Skip to main content
SpringerLink
Log in

Conservation metagenomics: a new branch of conservation biology

  • Review
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

Abstract

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 is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Alfano, N., Courtiol, A., Vielgrader, H., Timms, P., Roca, A.L., and Greenwood, A.D. (2015). Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep 5, 10189.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amato, K.R., Yeoman, C.J., Kent, A., Righini, N., Carbonero, F., Estrada, A., Rex Gaskins, H., Stumpf, R.M., Yildirim, S., Torralba, M., et al. (2013). Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J 7, 1344–1353.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Amato, K.R. (2013). Co-evolution in context: The importance of studying gut microbiomes in wild animals. Microbiome Sci Med 1, 10–29.

    Article  Google Scholar 

  • Amato, K.R., Leigh, S.R., Kent, A., Mackie, R.I., Yeoman, C.J., Stumpf, R. M., Wilson, B.A., Nelson, K.E., White, B.A., and Garber, P.A. (2014). The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol 69, 434–443.

    Article  CAS  PubMed  Google Scholar 

  • Amato, K.R., G. Sanders, J., Song, S.J., Nute, M., Metcalf, J.L., Thompson, L.R., Morton, J.T., Amir, A., J. McKenzie, V., Humphrey, G., et al. (2018). Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J 23, doi: 10.1038/s41396-018-0175-0.

  • Barker, C.J., Gillett, A., Polkinghorne, A., and Timms, P. (2013). Investigation of the koala (Phascolarctos cinereus) hindgut microbiome via 16S pyrosequencing. Vet Microbiol 167, 554–564.

    Article  CAS  PubMed  Google Scholar 

  • Bik, E.M., Costello, E.K., Switzer, A.D., Callahan, B.J., Holmes, S.P., Wells, R.S., Carlin, K.P., Jensen, E.D., Venn-Watson, S., and Relman, D.A. (2016). Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun 7, 10516.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Booijink, C.C.G.M., Boekhorst, J., Zoetendal, E.G., Smidt, H., Kleerebezem, M., and de Vos, W.M. (2010). Metatranscriptome analysis of the human fecal microbiota reveals subject-specific expression profiles, with genes encoding proteins involved in carbohydrate metabolism being dominantly expressed. Appl Environ Microbiol 76, 5533–5540.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bouchie, A. (2016). White house unveils national microbiome initiative. Nat Biotechnol 34, 580.

    Article  CAS  PubMed  Google Scholar 

  • Butchart, S.H.M., Walpole, M., Collen, B., van Strien, A., Scharlemann, J. P.W., Almond, R.E.A., Baillie, J.E.M., Bomhard, B., Brown, C., Bruno, J., et al. (2010). Global biodiversity: indicators of recent declines. Science 328, 1164–1168.

    Article  CAS  PubMed  Google Scholar 

  • Caporaso, J.G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F.D., Costello, E.K., Fierer, N., Peña, A.G., Goodrich, J.K., Gordon, J.I., et al. (2010). QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7, 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng, Y., Fox, S., Pemberton, D., Hogg, C., Papenfuss, A.T., and Belov, K. (2015). The Tasmanian devil microbiome—implications for conservation and management. Microbiome 3, 76.

    Article  PubMed  PubMed Central  Google Scholar 

  • Chu, H., Khosravi, A., Kusumawardhani, I.P., Kwon, A.H.K., Vasconcelos, A.C., Cunha, L.D., Mayer, A.E., Shen, Y., Wu, W.L., Kambal, A., et al. (2016). Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science 352, 1116–1120.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cleaveland, S., Laurenson, M.K., and Taylor, L.H. (2001). Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philos Trans R Soc B-Biol Sci 356, 991–999.

    Article  CAS  Google Scholar 

  • Costello, E.K., Gordon, J.I., Secor, S.M., and Knight, R. (2010). Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J 4, 1375–1385.

    Article  CAS  PubMed  Google Scholar 

  • de Groot, P.F., Frissen, M.N., de Clercq, N.C., and Nieuwdorp, M. (2017). Fecal microbiota transplantation in metabolic syndrome: History, present and future. Gut Microbes 8, 253–267.

