核心微生物组的研究及利用现状
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摘要
随着分子生物学和生物信息学的飞速发展,新一代测序技术可以轻松地检测不同样本中复杂的微生物分类单元。面对这些复杂而大量的微生物组数据带来的分析挑战,利用核心微生物组的方法来描述和分析样本中的核心微生物组和关键种是近年来新的研究热点,这些结果将揭示与宿主健康、生长和生产等密切相关的微生物种类,有助于深入认识微生物与宿主间的相互关系,深刻理解微生物对宿主的影响作用,更好地理解微生物组在自然生态系统中的功能。本文阐述了核心微生物组的定义、研究方法、与动植物的关系等方面的研究及利用现状,为更好地利用核心微生物组解决环境、人类健康和农业生产问题提供思路。
With the rapid development of molecular biology and bioinformatics, next-generation sequencing technology can easily detect complex microbial taxa in different samples. Being faced with the analytical challenges by these complex and large amounts of microbiome data, it is a new research hotspot that core microbiome and keystone species of samples are described and analyzed by using the core microbiome methods in recent years. The obtainment can reveal the important microorganisms closely related to health, growth and production of the host, and contribute to the understanding of the relationship between microorganisms and hosts. Ultimately, these studies can help understanding the effects of microorganisms on the host, and the functions of microorganisms in natural ecosystems. This review describes the definition and research methods of core microbiome, the relationships between core microbiome and animals and plants, and provides suggestions to better utilize core microbiome for solving practical problems of environment, human health and agricultural production and so on.
With the rapid development of molecular biology and bioinformatics, next-generation sequencing technology can easily detect complex microbial taxa in different samples. Being faced with the analytical challenges by these complex and large amounts of microbiome data, it is a new research hotspot that core microbiome and keystone species of samples are described and analyzed by using the core microbiome methods in recent years. The obtainment can reveal the important microorganisms closely related to health, growth and production of the host, and contribute to the understanding of the relationship between microorganisms and hosts. Ultimately, these studies can help understanding the effects of microorganisms on the host, and the functions of microorganisms in natural ecosystems. This review describes the definition and research methods of core microbiome, the relationships between core microbiome and animals and plants, and provides suggestions to better utilize core microbiome for solving practical problems of environment, human health and agricultural production and so on.
引文
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Lawrence K,Hyde J,2017.Microbiome restoration diet improves digestion,cognition and physical and emotional wellbeing.PLoS One,12(6):e0179017
Lawson CA,Raina JB,Kahlke T,Seymour JR,Suggett DJ,2018.Defining the core microbiome of the symbiotic dinoflagellate,Symbiodinium.Environmental Microbiology Reports,10(1):7-11
Lemanceau P,Blouin M,Muller D,Mo?nne-Loccoz Y,2017.Let the core microbiota be functional.Trends in Plant Science,22(7):583-595
Ley RE,Hamady M,Lozupone C,Turnbaugh PJ,Ramey RR,Bircher JS,Schlegel ML,Tucker TA,Schrenzel MD,Knight R,Gordon JI,2008.Evolution of mammals and their gut microbes.Science,320(5883):1647-1651
Little AE,Robinson CJ,Peterson SB,Raffa KF,Handelsman J,2008.Rules of engagement:interspecies interactions that regulate microbial communities.Annual Review of Microbiology,62:375-401
Liu WW,Wu B,Xiang MC,Liu XZ,2017.From microbiome to synthetic microbial community.Microbiology China,44(4):881-889(in Chinese)
Lloydprice J,Abuali G,Huttenhower C,2016.The healthy human microbiome.Genome Medicine,8(1):51-61
Lundberg DS,Lebeis SL,Paredes SH,Yourstone S,Gehring J,Malfatti S,Tremblay J,Engelbrektson A,Kunin V,Rio TG,Edgar RC,2012.Defining the core Arabidopsis thaliana root microbiome.Nature,488(7409):86-94
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McNally CP,Eng A,Noecker C,Gagne-Maynard WC,Borenstein E,2018.BURRITO:an Interactive multi-omic tool for visualizing taxa-function relationships in microbiome data.Frontiers in Microbiology,9:365-375
Mendes R,Garbeva P,Raaijmakers JM,2013.The rhizosphere microbiome:significance of plant beneficial,plant pathogenic,and human pathogenic microorganisms.FEMS Microbiology Reviews,37(5):634-663
Petrof EO,Gloor GB,Vanner SJ,Weese SJ,Carter D,Daigneault MC,Brown EM,Schroeter K,Allen-Vercoe E,2013.Stool substitute transplant therapy for the eradication of Clostridium difficile infection:‘RePOOPulating’the gut.Microbiome,1(1):3-15
Ren T,Wu M,2016.PhyloCore:a phylogenetic approach to identifying core taxa in microbial communities.Gene,593(2):330-333
Rodrigues RR,Moon J,Zhao B,Williams MA,2017.Microbial communities and diazotrophic activity differ in the root-zone of Alamo and Dacotah switchgrass feedstocks.Global Change Biology Bioenergy,9(6):1057-1070
Rodrigues RR,Rodgers NC,Wu X,Williams MA,2018.COREMIC:a web-tool to search for a niche associated CORE MICrobiome.PeerJ,6(2):e4395
Rui J,Li J,Zhang S,Yan X,Wang Y,Li X,2015.The core populations and co-occurrence patterns of prokaryotic communities in household biogas digesters.Biotechnology for Biofuels,8(1):158-170
Segata N,Baldini F,Pompon J,Garrett WS,Truong DT,DabiréRK,DiabatéA,Levashina EA,Catteruccia F,2016.The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender-and swarm-enriched microbial biomarkers.Scientific Reports,6:24207-24216
Sellart-Altisent M,Torres-Rodríguez JM,Gómez S,Alvarado-Ramírez E,2007.Nasal fungal microbiota in allergic and healthy subjects.Revista Iberoamericana de Micologia,24(2):125-130
Seymour JR,2014.A sea of microbes:the diversity and activity of marine microorganisms.Microbiology Australia,35(4):183-187
Shade A,Chiu CY,Mahon KD,2010.Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics.Microbial Ecology,59(3):546-554
Shade A,Handelsman J,2012.Beyond the Venn diagram:the hunt for a core microbiome.Environmental Microbiology,14(1):4-12
Singh BK,Trivedi P,Singh S,Macdonald CA,Verma JP,2018.Emerging microbiome technologies for sustainable increase in farm productivity and environmental security.Microbiology Australia,dio:10.1071/MA18006
Suskind DL,Brittnacher MJ,Wahbeh G,Shaffer ML,Hayden HS,Qin X,Singh N,Christopher J,Damman MD,Kyle R,Miller H,Nielson SI,2015.Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease.Inflammatory Bowel Diseases,21(3):556-563
Theis KR,Dheilly NM,Klassen JL,Brucker RM,Baines JF,Bosch TC,Cryan JF,Gilbert SF,Goodnight CJ,Lloyd EA,Vandenkoornhuyse JP,Zilber-Rosenberg I,Rosenberg E,Bordenstein SR,2016.Getting the hologenome concept right:an eco-evolutionary framework for hosts and their microbiomes.Msystems,1(2):e00028-16
Theriot CM,Koenigsknecht MJ,CarlsonJr PE,Hatton GE,Nelson AM,Li B,Huffnagle GB,Li JZ,Young VB,2014.Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection.Nature Communications,5(1):3114-3132
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