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      The Gut Microbiota of Marine Fish

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          Abstract

          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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          Most cited references236

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          Human gut microbiome viewed across age and geography

          Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ between human populations when viewed from the perspective of component microbial lineages, encoded metabolic functions, stage of postnatal development, and environmental exposures, we characterized bacterial species present in fecal samples obtained from 531 individuals representing healthy Amerindians from the Amazonas of Venezuela, residents of rural Malawian communities, and inhabitants of USA metropolitan areas, as well as the gene content of 110 of their microbiomes. This cohort encompassed infants, children, teenagers and adults, parents and offspring, and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the representation of genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial species assemblages and functional gene repertoires were noted between individuals residing in the USA compared to the other two countries. These distinctive features are evident in early infancy as well as adulthood. In addition, the similarity of fecal microbiomes among family members extends across cultures. These findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations, and the impact of Westernization.
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            Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics

            With the continued interest in the role of the gut microbiota in health, attention has now turned to how to harness the microbiota for the benefit of the host. This Consensus Statement outlines the definition and scope of the term 'prebiotic' as determined by an expert panel convened by the International Scientific Association for Probiotics and Prebiotics in December 2016.
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              Diversity, stability and resilience of the human gut microbiota.

              Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
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                Author and article information

                Contributors
                Journal
                Front Microbiol
                Front Microbiol
                Front. Microbiol.
                Frontiers in Microbiology
                Frontiers Media S.A.
                1664-302X
                04 May 2018
                2018
                : 9
                : 873
                Affiliations
                [1] 1School of Microbiology, University College Cork , Cork, Ireland
                [2] 2School of Biological, Earth and Environmental Sciences, University College Cork , Cork, Ireland
                [3] 3Environmental Research Institute, University College Cork , Cork, Ireland
                [4] 4Bio-marine Ingredients Ireland Ltd. , Killybegs, Ireland
                [5] 5Teagasc Research Centre , Fermoy, Ireland
                [6] 6APC Microbiome Ireland, Teagasc and University College Cork , Cork, Ireland
                Author notes

                Edited by: Michael Travisano, University of Minnesota, United States

                Reviewed by: Nastassia Virginia Patin, Georgia Institute of Technology, United States; Thomas Sharpton, Oregon State University, United States

                *Correspondence: R. Paul Ross, p.ross@ 123456ucc.ie

                This article was submitted to Microbial Symbioses, a section of the journal Frontiers in Microbiology

                Article
                10.3389/fmicb.2018.00873
                5946678
                29780377
                ce36e0fd-e147-41c0-b9f8-38b290d1daf0
                Copyright © 2018 Egerton, Culloty, Whooley, Stanton and Ross.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 20 December 2017
                : 16 April 2018
                Page count
                Figures: 1, Tables: 2, Equations: 0, References: 241, Pages: 17, Words: 0
                Funding
                Funded by: Irish Research Council for Science, Engineering and Technology 10.13039/501100001596
                Award ID: EPSPG/2015/57
                Funded by: Science Foundation Ireland 10.13039/501100001602
                Award ID: SFI/12/RC/2273
                Award ID: MFFRI/07/01
                Award ID: 13/F/411
                Categories
                Microbiology
                Review

                Microbiology & Virology
                intestinal bacteria,microbial ecology,metagenomics,dietary intervention,salmon,trophic levels,probiotics and prebiotics,aquaculture

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