SCIENCE CHINA Life Sciences, Volume 62 , Issue 2 : 168-178(2019) https://doi.org/10.1007/s11427-018-9423-3

Conservation metagenomics: a new branch of conservation biology

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  • ReceivedAug 30, 2018
  • AcceptedOct 6, 2018
  • PublishedDec 25, 2018


Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.


This work was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000), the National Key Program of Research and Development, Ministry of Science and Technology of China (2016YFC0503200), and the Creative Research Group Project of National Natural Science Foundation of China (31821001).

Interest statement

The author(s) declare that they have no conflict of interest.


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  • Figure 1

    (Color online) The metagenomics approaches used for gut microbiome. Middle panel shows a total pipeline of metagenomic analysis, comprising the following steps in turn: sample collection, sample DNA extraction, sequencing strategy selection based on the research aim. Targeted or shotgun genome sequencing strategies are chosen to acquire information for composition or function of the microbiome sample. Generally speaking, 16S rRNA targeting sequencing is applied for the studies on composition of microbiome while shotgun genome sequencing is performed for functional analysis of microbiome. Detailed steps of bioinformatics analyses used for targeted and shotgun genome sequencing are shown in left and right panels, respectively.

  • Table 1   Pioneering studies in application of gut microbiome approaches in conservation biology



    Host latin name

    Scientific issues





    60 species


    Diet and phylogeny



    Ley et al., 2008

    30 species



    Diet and phylogeny



    Muegge et al., 2011


    Tammar wallaby

    Macropus eugenii

    Adaptive evolution



    Pope et al., 2010


    Giant panda

    Ailuropoda melanoleuca

    Adaptive evolution, coevolution, Survivorship



    Zhu et al., 2011

    Diet seasonal variation



    Wu et al., 2017


    Acinonyx jubatus

    Oligotyping approach fordiversity



    Menke et al., 2014

    Black-backed jackal

    Canis mesomelas

    Brown bear

    Ursus arctos




    Sommer et al., 2016



    Bos grunniens

    Convergent evolution



    Zhang et al., 2016

    Tibetan sheep

    Ovis aries


    Bos taurus

    Ordinary sheep

    Ovis aries



    Homo sapiens




    Moeller et al., 2016



    Pan troglodytes

    Convergent evolution




    Moeller et al., 2013

    Moeller et al., 2016


    Gorilla gorilla


    Pan paniscus

    Black howler monkey

    Alouatta pigra

    Habitat degradation



    Amato et al., 2013


    Desert woodrats

    Neotoma lepida

    Function to consume plant toxins



    Kohl et al., 2014


    Pacific Humpback Whales

    Megaptera novaeangliae

    Composition and functions



    Sanders et al., 2015

    Atlantic white-sided dolphin

    Lagenorhynchus acutus

    Bottlenose dolphin

    Tursiops truncatus




    Soverini et al., 2016

    1, T means targeted sequencing (such as 16S rRNA); S means metagenomic shotgun sequencing; M means metabolomics methods. R means metatranscriptomic methods. P means (real time) PCR. 2, D means that the research focuses on the diversity of microbiome. F means that the research focuses on the function of microbiome. M means the metabolites of the microbiome.

  • Table 2   Comparison of different genome sequencing techniques applied in metagenomics

    ABI 3730

    Illumina HiSeq


    Illumina HiSeq 2500

    (Rapid Run)

    Illumina HiSeq


    Illumina MiSeq


    Maximum read length

    800 bp

    2×100 bp

    2×150 bp

    2×150 bp

    2×300 bp

    10--18 kb

    Reads per run







    Output range

    70--80 kb

    500--600 Gb

    150--180 Gb

    750--1,500 Gb

    15 Gb

    5--10 Gb/SMRT cell

    Run time

    2 h

    11 d

    40 h

    1--3.5 d

    4--55 h

    0.5--6 h/SMRT cell

    Raw error rate (%)







    Generational division

    The firstgeneration

    The secondgeneration

    The secondgeneration

    The secondgeneration

    The secondgeneration

    The thirdgeneration

    These parameters were cited from introductions of the commercial sequencer manufacturers

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