    Article  PubMed  PubMed Central  Google Scholar 

  • Delsuc, F., Metcalf, J.L., Wegener Parfrey, L., Song, S.J., González, A., and Knight, R. (2014). Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol 23, 1301–1317.

    Article  CAS  PubMed  Google Scholar 

  • Diaz Heijtz, R., Wang, S., Anuar, F., Qian, Y., Björkholm, B., Samuelsson, A., Hibberd, M.L., Forssberg, H., and Pettersson, S. (2011). Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA 108, 3047–3052.

    Article  PubMed  Google Scholar 

  • Ding, Y., Wu, Q., Hu, Y.B., Wang, X., Nie, Y.G., Wu, X.P., and Wei, F.W. (2017). Advances and prospects of gut microbiome in wild mammals. Acta Theriologica Sinica 37, 399–406.

    Google Scholar 

  • Ehrlich, S.D. (2011). MetaHIT: The European Union Project on metagenomics of the human intestinal tract. In Metagenomics of the Human Body, K.E. Nelson, ed. (New York: Springer), pp. 307–316.

    Chapter  Google Scholar 

  • Ezenwa, V.O., Gerardo, N.M., Inouye, D.W., Medina, M., and Xavier, J.B. (2012). Animal behavior and the microbiome. Science 338, 198–199.

    Article  CAS  PubMed  Google Scholar 

  • Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M.J., Valles-Colomer, M., Vandeputte, D., et al. (2016). Population-level analysis of gut microbiome variation. Science 352, 560–564.

    Article  CAS  PubMed  Google Scholar 

  • Ferreiro, A., Crook, N., Gasparrini, A.J., and Dantas, G. (2018). Multiscale evolutionary dynamics of host-associated microbiomes. Cell 172, 1216–1227.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fietz, K., Rye Hintze, C.O., Skovrind, M., Kjærgaard Nielsen, T., Limborg, M.T., Krag, M.A., Palsbøll, P.J., Hestbjerg Hansen, L., Rask Møller, P., and Gilbert, M.T.P. (2018). Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome 6, 82.

    Article  PubMed  PubMed Central  Google Scholar 

  • Flint, H.J., Scott, K.P., Louis, P., and Duncan, S.H. (2012). The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 9, 577–589.

    Article  CAS  PubMed  Google Scholar 

  • Foster, J.A., and McVey Neufeld, K.A. (2013). Gut–brain axis: how the microbiome influences anxiety and depression. Trends Neurosciences 36, 305–312.

    Article  CAS  Google Scholar 

  • Ghannoum, M.A., Jurevic, R.J., Mukherjee, P.K., Cui, F., Sikaroodi, M., Naqvi, A., and Gillevet, P.M. (2010). Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 6, e1000713.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B. S., Gordon, J.I., Relman, D.A., Fraser-Liggett, C.M., and Nelson, K.E. (2006). Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Godoy-Vitorino, F., Goldfarb, K.C., Karaoz, U., Leal, S., Garcia-Amado, M.A., Hugenholtz, P., Tringe, S.G., Brodie, E.L., and Dominguez-Bello, M.G. (2012). Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J 6, 531–541.

    Article  CAS  PubMed  Google Scholar 

  • Goldberg, T.L., Gillespie, T.R., Rwego, I.B., Estoff, E.L., and Chapman, C. A. (2008). Forest fragmentation as cause of bacterial transmission among nonhuman primates, humans, and livestock, Uganda. Emerg Infect Dis 14, 1375–1382.

    Article  PubMed  PubMed Central  Google Scholar 

  • Gomez, A., Petrzelkova, K., Yeoman, C.J., Vlckova, K., Mrázek, J., Koppova, I., Carbonero, F., Ulanov, A., Modry, D., Todd, A., et al. (2015). Gut microbiome composition and metabolomic profiles of wild western lowland gorillas (Gorilla gorilla gorilla) reflect host ecology. Mol Ecol 24, 2551–2565.

    Article  CAS  PubMed  Google Scholar 

  • Gomez, A., Rothman, J.M., Petrzelkova, K., Yeoman, C.J., Vlckova, K., Umaña, J.D., Carr, M., Modry, D., Todd, A., Torralba, M., et al. (2016). Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp. ISME J 10, 514–526.

