Research progress in metagenomics of fecal microorganisms in wild animals

doi:10.11853/j.issn.1003.8280.2022.03.026

Abstract

Abstract: The excrement of wild animals contains a complex and huge microbial community,which plays an important role in the survival history of wild animals. Studying fecal samples can provide an understanding of the species and composition of microorganisms in wild animals,the diversity and identity of microorganisms,and the symbiotic and evolutionary relationships between microorganisms and hosts,which provides a theoretical basis for the prevention and diagnosis of animal-borne infectious diseases and shows academic value and significance for choosing the future research focus and development trend of relevant disciplines. This paper summarizes the research progress in metagenomics and its application in fecal microorganisms of wild animals,and prospects the future development trend and research focus,in order to provide theoretical and technical support for the prevention and diagnosis of diseases caused by contact with wild animals.

Key words: Metagenomics, Wild animal, Fecal microorganism

摘要： 野生动物粪便中蕴含着复杂、庞大的微生物群体，这些微生物在野生动物的生存史中发挥重要作用。利用粪便样本可初步揭示野生动物体内微生物的种类与组成，探讨微生物间存在的多样性与同一性，了解微生物与宿主间的共生、进化关系，为防治、诊断动物源性传染病提供理论依据，对未来相应学科的研究重点与发展趋势判断具有学术价值和意义。该文概述了宏基因组学国内外研究进展及其在野生动物粪便微生物中的应用，展望未来的发展趋势与研究重点，为防治与诊断由于接触野生动物引起的疾病提供理论和技术支持。

关键词: 宏基因组, 野生动物, 粪便微生物

CLC Number:

Q347
R183

XU Peng, ZHANG Xue-fei, ZHAO Zhi-jun, MA Ying. Research progress in metagenomics of fecal microorganisms in wild animals[J]. Chinese Journal of Vector Biology and Control, 2022, 33(3): 446-452.

徐鹏, 张雪飞, 赵志军, 马英. 野生动物粪便微生物宏基因组学研究进展[J]. 中国媒介生物学及控制杂志, 2022, 33(3): 446-452.

