Reviews in Aquaculture Vol. 13 No. 2 pp. 1077-1096 · Wiley

View at Publisher Save 10.1111/raq.12513

Abstract

AbstractWith the continuous growth of the human population and associated need for high‐quality protein, the aquaculture sector will be required to increase significantly in productivity. This growth in productivity will be achieved through more efficient use of resources like feeds, genetic improvement and limiting the impacts of disease. One of the key links between animal productivity and disease is that of microbial diversity, with high‐throughput sequencing technologies increasing our understanding of the role microorganisms play in health, development and physiology of vertebrate and invertebrate hosts alike. Increasing our understanding of microbial–host interactions will help avoid or manage dysbiosis in aquaculture systems with the final aim of improving productivity. We review the current literature, which indicates that there is an association between productivity and microbial diversity in aquaculture systems, as changes in bacterial microbiomes are implicated in animal performance, in disease development associated with both bacterial and viral origin, and in dysbiosis triggered by environmental stressors or diet choice. Dysbiosis, whether in the form of the loss of beneficial bacteria, or the expansion of pathogens or potentially harmful microorganisms, can be used as an indicator tool for productivity monitoring purposes. Development of management strategies towards preserving the microbial balance, including maintaining or increasing diversity in the host, is critical for the health of cultured aquatic animals and will likely be critical for the expansion of aquaculture.

Topics

No keywords indexed for this article. Browse by subject →

References

160

[1]

10.1016/j.aquaculture.2016.05.028

[2]

Do Vertebrate Gut Metagenomes Confer Rapid Ecological Adaptation?

Antton Alberdi, Ostaizka Aizpurua, Kristine Bohmann et al.

Trends in Ecology & Evolution 10.1016/j.tree.2016.06.008

[3]

10.1111/jwas.12642

[4]

10.1186/s12866-017-1101-8

[5]

Opportunities and challenges in long-read sequencing data analysis

Shanika L. Amarasinghe, Shian Su, Xueyi Dong et al.

Genome Biology 10.1186/s13059-020-1935-5

[6]

10.1007/978-1-4939-8728-3

[7]

10.1111/1751-7915.12392

[8]

10.1152/physrev.1990.70.2.567

[9]

10.1128/msystems.00062-16

[10]

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen, Jai Ram Rideout, Matthew R. Dillon et al.

Nature Biotechnology 10.1038/s41587-019-0209-9

[11]

The Biodegradation of Poly-β-Hydroxybutyrate (PHB) by a Model Soil Community: The Effect of Cultivation Conditions on the Degradation Rate and the Physicochemical Characteristics of PHB

G. A. Bonartseva, V. L. Myshkina, D. A. Nikolaeva et al.

Microbiology 10.1023/a:1015162608031

[12]

10.1016/j.aquaculture.2017.10.025

[13]

10.1371/journal.pone.0084772

[14]

10.1073/pnas.0702059104

[15]

10.2307/1942268

[16]

10.1016/j.aquaculture.2018.01.006

[17]

10.3354/meps224187

[18]

10.1016/j.aquaculture.2017.12.022

[19]

Chao A "Non‐parametric estimation of the number of classes in a population" Scandinavian Journal of Statistics (1984)

[20]

10.1038/s41598-017-09923-6

[21]

10.1073/pnas.1000072107

[22]

10.1038/srep16350

[23]

10.1111/1748-5967.12043

[24]

Clarke KR (2001)

[25]

Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome

Camille Clerissi, Julien de Lorgeril, Bruno Petton et al.

Frontiers in Microbiology 10.3389/fmicb.2020.00311

[26]

10.1038/s41598-017-11805-w

[27]

10.1007/s00253-018-8891-y

[28]

10.1016/j.mimet.2009.11.009

[29]

10.1093/femsec/fix161

[30]

10.1007/s00253-009-2414-9

[31]

10.1111/1751-7915.12877

[32]

10.1146/annurev.ento.43.1.17

[33]

10.1111/are.14770

[34]

Conservation evaluation and phylogenetic diversity

Daniel P. Faith

Biological Conservation 10.1016/0006-3207(92)91201-3

[35]

10.1126/scitranslmed.3008051

[36]

10.1038/s41598-018-37042-3

[37]

FAO(2018)The State of World Fisheries and Aquaculture 2018. Meeting the sustainable development goals Rome.

[38]

10.1038/srep21192

[39]

10.1186/s12866-016-0738-z

[40]

Antinutritional factors present in plant-derived alternate fish feed ingredients and their effects in fish

George Francis, Harinder P.S Makkar, Klaus Becker

Aquaculture 10.1016/s0044-8486(01)00526-9

[41]

10.1111/j.1365-2109.2007.01704.x

[42]

10.1007/s00248-018-1242-9

[43]

10.1016/j.vetmic.2013.05.009

[44]

10.1007/978-1-4939-8728-3_8

[45]

10.1371/journal.pone.0202351

[46]

10.1016/j.fsi.2018.10.013

[47]

10.1016/j.fsi.2020.04.058

[48]

Harlystiarini H "In vitro antibacterial activity of black soldier fly (Hermetia illucens) larva extracts against gram‐negative bacteria" Bulletin of Animal Science. (2019)

[49]

10.1146/annurev.nutr.22.011602.092259

[50]

10.7717/peerj.8705

Showing 50 of 160 references

Cited By

151

Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management

Hirokazu Toju, Kenta Suzuki · 2026

The ISME Journal

Exploring the Molluscan Microbiome: Diversity, Function, and Ecological Implications

Tsireledzo Goodwill Makwarela, Nimmi Seoraj-Pillai · 2025

Biology

Effects of β-glucan combined with the gut probiotic Klebsiella sp. E26 on growth, energy metabolism, and immune response in pacific white shrimp (Penaeus vannamei) under low salinity stress

Tong Chang, Kunyu Lu · 2025

Aquaculture

Core species and interactions prominent in fish-associated microbiome dynamics

Daii Yajima, Hiroaki Fujita · 2023

Microbiome

Fish disease and intestinal microbiota: A close and indivisible relationship

Diana Medina‐Félix, Estefanía Garibay‐Valdez · 2022

Reviews in Aquaculture

Metrics

151

Citations

160

References

Details

Published: Oct 27, 2020
Vol/Issue: 13(2)
Pages: 1077-1096
License: View

Authors

S

Sandra Infante‐Villamil

Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding Townsville QLD Australia; College of Science and Engineering Centre for Sustainable Tropical Fisheries and Aquaculture James Cook University Townsville QLD Australia

R

Roger Huerlimann

Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding Townsville QLD Australia; College of Science and Engineering Centre for Sustainable Tropical Fisheries and Aquaculture James Cook University Townsville QLD Australia

D

Dean R. Jerry

Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding Townsville QLD Australia; College of Science and Engineering Centre for Sustainable Tropical Fisheries and Aquaculture James Cook University Townsville QLD Australia; Tropical Futures Institute James Cook University Singapore

Cite This Article

Sandra Infante‐Villamil, Roger Huerlimann, Dean R. Jerry (2020). Microbiome diversity and dysbiosis in aquaculture. Reviews in Aquaculture, 13(2), 1077-1096. https://doi.org/10.1111/raq.12513

Microbiome diversity and dysbiosis in aquaculture

You May Also Like