logo

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

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

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.


Acknowledgment

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.


References

[1] Alfano N., Courtiol A., Vielgrader H., Timms P., Roca A.L., Greenwood A.D.. Variation in koala microbiomes within and between individuals: effect of body region and captivity status. Sci Rep, 2015, 5: 10189 CrossRef PubMed ADS Google Scholar

[2] 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. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes. ISME J, 2013, 7: 1344-1353 CrossRef PubMed Google Scholar

[3] Amato K.R.. Co-evolution in context: The importance of studying gut microbiomes in wild animals. Microbiome Sci Med, 2013, 1: 10-29 CrossRef Google Scholar

[4] 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., Garber P.A.. The gut microbiota appears to compensate for seasonal diet variation in the wild black howler monkey (Alouatta pigra). Microb Ecol, 2014, 69: 434-443 CrossRef PubMed Google Scholar

[5] 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. Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes. ISME J, 2018, 23: doi: 10.1038/s41396-018-0175-0 CrossRef PubMed Google Scholar

[6] Barker C.J., Gillett A., Polkinghorne A., Timms P.. Investigation of the koala (Phascolarctos cinereus) hindgut microbiome via 16S pyrosequencing. Vet Microbiol, 2013, 167: 554-564 CrossRef PubMed Google Scholar

[7] 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., Relman D.A.. Marine mammals harbor unique microbiotas shaped by and yet distinct from the sea. Nat Commun, 2016, 7: 10516 CrossRef PubMed ADS Google Scholar

[8] Booijink C.C.G.M., Boekhorst J., Zoetendal E.G., Smidt H., Kleerebezem M., de Vos W.M.. 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, 2010, 76: 5533-5540 CrossRef PubMed Google Scholar

[9] Bouchie A.. White house unveils national microbiome initiative. Nat Biotechnol, 2016, 34: 580 CrossRef PubMed Google Scholar

[10] 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. Global biodiversity: indicators of recent declines. Science, 2010, 328: 1164-1168 CrossRef PubMed ADS Google Scholar

[11] 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. QIIME allows analysis of high-throughput community sequencing data. Nat Methods, 2010, 7: 335-336 CrossRef PubMed Google Scholar

[12] Cheng Y., Fox S., Pemberton D., Hogg C., Papenfuss A.T., Belov K.. The Tasmanian devil microbiome—implications for conservation and management. Microbiome, 2015, 3: 76 CrossRef PubMed Google Scholar

[13] 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. Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease. Science, 2016, 352: 1116-1120 CrossRef PubMed ADS Google Scholar

[14] Cleaveland S., Laurenson M.K., Taylor L.H.. Diseases of humans and their domestic mammals: pathogen characteristics, host range and the risk of emergence. Philos Trans R Soc B-Biol Sci, 2001, 356: 991-999 CrossRef PubMed Google Scholar

[15] Costello E.K., Gordon J.I., Secor S.M., Knight R.. Postprandial remodeling of the gut microbiota in Burmese pythons. ISME J, 2010, 4: 1375-1385 CrossRef PubMed Google Scholar

[16] de Groot P.F., Frissen M.N., de Clercq N.C., Nieuwdorp M.. Fecal microbiota transplantation in metabolic syndrome: History, present and future. Gut Microbes, 2017, 8: 253-267 CrossRef PubMed Google Scholar

[17] Delsuc F., Metcalf J.L., Wegener Parfrey L., Song S.J., González A., Knight R.. Convergence of gut microbiomes in myrmecophagous mammals. Mol Ecol, 2014, 23: 1301-1317 CrossRef PubMed Google Scholar

[18] Diaz Heijtz R., Wang S., Anuar F., Qian Y., Björkholm B., Samuelsson A., Hibberd M.L., Forssberg H., Pettersson S.. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA, 2011, 108: 3047-3052 CrossRef PubMed ADS Google Scholar

[19] 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

[20] 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. Google Scholar

[21] Ezenwa V.O., Gerardo N.M., Inouye D.W., Medina M., Xavier J.B.. Animal behavior and the microbiome. Science, 2012, 338: 198-199 CrossRef PubMed ADS Google Scholar

