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      The characteristics of gut microbiota and commensal Enterobacteriaceae isolates in tree shrew ( Tupaia belangeri)

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          Abstract

          Background

          Tree shrew is a novel laboratory animal with specific characters for human disease researches in recent years. However, little is known about its characteristics of gut microbial community and intestinal commensal bacteria. In this study, 16S rRNA sequencing method was used to illustrate the gut microbiota structure and commensal Enterobacteriaceae bacteria were isolated to demonstrate their features.

          Results

          The results showed Epsilonbacteraeota (30%), Proteobacteria (25%), Firmicutes (19%), Fusobacteria (13%), and Bacteroidetes (8%) were the most abundant phyla in the gut of tree shrew. Campylobacteria, Campylobacterales, Helicobacteraceae and Helicobacter were the predominant abundance for class, order, family and genus levels respectively. The alpha diversity analysis showed statistical significance ( P < 0.05) for operational taxonomic units (OTUs), the richness estimates, and diversity indices for age groups of tree shrew. Beta diversity revealed the significant difference (P < 0.05) between age groups, which showed high abundance of Epsilonbacteraeota and Spirochaetes in infant group, Proteobacteria in young group, Fusobacteria in middle group, and Firmicutes in senile group. The diversity of microbial community was increased followed by the aging process of this animal. 16S rRNA gene functional prediction indicated that highly hot spots for infectious diseases, and neurodegenerative diseases in low age group of tree shrew (infant and young). The most isolated commensal Enterobacteriaceae bacteria from tree shrew were Proteus spp. (67%) and Escherichia coli (25%). Among these strains, the antibiotic resistant isolates were commonly found, and pulsed-field gel electrophoresis (PFGE) results of Proteus spp. indicated a high degree of similarity between isolates in the same age group, which was not observed for other bacteria.

          Conclusions

          In general, this study made understandings of the gut community structure and diversity of tree shrew.

          Electronic supplementary material

          The online version of this article (10.1186/s12866-019-1581-9) contains supplementary material, which is available to authorized users.

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          Genome of the Chinese tree shrew.

          Bing Zhu, Jian-Guo Zhang, Qiang Xiong … (2012)
          Chinese tree shrews (Tupaia belangeri chinensis) possess many features valuable in animals used as experimental models in biomedical research. Currently, there are numerous attempts to employ tree shrews as models for a variety of human disorders: depression, myopia, hepatitis B and C virus infections, and hepatocellular carcinoma, to name a few. Here we present a publicly available annotated genome sequence for the Chinese tree shrew. Phylogenomic analysis of the tree shrew and other mammalians highly support its close affinity to primates. By characterizing key factors and signalling pathways in nervous and immune systems, we demonstrate that tree shrews possess both shared common and unique features, and provide a genetic basis for the use of this animal as a potential model for biomedical research.
          Article 0 comments Cited 148 times – based on 0 reviews     Review now
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            Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

            David Waite, Inka Vanwonterghem, Christian Rinke … (2017)
            The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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              Detection of erythromycin-resistant determinants by PCR.

              J. SUTCLIFFE, T Grebe, A Tait-Kamradt … (1996)
              Erythromycin resistance determinants include Erm methylases, efflux pumps, and inactivating enzymes. To distinguish the different mechanisms of resistance in clinical isolates, PCR primers were designed so that amplification of the partial gene products could be detected in multiplex PCRs. This methodology enables the direct sequencing of amplified PCR products that can be used to compare resistance determinants in clinical strains. Further, this methodology could be useful in surveillance studies of erythromycin-resistant determinants.
              Article 0 comments Cited 142 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Wenpeng Gu: gu_02788@163.com
                Pinfen Tong: 1254489442@qq.com
                Chenxiu Liu: 705588188@qq.com
                Wenguang Wang: 346560005@qq.com
                Caixia Lu: 37364598@qq.com
                Yuanyuan Han: 46900014@qq.com
                Xiaomei Sun: 1023650688@qq.com
                De Xuan Kuang: 457221197@qq.com
                Na Li: 1107276856@qq.com
                Jiejie Dai:
                ORCID: http://orcid.org/0000-0003-3981-2164
                djj@imbcams.com.cn
                Journal
                Journal ID (nlm-ta): BMC Microbiol
                Journal ID (iso-abbrev): BMC Microbiol
                Title: BMC Microbiology
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2180
                Publication date (Electronic): 2 September 2019
                Publication date PMC-release: 2 September 2019
                Publication date Collection: 2019
                Volume: 19
                Electronic Location Identifier: 203
                Affiliations
                [1 ]Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Zhao zong Road 66, Kunming, 650118 China
                [2 ]Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, 650022 China
                Author information
                http://orcid.org/0000-0003-3981-2164
                Article
                Publisher ID: 1581
                DOI: 10.1186/s12866-019-1581-9
                PMC ID: 6721287
                PubMed ID: 31477004
                SO-VID: 5d50618c-92f6-41d4-b4b7-2840e0ff401f
                Copyright © © The Author(s). 2019
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 15 October 2018
                Date accepted : 27 August 2019
                Funding
                Funded by: Yunnan Science and Technology Talent and Platform Program
                Award ID: 2017HC019
                Award Recipient :
                Funded by: Yunnan Joint Support for National Program
                Award ID: 2015GA009
                Award Recipient :
                Funded by: Yunnan Province Major Science and Technology Project
                Award ID: 2017ZF007
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: U1702282
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2019

                ScienceOpen disciplines: Microbiology & Virology
                Keywords: tree shrew,gut microbiota,commensal enterobacteriaceae,susceptible age groups,proteus spp.
                Data availability:
                ScienceOpen disciplines: Microbiology & Virology
                Keywords: tree shrew, gut microbiota, commensal enterobacteriaceae, susceptible age groups, proteus spp.

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