References

[1] Cutler SJ, Fooks AR, van der Poel WH. Public health threat of new, reemerging, and neglected zoonoses in the industrialized world[J]. Emerg Infect Dis, 2010, 16(1):1-7. DOI:10.3201/eid1601.081467.
[2] Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes:A new frontier for natural products[J]. Chem Biol, 1998, 5(10):R245-R249. DOI:10.1016/s1074-5521(98)90108-9.
[3] Ericsson AC, Busi SB, Amos-Landgraf JM. Characterization of the rat gut Microbiota via 16S rRNA amplicon library sequencing[M]//Hayman G, Smith J, Dwinell M, et al. Rat genomics. New York, NY:Humana, 2019, 2018:195-212. DOI:10.1007/978-1-4939-9581-3_9.
[4] Walters W, Hyde ER, Berg-Lyons D, et al. Improved bacterial 16S rRNA Gene (V4 and V4-5) and fungal internal transcribed spacer marker gene primers for microbial community surveys[J]. mSystems, 2016, 1(1):e00009-15. DOI:10.1128/mSystems. 00009-15.
[5] Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data[J]. Nat Methods, 2010, 7(5):335-336. DOI:10.1038/nmeth.f.303.
[6] Jovel J, Patterson J, Wang WW, et al. Characterization of the gut microbiome using 16S or shotgun metagenomics[J]. Front Microbiol, 2016, 7:459. DOI:10.3389/fmicb.2016.00459.
[7] Quince C, Walker AW, Simpson JT, et al. Shotgun metagenomics, from sampling to analysis[J]. Nat Biotechnol, 2017, 35(9):833-844. DOI:10.1038/nbt.3935.
[8] 张翠媛. 高通量测序技术应用于野生动物粪便中病毒的发现与分析[D]. 长沙:湖南师范大学, 2016. DOI:10.7666/d.Y3012807. Zhang CY. Application of high-throughput sequencing for virus detection and analysis in wild animal feces[D]. Changsha:Hunan Normal University, 2016. DOI:10.7666/d.Y3012807.(in Chinese)
[9] Miller DN, Bryant JE, Madsen EL, et al. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples[J]. Appl Environ Microbiol, 1999, 65(11):4715-4724. DOI:10.1128/AEM.65.11.4715-4724.1999.
[10] Gupta R, Beg Q, Lorenz P. Bacterial alkaline proteases:Molecular approaches and industrial applications[J]. Appl Microbiol Biotechnol, 2002, 59(1):15-32. DOI:10.1007/s00253-002-0975-y.
[11] Diaz-Torres ML, McNab R, Spratt DA, et al. Novel tetracycline resistance determinant from the oral metagenome[J]. Antimicrob Agents Chemother, 2003, 47(4):1430-1432. DOI:10.1128/aac. 47.4.1430-1432.2003.
[12] Desai N, Antonopoulos D, Gilbert JA, et al. From genomics to metagenomics[J]. Curr Opin Biotechnol, 2012, 23(1):72-76. DOI:10.1016/j.copbio.2011.12.017.
[13] 张冰, 崔岱宗, 赵敏. 宏基因组学技术及其在微生物学研究中的应用[J]. 黑龙江医药, 2014, 27(2):267-271. DOI:10.14035/j.cnki.hljyy.2014.02.001. Zhang B, Cui DZ, Zhao M. Application of metagenomics for understanding of environmental microbiology[J]. Heilongjiang Med J, 2014, 27(2):267-271. DOI:10.14035/j.cnki.hljyy.2014. 02.001.(in Chinese)
[14] Willner D, Furlan M, Schmieder R, et al. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity[J]. Proc Natl Acad Sci USA, 2011, 108(S1):4547-4553. DOI:10.1073/pnas.1000089107.
[15] Breitbart M, Rohwer F. Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing[J]. Biotechniques, 2005, 39(5):729-736. DOI:10.2144/000112019.
[16] 吴莎莎, 卢向阳, 许源, 等. 宏基因组学在胃肠道微生物研究中的应用[J]. 激光生物学报, 2012, 21(1):91-96. DOI:10.3969/j.issn.1007-7146.2012.01.018. Wu SS, Lu XY, Xu Y, et al. The application of metagenomic in the research of the microbiology in the gastrointestinal tract[J]. Chin J Laser Biol, 2012, 21(1):91-96. DOI:10.3969/j.issn.1007-7146.2012.01.018.(in Chinese)
[17] Wang J, Linnenbrink M, Künzel S, et al. Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice[J]. Proc Natl Acad Sci USA, 2014, 111(26):E2703-E2710. DOI:10.1073/pnas.1402342111.
[18] Kreisinger J, Čížková D, Vohánka J, et al. Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing[J]. Mol Ecol, 2014, 23(20):5048-5060. DOI:10.1111/mec.12909.
[19] De Filippo C, Cavalieri D, Di Paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa[J]. Proc Natl Acad Sci USA, 2010, 107(33):14691-14696. DOI:10.1073/pnas. 1005963107.
[20] Li H, Li TT, Beasley DE, et al. Diet diversity is associated with beta but not alpha diversity of pika gut microbiota[J]. Front Microbiol, 2016, 7:1169. DOI:10.3389/fmicb.2016.01169.
