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      Bacterial Community Associated with the Intestinal Tract of Chinese Mitten Crab ( Eriocheir sinensis) Farmed in Lake Tai, China

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          Abstract

          Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal >95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host.

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          Evidence for a core gut microbiota in the zebrafish.

          Experimental analysis of gut microbial communities and their interactions with vertebrate hosts is conducted predominantly in domesticated animals that have been maintained in laboratory facilities for many generations. These animal models are useful for studying coevolved relationships between host and microbiota only if the microbial communities that occur in animals in lab facilities are representative of those that occur in nature. We performed 16S rRNA gene sequence-based comparisons of gut bacterial communities in zebrafish collected recently from their natural habitat and those reared for generations in lab facilities in different geographic locations. Patterns of gut microbiota structure in domesticated zebrafish varied across different lab facilities in correlation with historical connections between those facilities. However, gut microbiota membership in domesticated and recently caught zebrafish was strikingly similar, with a shared core gut microbiota. The zebrafish intestinal habitat therefore selects for specific bacterial taxa despite radical differences in host provenance and domestication status.
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            Characterization of the gut microbiota of three commercially valuable warmwater fish species.

            Due to the strong influence of the gut microbiota on fish health, dominant bacterial species in the gut are strong candidates for probiotics. This study aimed to characterize the gut microbiota of channel catfish Ictalurus punctatus, largemouth bass Micropterus salmoides and bluegill Lepomis macrochirus to provide a baseline for future probiotic studies. The gut microbiota of five pooled individuals from each fish species was identified using 16S rRNA pyrosequencing. Microbiota differed significantly between fish species in terms of bacterial species evenness. However, all gut communities analysed were dominated by the phylum Fusobacteria, specifically the species Cetobacterium somerae. Relatively high abundances of the human pathogens Plesiomonas shigelloides and Fusobacterium mortiferum, as well as members of the genus Aeromonas, suggest these species are normal inhabitants of the gut. The overwhelming dominance of the genus Cetobacterium in all species warrants further investigation into its role in the fish gut microbiota. This study provides the first characterization of the gut microbiota of three economically significant fishes and establishes a baseline for future probiotic trials. © 2014 The Society for Applied Microbiology.
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              Novel primers for 16S rRNA-based archaeal community analyses in environmental samples.

              Next generation sequencing technologies for in depth analyses of complex microbial communities rely on rational primer design based on up-to-date reference databases. Most of the 16S rRNA-gene based analyses of environmental Archaea community composition use PCR primers developed from small data sets several years ago, making an update long overdue. Here we present a new set of archaeal primers targeting the 16S rRNA gene designed from 8500 aligned archaeal sequences in the SILVA database. The primers 340F-1000R showed a high archaeal specificity (<1% bacteria amplification) covering 93 and 97% of available sequences for Crenarchaeota and Euryarchaeota respectively. In silico tests of the primers revealed at least 38% higher coverage for Archaea compared to other commonly used primers. Empirical tests with clone libraries confirmed the high specificity of the primer pair to Archaea in three biomes: surface waters in the Arctic Ocean, the pelagic zone of a temperate lake and a methanogenic bioreactor. The clone libraries featured both Euryarchaeota and Crenarchaeota in variable proportions and revealed dramatic differences in the archaeal community composition and minimal phylogenetic overlap between samples. Copyright © 2010 Elsevier B.V. All rights reserved.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                13 April 2015
                2015
                : 10
                : 4
                : e0123990
                Affiliations
                [1 ]Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage & Preservation, Ministry of Agriculture, Shanghai, China
                [2 ]Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
                [3 ]College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
                [4 ]Institute of Biochemistry and Molecular Cell Biology, University of Goettingen, Goettingen, Germany
                Fish Vet Group, THAILAND
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SY YW. Performed the experiments: XC PD HW. Analyzed the data: XC PD HW SY YW. Contributed reagents/materials/analysis tools: BL YP. Wrote the paper: XC PD YW.

                Article
                PONE-D-14-48068
                10.1371/journal.pone.0123990
                4395229
                25875449
                929a5e8d-0430-495e-a83b-470111124b01
                Copyright @ 2015

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 28 October 2014
                : 25 February 2015
                Page count
                Figures: 10, Tables: 5, Pages: 21
                Funding
                This work was supported by the National Natural Science Foundation of China (No. 41376135), Doctoral Fund of Ministry of Education of China (20133104110006), Innovation Program of Shanghai Municipal Education Commission (14ZZ144), China, to YW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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                Research Article
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