[22] 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. Population-level analysis of gut microbiome variation. Science, 2016, 352: 560-564 CrossRef PubMed ADS Google Scholar

[23] Ferreiro A., Crook N., Gasparrini A.J., Dantas G.. Multiscale evolutionary dynamics of host-associated microbiomes. Cell, 2018, 172: 1216-1227 CrossRef PubMed Google Scholar

[24] 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., Gilbert M.T.P.. Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species. Microbiome, 2018, 6: 82 CrossRef PubMed Google Scholar

[25] Flint H.J., Scott K.P., Louis P., Duncan S.H.. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol, 2012, 9: 577-589 CrossRef PubMed Google Scholar

[26] Foster J.A., McVey Neufeld K.A.. Gut–brain axis: how the microbiome influences anxiety and depression. Trends Neurosciences, 2013, 36: 305-312 CrossRef PubMed Google Scholar

[27] Ghannoum M.A., Jurevic R.J., Mukherjee P.K., Cui F., Sikaroodi M., Naqvi A., Gillevet P.M.. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog, 2010, 6: e1000713 CrossRef PubMed Google Scholar

[28] 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., Nelson K.E.. Metagenomic analysis of the human distal gut microbiome. Science, 2006, 312: 1355-1359 CrossRef PubMed ADS Google Scholar

[29] Godoy-Vitorino F., Goldfarb K.C., Karaoz U., Leal S., Garcia-Amado M.A., Hugenholtz P., Tringe S.G., Brodie E.L., Dominguez-Bello M.G.. Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows. ISME J, 2012, 6: 531-541 CrossRef PubMed Google Scholar

[30] Goldberg T.L., Gillespie T.R., Rwego I.B., Estoff E.L., Chapman C.A.. Forest fragmentation as cause of bacterial transmission among nonhuman primates, humans, and livestock, Uganda. Emerg Infect Dis, 2008, 14: 1375-1382 CrossRef PubMed Google Scholar

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

[32] 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. Temporal variation selects for diet–microbe co-metabolic traits in the gut of Gorilla spp. ISME J, 2016, 10: 514-526 CrossRef PubMed Google Scholar

[33] Groussin M., Mazel F., Sanders J.G., Smillie C.S., Lavergne S., Thuiller W., Alm E.J.. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun, 2017, 8: 14319 CrossRef PubMed ADS Google Scholar

[34] Handelsman J.. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev, 2004, 68: 669-685 CrossRef PubMed Google Scholar

[35] Hooper L.V., Littman D.R., Macpherson A.J.. Interactions between the microbiota and the immune system. Science, 2012, 336: 1268-1273 CrossRef PubMed ADS Google Scholar

[36] Huson D.H., Auch A.F., Qi J., Schuster S.C.. MEGAN analysis of metagenomic data. Genome Res, 2007, 17: 377-386 CrossRef PubMed Google Scholar

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

[38] Kau A.L., Ahern P.P., Griffin N.W., Goodman A.L., Gordon J.I.. Human nutrition, the gut microbiome and the immune system. Nature, 2011, 474: 327-336 CrossRef PubMed Google Scholar

[39] Klaassens E.S., de Vos W.M., Vaughan E.E.. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl Environ Microbiol, 2007, 73: 1388-1392 CrossRef PubMed Google Scholar

[40] Kohl K.D., Weiss R.B., Cox J., Dale C., Dearing M.D.. Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol Lett, 2014, 17: 1238-1246 CrossRef PubMed Google Scholar

[41] Kong F., Zhao J., Han S., Zeng B., Yang J., Si X., Yang B., Yang M., Xu H., Li Y.. Characterization of the gut microbiota in the red panda (Ailurus fulgens). PLoS ONE, 2014, 9: e87885 CrossRef PubMed ADS Google Scholar

[42] Lagier J.C., Armougom F., Million M., Hugon P., Pagnier I., Robert C., Bittar F., Fournous G., Gimenez G., Maraninchi M., et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clinical Microbiol Infection, 2012, 18: 1185-1193 CrossRef PubMed Google Scholar

[43] 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. Evolution of mammals and their gut microbes. Science, 2008, 320: 1647-1651 CrossRef PubMed ADS Google Scholar