[21] 尚立强, 薛世魁, 王惜婧, 等. 西北高海拔地区放养偶蹄类动物肠道微生物多样性的宏基因组比较研究[J]. 安徽农业科学, 2019, 47(7):98-101. DOI:10.3969/j.issn.0517-6611.2019. 07.031. Shang LQ, Xue SK, Wang XJ, et al. Metagenomic comparative study on the the intestinal microbial diversity of stocked cloven-hoofed animals in high elevation area of northwest China[J]. J Anhui Agric Sci, 2019, 47(7):98-101. DOI:10.3969/j.issn.0517-6611.2019.07.031.(in Chinese)
[22] Sun GL, Zhang HH, Wei QG, et al. Comparative analyses of fecal microbiota in European mouflon (Ovis orientalis musimon) and blue sheep (Pseudois nayaur) living at low or high altitudes[J]. Front Microbiol, 2019, 10:1735. DOI:10.3389/fmicb.2019.01735.
[23] Sun YW, Sun YJ, Shi ZH, et al. Gut microbiota of wild and captive alpine musk deer (Moschus chrysogaster)[J]. Front Microbiol, 2020, 10:3156. DOI:10.3389/fmicb.2019.03156.
[24] 谭春桃, 李欢, 曲家鹏. 野生和室内饲养高原鼠兔肠道菌群多样性的比较[J]. 草业科学, 2019, 36(2):531-539. DOI:10. 11829/j.issn.1001-0629.2018-0324. Tan CT, Li H, Qu JP. Comparison of gut microbial diversity between wild and laboratory-reared plateau pika (Ochotona curzoniae)[J]. Pratacult Sci, 2019, 36(2):531-539. DOI:10.11829/j.issn.1001-0629.2018-0324.(in Chinese)
[25] Ley RE, Hamady M, Lozupone C, et al. Evolution of mammals and their gut microbes[J]. Science, 2008, 320(5883):1647-1651. DOI:10.1126/science.1155725.
[26] Lau SKP, Woo PCY, Li KSM, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats[J]. Proc Natl Acad Sci USA, 2005, 102(39):14040-14045. DOI:10. 1073/pnas.0506735102.
[27] Reusken CB, Haagmans BL, Müller MA, et al. Middle East respiratory syndrome coronavirus neutralising serum antibodies in dromedary camels:A comparative serological study[J]. Lancet Infect Dis, 2013, 13(10):859-866. DOI:10.1016/S1473-3099(13)70164-6.
[28] Gao RB, Cao B, Hu YW, et al. Human infection with a novel avian-origin influenza A (H7N9) virus[J]. N Engl J Med, 2013, 368(20):1888-1897. DOI:10.1056/NEJMoa1304459.
[29] Lu RJ, Zhao X, Li J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus:Implications for virus origins and receptor binding[J]. Lancet, 2020, 395(10224):565-574. DOI:10.1016/S0140-6736(20)30251-8.
[30] Zhou P, Yang XL, Wang XG, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin[J]. Nature, 2020, 579(7798):270-273. DOI:10.1038/s41586-020-2012-7.
[31] Liu P, Chen W, Chen JP. Viral metagenomics revealed Sendai virus and coronavirus infection of Malayan pangolins (Manis javanica)[J]. Viruses, 2019, 11(11):979. DOI:10.3390/v11110979.
[32] Kocher JF, Lindesmith LC, Debbink K, et al. Bat caliciviruses and human noroviruses are antigenically similar and have overlapping histo-blood group antigen binding profiles[J]. mBio, 2018, 9(3):e00869-18. DOI:10.1128/mBio.00869-18.
[33] Sachsenröder J, Braun A, Machnowska P, et al. Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus[J]. J Gen Virol, 2014, 95(12):2734-2747. DOI:10.1099/vir.0.070029-0.
[34] Simmonds P, Adams MJ, Benkő M, et al. Virus taxonomy in the age of metagenomics[J]. Nat Rev Microbiol, 2017, 15(3):161-168. DOI:10.1038/nrmicro.2016.177.
[35] Konstantinov OK, Diallo SM, Inapogi AP, et al. The mammals of Guinea as reservoirs and carriers of arboviruses[J]. Med Parazitol (Mosk), 2006(1):34-39.
[36] Li LL, Victoria JG, Wang CL, et al. Bat guano virome:Predominance of dietary viruses from insects and plants plus novel mammalian viruses[J]. J Virol, 2010, 84(14):6955-6965. DOI:10.1128/JVI.00501-10.
[37] Phan TG, Kapusinszky B, Wang CL, et al. The fecal viral flora of wild rodents[J]. PLoS Pathog, 2011, 7(9):e1002218. DOI:10.1371/journal.ppat.1002218.
[38] 李旺. 鼠肠道病毒宏基因组学研究[D]. 镇江:江苏大学, 2016. DOI:10.7666/d.D01003085. Li W. Identification of the intestinal virome of rats using viral metagenomics[D]. Zhenjiang:Jiangsu University, 2016. DOI:10.7666/d.D01003085.(in Chinese)
[39] Donaldson EF, Haskew AN, Gates JE, et al. Metagenomic analysis of the viromes of three North American bat species:Viral diversity among different bat species that share a common habitat[J]. J Virol, 2010, 84(24):13004-13018. DOI:10.1128/JVI.01255-10.
[40] Mishra N, Fagbo SF, Alagaili AN, et al. A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia[J]. PLoS One, 2019, 14(4):e0214227. DOI:10.1371/journal.pone.0214227.
[41] Duarte MA, Silva JMF, Brito CR, et al. Faecal virome analysis of wild animals from Brazil[J]. Viruses, 2019, 11(9):803. DOI:10.3390/v11090803.