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      Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish ( Seriola lalandi)

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          Summary

          The supply of quality juveniles via land‐based larviculture represents a major bottleneck to the growing finfish aquaculture industry. As the microbiome plays a key role in animal health, this study aimed to assess the microbial community associated with early larval development of commercially raised Yellowtail Kingfish ( Seriola lalandi). We used qPCR and 16S rRNA gene amplicon sequencing to monitor changes in the microbiome associated with the development of S. lalandi from larvae to juveniles. We observed an increase in the bacterial load during larval development, which consisted of a small but abundant core microbiota including taxa belonging to the families Rhodobacteraceae, Lactobacillaceae and Vibrionaceae. The greatest change in the microbiome occurred as larvae moved from a diet of live feeds to formulated pellets, characterized by a transition from Proteobacteria to Firmicutes as the dominant phylum. A prediction of bacterial gene functions found lipid metabolism and secondary metabolite production were abundant in the early larval stages, with carbohydrate and thiamine metabolism functions increasing in abundance as the larvae age and are fed formulated diets. Together, these results suggest that diet is a major contributor to the early microbiome development of commercially raised S. lalandi.

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            Environmental and ecological factors that shape the gut bacterial communities of fish: a meta-analysis.

            Symbiotic bacteria often help their hosts acquire nutrients from their diet, showing trends of co-evolution and independent acquisition by hosts from the same trophic levels. While these trends hint at important roles for biotic factors, the effects of the abiotic environment on symbiotic community composition remain comparably understudied. In this investigation, we examined the influence of abiotic and biotic factors on the gut bacterial communities of fish from different taxa, trophic levels and habitats. Phylogenetic and statistical analyses of 25 16S rRNA libraries revealed that salinity, trophic level and possibly host phylogeny shape the composition of fish gut bacteria. When analysed alongside bacterial communities from other environments, fish gut communities typically clustered with gut communities from mammals and insects. Similar consideration of individual phylotypes (vs. communities) revealed evolutionary ties between fish gut microbes and symbionts of animals, as many of the bacteria from the guts of herbivorous fish were closely related to those from mammals. Our results indicate that fish harbour more specialized gut communities than previously recognized. They also highlight a trend of convergent acquisition of similar bacterial communities by fish and mammals, raising the possibility that fish were the first to evolve symbioses resembling those found among extant gut fermenting mammals. © 2012 Blackwell Publishing Ltd.
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              The Gut Microbiota of Marine Fish

              The body of work relating to the gut microbiota of fish is dwarfed by that on humans and mammals. However, it is a field that has had historical interest and has grown significantly along with the expansion of the aquaculture industry and developments in microbiome research. Research is now moving quickly in this field. Much recent focus has been on nutritional manipulation and modification of the gut microbiota to meet the needs of fish farming, while trying to maintain host health and welfare. However, the diversity amongst fish means that baseline data from wild fish and a clear understanding of the role that specific gut microbiota play is still lacking. We review here the factors shaping marine fish gut microbiota and highlight gaps in the research.
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                Author and article information

                Contributors
                s.egan@unsw.edu.au
                Journal
                Microb Biotechnol
                Microb Biotechnol
                10.1111/(ISSN)1751-7915
                MBT2
                Microbial Biotechnology
                John Wiley and Sons Inc. (Hoboken )
                1751-7915
                01 December 2018
                March 2019
                : 12
                : 2 ( doiID: 10.1111/mbt2.2019.12.issue-2 )
                : 275-288
                Affiliations
                [ 1 ] Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences University of New South Wales Sydney NSW Australia
                [ 2 ] NSW Department of Primary Industries Port Stephens Fisheries Institute (PSFI) Taylors Beach NSW Australia
                Author notes
                [*] [* ]For correspondence. E‐mail s.egan@ 123456unsw.edu.au ; Tel. +61 (0) 2 93858569; Fax +61 2 9385 3327.
                Author information
                http://orcid.org/0000-0003-3286-4279
                Article
                MBT213323
                10.1111/1751-7915.13323
                6389859
                30506824
                51676044-ec23-4f98-a8a9-13cf5261c386
                © 2018 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 07 July 2018
                : 07 September 2018
                : 12 September 2018
                Page count
                Figures: 7, Tables: 2, Pages: 14, Words: 9832
                Categories
                Research Article
                Research Articles
                Custom metadata
                2.0
                mbt213323
                March 2019
                Converter:WILEY_ML3GV2_TO_NLMPMC version:5.6.0 mode:remove_FC converted:26.02.2019

                Biotechnology
                Biotechnology

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