    Article  CAS  PubMed  Google Scholar 

  • Groussin, M., Mazel, F., Sanders, J.G., Smillie, C.S., Lavergne, S., Thuiller, W., and Alm, E.J. (2017). Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 8, 14319.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Handelsman, J. (2004). Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68, 669–685.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hooper, L.V., Littman, D.R., and Macpherson, A.J. (2012). Interactions between the microbiota and the immune system. Science 336, 1268–1273.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huson, D.H., Auch, A.F., Qi, J., and Schuster, S.C. (2007). MEGAN analysis of metagenomic data. Genome Res 17, 377–386.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingala, M.R., Simmons, N.B., Wultsch, C., Krampis, K., Speer, K.A., and Perkins, S.L. (2018). Comparing microbiome sampling methods in a wild mammal: fecal and intestinal samples record different signals of host ecology, evolution. Front Microbiol 9, 803.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kau, A.L., Ahern, P.P., Griffin, N.W., Goodman, A.L., and Gordon, J.I. (2011). Human nutrition, the gut microbiome and the immune system. Nature 474, 327–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Klaassens, E.S., de Vos, W.M., and Vaughan, E.E. (2007). Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol 73, 1388–1392.

    Article  CAS  PubMed  Google Scholar 

  • Kohl, K.D., Weiss, R.B., Cox, J., Dale, C., and Dearing, M.D. (2014). Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol Lett 17, 1238–1246.

    Article  PubMed  Google Scholar 

  • Kong, F., Zhao, J., Han, S., Zeng, B., Yang, J., Si, X., Yang, B., Yang, M., Xu, H., and Li, Y. (2014). Characterization of the gut microbiota in the red panda (Ailurus fulgens). PLoS ONE 9, e87885.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lagier, J.C., Armougom, F., Million, M., Hugon, P., Pagnier, I., Robert, C., Bittar, F., Fournous, G., Gimenez, G., Maraninchi, M., et al. (2012). Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiol Infection 18, 1185–1193.

    Article  CAS  Google Scholar 

  • Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., et al. (2008). Evolution of mammals and their gut microbes. Science 320, 1647–1651.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li, Y., Guo, W., Han, S., Kong, F., Wang, C., Li, D., Zhang, H., Yang, M., Xu, H., Zeng, B., et al. (2015). The evolution of the gut microbiota in the giant and the red pandas. Sci Rep 5, 10185.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marchesi, J.R., Adams, D.H., Fava, F., Hermes, G.D.A., Hirschfield, G.M., Hold, G., Quraishi, M.N., Kinross, J., Smidt, H., Tuohy, K.M., et al. (2016). The gut microbiota and host health: a new clinical frontier. Gut 65, 330–339.

    Article  PubMed  Google Scholar 

  • Menke, S., Wasimuddin, S., Meier, M., Melzheimer, J., Mfune, J.K.E., Heinrich, S., Thalwitzer, S., Wachter, B., and Sommer, S. (2014). Oligotyping reveals differences between gut microbiomes of freeranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level. Front Microbiol 5, 526.

    Article  PubMed  PubMed Central  Google Scholar 

  • Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Rodriguez, A., Stevens, R., Wilke, A., et al. (2008). The metagenomics RAST server–a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinf 9, 386.

    Article  CAS  Google Scholar 

  • Moeller, A.H., Peeters, M., Ndjango, J.B., Li, Y., Hahn, B.H., and Ochman, H. (2013). Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res 23, 1715–1720.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moeller, A.H., Caro-Quintero, A., Mjungu, D., Georgiev, A.V., Lonsdorf, E.V., Muller, M.N., Pusey, A.E., Peeters, M., Hahn, B.H., and Ochman, H. (2016). Cospeciation of gut microbiota with hominids. Science 353, 380–382.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moran, N.A., and Sloan, D.B. (2015). The hologenome concept: helpful or hollow? PLoS Biol 13, e1002311.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muegge, B.D., Kuczynski, J., Knights, D., Clemente, J.C., González, A., Fontana, L., Henrissat, B., Knight, R., and Gordon, J.I. (2011). Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970–974.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nelson, T.M., Rogers, T.L., Carlini, A.R., and Brown, M.V. (2013). Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol 15, 1132–1145.