[44] Li Y., Guo W., Han S., Kong F., Wang C., Li D., Zhang H., Yang M., Xu H., Zeng B., et al. The evolution of the gut microbiota in the giant and the red pandas. Sci Rep, 2015, 5: 10185 CrossRef PubMed ADS Google Scholar

[45] 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. The gut microbiota and host health: a new clinical frontier. Gut, 2016, 65: 330-339 CrossRef PubMed Google Scholar

[46] Menke S., Wasimuddin S., Meier M., Melzheimer J., Mfune J.K.E., Heinrich S., Thalwitzer S., Wachter B., Sommer S.. Oligotyping reveals differences between gut microbiomes of free-ranging sympatric Namibian carnivores (Acinonyx jubatus, Canis mesomelas) on a bacterial species-like level. Front Microbiol, 2014, 5: 526 CrossRef Google Scholar

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

[48] Moeller A.H., Peeters M., Ndjango J.B., Li Y., Hahn B.H., Ochman H.. Sympatric chimpanzees and gorillas harbor convergent gut microbial communities. Genome Res, 2013, 23: 1715-1720 CrossRef PubMed Google Scholar

[49] 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., Ochman H.. Cospeciation of gut microbiota with hominids. Science, 2016, 353: 380-382 CrossRef PubMed ADS Google Scholar

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

[51] Muegge B.D., Kuczynski J., Knights D., Clemente J.C., González A., Fontana L., Henrissat B., Knight R., Gordon J.I.. Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science, 2011, 332: 970-974 CrossRef PubMed ADS Google Scholar

[52] Nelson T.M., Rogers T.L., Carlini A.R., Brown M.V.. Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals. Environ Microbiol, 2013, 15: 1132-1145 CrossRef PubMed Google Scholar

[53] Nicholson J.K., Holmes E., Kinross J., Burcelin R., Gibson G., Jia W., Pettersson S.. Host-gut microbiota metabolic interactions. Science, 2012, 336: 1262-1267 CrossRef PubMed ADS Google Scholar

[54] Nishida A.H., Ochman H.. Rates of gut microbiome divergence in mammals. Mol Ecol, 2018, 27: 1884-1897 CrossRef PubMed Google Scholar

[55] O'Toole P.W., Jeffery I.B.. Gut microbiota and aging. Science, 2015, 350: 1214-1215 CrossRef PubMed ADS Google Scholar

[56] Palmer C., Bik E.M., DiGiulio D.B., Relman D.A., Brown P.O.. Development of the human infant intestinal microbiota. PLoS Biol, 2007, 5: e177-1573 CrossRef PubMed Google Scholar

[57] 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. Adaptation to herbivory by the tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores. Proc Natl Acad Sci USA, 2010, 107: 14793-14798 CrossRef PubMed ADS Google Scholar

[58] Qin N., Dong X., Zhao L.. Microbiome: from community metabolism to host diseases. Sci China Life Sci, 2018, 61: 741-743 CrossRef PubMed Google Scholar

[59] Reyes A., Haynes M., Hanson N., Angly F.E., Heath A.C., Rohwer F., Gordon J.I.. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature, 2010, 466: 334-338 CrossRef PubMed ADS Google Scholar

[60] Rosenberg D.K., Noon B.R., Meslow E.C.. Biological corridors: Form, function, and efficacy. BioScience, 1997, 47: 677-687 CrossRef Google Scholar

[61] Round J.L., Mazmanian S.K.. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol, 2009, 9: 313-323 CrossRef PubMed Google Scholar

[62] Sanders J.G., Beichman A.C., Roman J., Scott J.J., Emerson D., McCarthy J.J., Girguis P.R.. Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. Nat Commun, 2015, 6: 8285 CrossRef PubMed ADS Google Scholar

[63] Schmidt C.. thinking from the gut. Nature, 2015, 518: S12-S14 CrossRef PubMed ADS Google Scholar

[64] Sharpton T.J.. Role of the gut microbiome in vertebrate evolution. mSystems, 2018, 3: e00174-17-17 CrossRef PubMed Google Scholar

