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Journal ArticleDOI

Fish intestinal microbiome: diversity and symbiosis unravelled by metagenomics.

TL;DR: This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.
Abstract: The gut microbiome of vertebrates plays an integral role in host health by stimulating development of the immune system, aiding in nutrient acquisition and outcompeting opportunistic pathogens. Development of next-generation sequencing technologies allows researchers to survey complex communities of microorganisms within the microbiome at great depth with minimal costs, resulting in a surge of studies investigating bacterial diversity of fishes. Many of these studies have focused on the microbial structure of economically significant aquaculture species with the goal of manipulating the microbes to increase feed efficiency and decrease disease susceptibility. The unravelling of intricate host-microbe symbioses and identification of core microbiome functions is essential to our ability to use the benefits of a healthy microbiome to our advantage in fish culture, as well as gain deeper understanding of bacterial roles in vertebrate health. This review aims to summarize the available knowledge on fish gastrointestinal communities obtained from metagenomics, including biases from sample processing, factors influencing assemblage structure, intestinal microbiology of important aquaculture species and description of the teleostean core microbiome.
Citations
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Journal ArticleDOI

643 citations

Journal ArticleDOI
TL;DR: The factors shaping marine fish gut microbiota are reviewed and gaps in the research are highlighted and a clear understanding of the role that specific gut microbiota play is still lacking.
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.

481 citations


Cites methods from "Fish intestinal microbiome: diversi..."

  • ...These have been discussed in detail in some recent reviews (Zhou et al., 2014; Tarnecki et al., 2017) Briefly, they include quantitative real-time PCR (qPCR), used for quantitative analysis of taxa; clone libraries for identification of microbiota composition; finger-printing methods such as temporal temperature gradient electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE), and fluorescent in situ hybridization (FISH) used to determine the abundance of particular taxa, total microbial levels and assess bacterial–host interactions at the mucosal brush border (Zhou et al....

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  • ...These have been discussed in detail in some recent reviews (Zhou et al., 2014; Tarnecki et al., 2017) Briefly, they include quantitative real-time PCR (qPCR), used for quantitative analysis of taxa; clone libraries for identification of microbiota composition; finger-printing methods such as…...

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Journal ArticleDOI
TL;DR: Current knowledge on the possible effects of microbiota on feeding, digestive processes, growth, and energy homeostasis in fish is described, with emphasis on the influence of brain and gut hormones, environmental factors, and inter-specific differences.
Abstract: The microorganisms within the intestinal tract (termed gut microbiota) have been shown to interact with the gut-brain axis, a bidirectional communication system between the gut and the brain mediated by hormonal, immune, and neural signals. Through these interactions, the microbiota might affect behaviors, including feeding behavior, digestive/absorptive processes (e.g., by modulating intestinal motility and the intestinal barrier), metabolism, as well as the immune response, with repercussions on the energy homeostasis and health of the host. To date, research in this field has mostly focused on mammals. Studies on non-mammalian models such as fish may provide novel insights into the specific mechanisms involved in the microbiota-brain-gut axis. This review describes our current knowledge on the possible effects of microbiota on feeding, digestive processes, growth, and energy homeostasis in fish, with emphasis on the influence of brain and gut hormones, environmental factors, and inter-specific differences.

247 citations


Cites background from "Fish intestinal microbiome: diversi..."

  • ...To date, most of the studies on gut microbiota have focused on mammals, in particular rodents, and in comparison, little is known about the host-microbe interactions in fish (5)....