    Article  CAS  PubMed  Google Scholar 

  • Nicholson, J.K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., and Pettersson, S. (2012). Host-gut microbiota metabolic interactions. Science 336, 1262–1267.

    Article  CAS  PubMed  Google Scholar 

  • Nishida, A.H., and Ochman, H. (2018). Rates of gut microbiome divergence in mammals. Mol Ecol 27, 1884–1897.

    Article  PubMed  PubMed Central  Google Scholar 

  • O'Toole, P.W., and Jeffery, I.B. (2015). Gut microbiota and aging. Science 350, 1214–1215.

    Article  CAS  PubMed  Google Scholar 

  • Palmer, C., Bik, E.M., DiGiulio, D.B., Relman, D.A., and Brown, P.O. (2007). Development of the human infant intestinal microbiota. PLoS Biol 5, e177–1573.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pope, P.B., Denman, S.E., Jones, M., Tringe, S.G., Barry, K., Malfatti, S.A., McHardy, A.C., Cheng, J.F., Hugenholtz, P., McSweeney, C.S., et al. (2010). Adaptation to herbivory by the tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci USA 107, 14793–14798.

    Article  PubMed  PubMed Central  Google Scholar 

  • Qin, N., Dong, X., and Zhao, L. (2018). Microbiome: from community metabolism to host diseases. Sci China Life Sci 61, 741–743.

    Article  PubMed  Google Scholar 

  • Reyes, A., Haynes, M., Hanson, N., Angly, F.E., Heath, A.C., Rohwer, F., and Gordon, J.I. (2010). Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 466, 334–338.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rosenberg, D.K., Noon, B.R., and Meslow, E.C. (1997). Biological corridors: Form, function, and efficacy. BioScience 47, 677–687.

    Article  Google Scholar 

  • Round, J.L., and Mazmanian, S.K. (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9, 313–323.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanders, J.G., Beichman, A.C., Roman, J., Scott, J.J., Emerson, D., McCarthy, J.J., and Girguis, P.R. (2015). Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nat Commun 6, 8285.

    Article  CAS  PubMed  Google Scholar 

  • Schmidt, C. (2015). thinking from the gut. Nature 518, S12–S14.

    Article  CAS  PubMed  Google Scholar 

  • Sharpton, T.J. (2018). Role of the gut microbiome in vertebrate evolution. mSystems 3, e00174–17–17.

    Article  PubMed  PubMed Central  Google Scholar 

  • Shapira, M. (2016). Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol Evol 31, 539–549.

    Article  PubMed  Google Scholar 

  • Simpson, S., Ash, C., Pennisi, E., and Travis, J. (2005). The gut: inside out. Science 307, 1895.

    Article  CAS  Google Scholar 

  • Sommer, F., and Bäckhed, F. (2013). The gut microbiota — masters of host development and physiology. Nat Rev Microbiol 11, 227–238.

    Article  CAS  PubMed  Google Scholar 

  • Sommer, F., Ståhlman, M., Ilkayeva, O., Arnemo, J.M., Kindberg, J., Josefsson, J., Newgard, C.B., Fröbert, O., and Bäckhed, F. (2016). The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep 14, 1655–1661.

    Article  CAS  PubMed  Google Scholar 

  • Soverini, M., Quercia, S., Biancani, B., Furlati, S., Turroni, S., Biagi, E., Consolandi, C., Peano, C., Severgnini, M., Rampelli, S., et al. (2016). The bottlenose dolphin (Tursiops truncatus) faecal microbiota. FEMS Microbiol Ecol 92, fiw055.

    Article  CAS  PubMed  Google Scholar 

  • Spor, A., Koren, O., and Ley, R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9, 279–290.

    Article  CAS  PubMed  Google Scholar 

  • Srivathsan, A., Ang, A., Vogler, A.P., and Meier, R. (2016). Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Front Zool 13, 17.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stumpf, R.M., Gomez, A., Amato, K.R., Yeoman, C.J., Polk, J.D., Wilson, B.A., Nelson, K.E., White, B.A., and Leigh, S.R. (2016). Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biol Conserv 199, 56–66.