[65] Shapira M.. Gut microbiotas and host evolution: scaling up symbiosis. Trends Ecol Evol, 2016, 31: 539-549 CrossRef PubMed Google Scholar

[66] Simpson S., Ash C., Pennisi E., Travis J.. The gut: inside out. Science, 2005, 307: 1895 CrossRef Google Scholar

[67] Sommer F., Bäckhed F.. The gut microbiota — masters of host development and physiology. Nat Rev Microbiol, 2013, 11: 227-238 CrossRef PubMed Google Scholar

[68] Sommer F., Ståhlman M., Ilkayeva O., Arnemo J.M., Kindberg J., Josefsson J., Newgard C.B., Fröbert O., Bäckhed F.. The gut microbiota modulates energy metabolism in the hibernating brown bear Ursus arctos. Cell Rep, 2016, 14: 1655-1661 CrossRef PubMed Google Scholar

[69] Soverini M., Quercia S., Biancani B., Furlati S., Turroni S., Biagi E., Consolandi C., Peano C., Severgnini M., Rampelli S., et al. The bottlenose dolphin (Tursiops truncatus ) faecal microbiota. FEMS Microbiol Ecol, 2016, 92: fiw055 CrossRef PubMed Google Scholar

[70] Spor A., Koren O., Ley R.. Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol, 2011, 9: 279-290 CrossRef PubMed Google Scholar

[71] Srivathsan A., Ang A., Vogler A.P., Meier R.. Fecal metagenomics for the simultaneous assessment of diet, parasites, and population genetics of an understudied primate. Front Zool, 2016, 13: 17 CrossRef PubMed Google Scholar

[72] Stumpf R.M., Gomez A., Amato K.R., Yeoman C.J., Polk J.D., Wilson B.A., Nelson K.E., White B.A., Leigh S.R.. Microbiomes, metagenomics, and primate conservation: New strategies, tools, and applications. Biol Conserv, 2016, 199: 56-66 CrossRef Google Scholar

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

[74] Tremaroli V., Bäckhed F.. Functional interactions between the gut microbiota and host metabolism. Nature, 2012, 489: 242-249 CrossRef PubMed ADS Google Scholar

[75] Trosvik P., Rueness E.K., de Muinck E.J., Moges A., Mekonnen A.. Ecological plasticity in the gastrointestinal microbiomes of Ethiopian Chlorocebus monkeys. Sci Rep, 2018, 8: 20 CrossRef PubMed ADS Google Scholar

[76] Turnbaugh P.J., Ley R.E., Hamady M., Fraser-Liggett C.M., Knight R., Gordon J.I.. The human microbiome project. Nature, 2007, 449: 804-810 CrossRef PubMed ADS Google Scholar

[77] 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

[78] Wei F., Swaisgood R., Hu Y., Nie Y., Yan L., Zhang Z., Qi D., Zhu L.. Progress in the ecology and conservation of giant pandas. Conserv Biol, 2015, 29: 1497-1507 CrossRef PubMed Google Scholar

[79] Wei F., Wang X., Wu Q.. The giant panda gut microbiome. Trends Microbiol, 2015, 23: 450-452 CrossRef PubMed Google Scholar

[80] Weng F.C.H., Yang Y.J., Wang D.. Functional analysis for gut microbes of the brown tree frog (Polypedates megacephalus) in artificial hibernation. BMC Genomics, 2016, 17: 1024 CrossRef PubMed Google Scholar

[81] Wiebler J.M., Kohl K.D., Lee Jr R.E., Costanzo J.P.. Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia. Proc R Soc B, 2018, 285: 20180241 CrossRef PubMed Google Scholar

[82] Wu Q., Wang X., Ding Y., Hu Y., Nie Y., Wei W., Ma S., Yan L., Zhu L., Wei F.. Seasonal variation in nutrient utilization shapes gut microbiome structure and function in wild giant pandas. Proc R Soc B, 2017, 284: 20170955 CrossRef PubMed Google Scholar

[83] Zhang X.Y., Sukhchuluun G., Bo T.B., Chi Q.S., Yang J.J., Chen B., Zhang L., Wang D.H.. Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure. Microbiome, 2018, 6: 103 CrossRef PubMed Google Scholar

