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      Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing

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          Abstract

          The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François’ langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François’ langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.

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          Most cited references47

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          Metagenomic biomarker discovery and explanation

          This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/.
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            MultiQC: summarize analysis results for multiple tools and samples in a single report

            Motivation: Fast and accurate quality control is essential for studies involving next-generation sequencing data. Whilst numerous tools exist to quantify QC metrics, there is no common approach to flexibly integrate these across tools and large sample sets. Assessing analysis results across an entire project can be time consuming and error prone; batch effects and outlier samples can easily be missed in the early stages of analysis. Results: We present MultiQC, a tool to create a single report visualising output from multiple tools across many samples, enabling global trends and biases to be quickly identified. MultiQC can plot data from many common bioinformatics tools and is built to allow easy extension and customization. Availability and implementation: MultiQC is available with an GNU GPLv3 license on GitHub, the Python Package Index and Bioconda. Documentation and example reports are available at http://multiqc.info Contact: phil.ewels@scilifelab.se
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              Improved metagenomic analysis with Kraken 2

              Although Kraken’s k-mer-based approach provides a fast taxonomic classification of metagenomic sequence data, its large memory requirements can be limiting for some applications. Kraken 2 improves upon Kraken 1 by reducing memory usage by 85%, allowing greater amounts of reference genomic data to be used, while maintaining high accuracy and increasing speed fivefold. Kraken 2 also introduces a translated search mode, providing increased sensitivity in viral metagenomics analysis.
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                Author and article information

                Contributors
                Journal
                Front Cell Infect Microbiol
                Front Cell Infect Microbiol
                Front. Cell. Infect. Microbiol.
                Frontiers in Cellular and Infection Microbiology
                Frontiers Media S.A.
                2235-2988
                04 May 2022
                2022
                : 12
                : 872841
                Affiliations
                [1] 1 Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi , Nanning, China
                [2] 2 Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application, Guangxi Medical University , Nanning, China
                [3] 3 Guangxi Center for Disease Control and Prevention , Nanning, China
                [4] 4 The First Affiliated Hospital of Guangxi Medical University , Nanning, Guangxi, China
                [5] 5 Life Sciences Institute, Guangxi Medical University , Nanning, China
                [6] 6 School of Information and Management, Guangxi Medical University , Nanning, China
                [7] 7 Acdemy of Inventory and Planning, National Forestry and Grassland Administration , Beijing, China
                [8] 8 Center for Genomic and Personalized Medicine, Guangxi key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University , Nanning, China
                Author notes

                Edited by: Crystal Richards, National Institutes of Health, United States

                Reviewed by: Leandro Nascimento Lemos, National Laboratory for Scientific Computing (LNCC), Brazil; Luisa I. Falcon, National Autonomous University of Mexico, Mexico

                *Correspondence: Yanling Hu, huyanling@ 123456gxmu.edu.cn

                This article was submitted to Bacteria and Host, a section of the journal Frontiers in Cellular and Infection Microbiology

                †These authors have contributed equally to this work and share first authorship

                Article
                10.3389/fcimb.2022.872841
                9114771
                35601103
                a7c79fff-b4a0-4d8b-a94f-1a4646dd16d0
                Copyright © 2022 Que, Pang, Huang, Chen, Wei, Hua, Liao, Wu, Li, Wu, He, Ruan and Hu

                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(s) 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
                : 10 February 2022
                : 29 March 2022
                Page count
                Figures: 8, Tables: 0, Equations: 0, References: 47, Pages: 11, Words: 4025
                Funding
                Funded by: Guangxi Key Research and Development Program , doi 10.13039/501100017691;
                Award ID: Guike AB20059002
                Categories
                Cellular and Infection Microbiology
                Original Research

                Infectious disease & Microbiology
                trachypithecus leucocephalus,gut microbiome,dietary,karst limestone,metagenomic sequencing

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