    Article  Google Scholar 

  • Sun, B., Wang, X., Bernstein, S., Huffman, M.A., Xia, D.P., Gu, Z., Chen, R., Sheeran, L.K., Wagner, R.S., and Li, J. (2016). Marked variation between winter and spring gut microbiota in free-ranging Tibetan Macaques (Macaca thibetana). Sci Rep 6, 26035.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tremaroli, V., and Bäckhed, F. (2012). Functional interactions between the gut microbiota and host metabolism. Nature 489, 242–249.

    Article  CAS  PubMed  Google Scholar 

  • Trosvik, P., Rueness, E.K., de Muinck, E.J., Moges, A., and Mekonnen, A. (2018). Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys. Sci Rep 8, 20.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turnbaugh, P.J., Ley, R.E., Hamady, M., Fraser-Liggett, C.M., Knight, R., and Gordon, J.I. (2007). The human microbiome project. Nature 449, 804–810.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wall, R., Ross, R.P., Ryan, C.A., Hussey, S., Murphy, B., Fitzgerald, G.F., and Stanton, C. (2009). Role of gut microbiota in early infant development. Clin Med Pediatr 2009, 45–54.

    Google Scholar 

  • Wei, F., Swaisgood, R., Hu, Y., Nie, Y., Yan, L., Zhang, Z., Qi, D., and Zhu, L. (2015). Progress in the ecology and conservation of giant pandas. Conserv Biol 29, 1497–1507.

    Article  PubMed  Google Scholar 

  • Wei, F., Wang, X., and Wu, Q. (2015). The giant panda gut microbiome. Trends Microbiol 23, 450–452.

    Article  CAS  PubMed  Google Scholar 

  • Weng, F.C.H., Yang, Y.J., and Wang, D. (2016). Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. BMC Genomics 17, 1024.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wiebler, J.M., Kohl, K.D., Lee Jr, R.E., and Costanzo, J.P. (2018). Urea hydrolysis by gut bacteria in a hibernating frog: evidence for ureanitrogen recycling in Amphibia. Proc R Soc B 285, 20180241.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu, Q., Wang, X., Ding, Y., Hu, Y., Nie, Y., Wei, W., Ma, S., Yan, L., Zhu, L., and Wei, F. (2017). Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas. Proc R Soc B 284, 20170955.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, X.Y., Sukhchuluun, G., Bo, T.B., Chi, Q.S., Yang, J.J., Chen, B., Zhang, L., and Wang, D.H. (2018). Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure. Microbiome 6, 103.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang, Z., Xu, D., Wang, L., Hao, J., Wang, J., Zhou, X., Wang, W., Qiu, Q., Huang, X., Zhou, J., et al. (2016). Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol 26, 1873–1879.

    Article  CAS  PubMed  Google Scholar 

  • Zhernakova, A., Kurilshikov, A., Bonder, M.J., Tigchelaar, E.F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A.V., Falony, G., Vieira-Silva, S., et al. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565–569.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu, L., Wu, Q., Dai, J., Zhang, S., and Wei, F. (2011). Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci USA 108, 17714–17719.

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhu, L., Wu, Q., Deng, C., Zhang, M., Zhang, C., Chen, H., Lu, G., and Wei, F. (2018a). Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes. Environ Microbiol 20, 1711–1722.

    Article  CAS  PubMed  Google Scholar 

  • Zhu, L.F., Yang, Z.S., Yao, R., Xu, L.L., Chen, H., Gu, X.D., Wu, T.G., and Yang, X.Y. (2018b). Potential mechanism of detoxification of cyanide compounds by gut microbiomes of bamboo-eating pandas. MSphere 3, e00229–18.

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

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).

Author information

Authors and Affiliations

  1. CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China

    Fuwen Wei, Qi Wu, Yibo Hu, Guangping Huang, Yonggang Nie & Li Yan

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Fuwen Wei

  3. Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China

    Fuwen Wei, Yibo Hu & Yonggang Nie

Authors
  1. Fuwen Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Qi Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yibo Hu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Guangping Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yonggang Nie
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Li Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fuwen Wei.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wei, F., Wu, Q., Hu, Y. et al. Conservation metagenomics: a new branch of conservation biology. Sci. China Life Sci. 62, 168–178 (2019). https://doi.org/10.1007/s11427-018-9423-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-018-9423-3

Keywords

Search

Navigation