[84] Zhang Z., Xu D., Wang L., Hao J., Wang J., Zhou X., Wang W., Qiu Q., Huang X., Zhou J., et al. Convergent evolution of rumen microbiomes in high-altitude mammals. Curr Biol, 2016, 26: 1873-1879 CrossRef PubMed Google Scholar

[85] 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. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 2016, 352: 565-569 CrossRef PubMed ADS Google Scholar

[86] Zhu L., Wu Q., Dai J., Zhang S., Wei F.. Evidence of cellulose metabolism by the giant panda gut microbiome. Proc Natl Acad Sci USA, 2011, 108: 17714-17719 CrossRef PubMed ADS Google Scholar

[87] Zhu L., Wu Q., Deng C., Zhang M., Zhang C., Chen H., Lu G., Wei F.. Adaptive evolution to a high purine and fat diet of carnivorans revealed by gut microbiomes and host genomes. Environ Microbiol, 2018a, 20: 1711-1722 CrossRef PubMed Google Scholar

[88] 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. Google Scholar

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

    Taxa

    Host

    Host latin name

    Scientific issues

    Methods1

    Microbiomefocus2

    References

    Mammalia

    60 species

    --

    Diet and phylogeny

    T

    D

    Ley et al., 2008

    30 species

    human

    --

    Diet and phylogeny

    T/S

    D/F

    Muegge et al., 2011

    Marsupialia

    Tammar wallaby

    Macropus eugenii

    Adaptive evolution

    T/S

    D/F

    Pope et al., 2010

    Carnivora

    Giant panda

    Ailuropoda melanoleuca

    Adaptive evolution, coevolution, Survivorship

    S/P

    D/F

    Zhu et al., 2011

    Diet seasonal variation

    S/P

    D/F

    Wu et al., 2017

    Cheetah

    Acinonyx jubatus

    Oligotyping approach fordiversity

    T

    D

    Menke et al., 2014

    Black-backed jackal

    Canis mesomelas

    Brown bear

    Ursus arctos

    Hibernation

    T/S

    D/F

    Sommer et al., 2016

    Artiodactyla

    Yaks

    Bos grunniens

    Convergent evolution

    T/R

    D/F

    Zhang et al., 2016

    Tibetan sheep

    Ovis aries

    Cattle

    Bos taurus

    Ordinary sheep

    Ovis aries

    Hominid

    Human

    Homo sapiens

    Codiversification

    T

    D

    Moeller et al., 2016

    Primates

    Chimpanzee

    Pan troglodytes

    Convergent evolution

    Codiversification

    T

    D/M

    Moeller et al., 2013

    Moeller et al., 2016

    Gorilla

    Gorilla gorilla

    Bonobo

    Pan paniscus

    Black howler monkey

    Alouatta pigra

    Habitat degradation

    T

    D

    Amato et al., 2013

    Rodentia

    Desert woodrats

    Neotoma lepida

    Function to consume plant toxins

    T/S

    D/F

    Kohl et al., 2014

    Cetacea

    Pacific Humpback Whales

    Megaptera novaeangliae

    Composition and functions

    T/S

    D/F

    Sanders et al., 2015

    Atlantic white-sided dolphin

    Lagenorhynchus acutus

    Bottlenose dolphin

    Tursiops truncatus

    Composition

    T

    D

    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   Table 2 Comparison of different genome sequencing techniques applied in metagenomicsa)

    ABI 3730

    Illumina HiSeq

    2000

    Illumina HiSeq 2500

    (Rapid Run)

    Illumina HiSeq

    3000/4000

    Illumina MiSeq

    PacBio

    Maximum read length

    800 bp

    2×100 bp

    2×150 bp

    2×150 bp

    2×300 bp

    10--18 kb

    Reads per run

    96

    3×109

    6×108

    2.5×109--5×109

    2.5×107

    --

    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 (%)

    <0.001

    <1

    <1

    <1

    <1

    12

    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

Copyright 2019 Science China Press Co., Ltd. 《中国科学》杂志社有限责任公司 版权所有

京ICP备18024590号-1