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Journal ArticleDOI
TL;DR: Results indicate that LAB may vary in their immunological effects depending on the species and hosts, which includes their impacts on finfish aquaculture, possible routes for treatment and their interaction with fish immune responses.
Abstract: Fish intestinal mucosal surfaces comprise of a complex and dynamic community of microorganisms, which play important roles within the gastrointestinal (GI) tract. Of the bacteria colonising the GI tract, lactic acid bacteria (LAB), are generally considered as favourable bacteria due to their abilities to stimulating host GI development, digestive function, maintaining mucosal tolerance, stimulating immune response and provide protection towards bacterial pathogens. In early finfish studies culture-dependent methods were used to enumerate bacterial population levels within the GI tract; members of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus and Carnobacterium genera were isolated. However, due to limitations by using culture media, techniques such as denaturing gradient gel electrophoresis (DGGE), temporal temperature gradient electrophoresis (TTGE), 16S rRNA clone libraries, and MiSeq sequencing of 16S rRNA genes have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella and Pediococcus as indigenous species. In the GI tract of warm water fish species, members of the genera Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Weissella and Pediococcus have commonly been identified, however, Carnobacterium are rarely identified. Numerous strains of LAB isolated from finfish are capable of producing antibacterial substances against different potential fish pathogenic bacteria as well as human pathogens. In addition, many LAB have the ability to inhibit growth of closely related bacteria including strains of carnobacteria, lactobacilli, lactococci, leuconostoc and pediococci. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade increasing number of research attempts are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains showed beneficial effects on growth performance, reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB such as members of the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium and Lactococcus have been detected from ascites, kidney, liver, heart and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment.

222 citations

References
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Journal ArticleDOI
TL;DR: Phylogenetic analysis of the retrieved rRNA sequence of an uncultured microorganism reveals its closest culturable relatives and may, together with information on the physicochemical conditions of its natural habitat, facilitate more directed cultivation attempts.

9,017 citations


"Fish intestinal microbiome: diversi..." refers background or methods in this paper

  • ...The first attempts to explore fish intestinal microbiology used culture-based methods that vastly underestimate the diversity of these communities, as <10% of bacteria can be isolated and cultured under laboratory conditions (Amann et al. 1995)....

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  • ...Fluorescence in situ hybridization (FISH) uses fluorescent-label probes to directly observe microbes, with minimal processing, using fluorescence or confocal microscopy (Amann et al. 1995)....

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Journal ArticleDOI
TL;DR: A technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments is presented.
Abstract: Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications for NGS technologies, in addition to providing guidelines for platform selection to address biological questions of interest.

7,023 citations


"Fish intestinal microbiome: diversi..." refers background in this paper

  • ...Numerous reviews address NGS sequencing technologies, including sample preparation, sequencing chemistry and pros and cons (Metzker 2010; Mardis 2013; Chiu and Miller 2016)....

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Journal ArticleDOI
17 Oct 2007-Nature
TL;DR: A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.
Abstract: A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

4,730 citations


"Fish intestinal microbiome: diversi..." refers background in this paper

  • ...Discovering a core microbiome, that is, members of the microbial community present in all individuals of a species, has been a primary goal for many researchers interested in understanding gut microbial communities (Turnbaugh et al. 2007)....

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Journal ArticleDOI
TL;DR: This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea.
Abstract: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.

1,755 citations

Journal ArticleDOI
TL;DR: It is indicated that a core microbiome can be found at the gene level, despite large variation in community membership, and that variations from the core are associated with obesity.
Abstract: Metagenomics is an emerging field focused on characterizing the structures, functions and dynamic operations of microbial communities sampled in their native habitats without the need for culture. Here, we present findings from a 16S rRNA gene sequence- and whole community DNA shotgun sequencing-based analysis of the adult human gut microbiomes of lean and obese mono- and dizygotic twins. Our findings indicate that a core microbiome can be found at the gene level, despite large variation in community membership, and that variations from the core are associated with obesity. These findings have implications for ongoing Human Microbiome Project(s), and highlight important challenges to the field of metagenomics.

912 citations


"Fish intestinal microbiome: diversi..." refers background in this paper

  • ...The theory of a core gut microbiome has primarily been explored in humans and mammalian models (Tap et al. 2009; Turnbaugh and Gordon 2009), but many authors believe that the same concept applies to bony fish....

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  • ...The theory of a core gut microbiome has primarily been explored in humans and mammalian models (Tap et al. 2009; Turnbaugh and Gordon 2009), but many authors believe the same concept applies to bony fish....

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