Metagenomic tools in microbial ecology research

被引：112

作者：

Tas, Neslihan ^{[1
,2
]}

de Jong, Anniek E. E. ^{[3
,4
]}

Li, Yaoming ^{[5
,6
]}

Trubl, Gareth ^{[7
]}

Xue, Yaxin ^{[8
]}

Dove, Nicholas C. ^{[9
]}

机构：

[1] Lawrence Berkeley Natl Lab, Div Earth & Environm Sci, Berkeley, CA 94720 USA

[2] Lawrence Berkeley Natl Lab, Biosci Area, Berkeley, CA 94720 USA

[3] Deltares, Daltonlaan 600, NL-3584 BK Utrecht, Netherlands

[4] Radboud Univ Nijmegen, Inst Water & Wetland Res, Dept Microbiol, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands

[5] Beijing Forest Univ, Sch Grassland Sci, Beijing 100083, Peoples R China

[6] Zhejiang Tiantong Forest Ecosyst Natl Observat &, Shanghai 200241, Peoples R China

[7] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Livermore, CA 94550 USA

[8] Univ Bergen, Dept Informat, Computat Biol Unit, N-5008 Bergen, Norway

[9] Oak Ridge Natl Lab, Biosci Div, POB 2009, Oak Ridge, TN 37831 USA

来源：

CURRENT OPINION IN BIOTECHNOLOGY | 2021年 / 67卷

基金：

中国国家自然科学基金;

关键词：

METABOLISM; VIRUS; BIOLOGY; SYSTEMS; GENOMES;

D O I：

10.1016/j.copbio.2021.01.019

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via genecentric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.

引用

页码：184 / 191

页数：8

共 60 条

[1] Functional metagenomic analysis of dust-associated microbiomes above the Red Sea [J].

Aalismail, Nojood A. ;

Ngugi, David K. ;

Diaz-Rua, Ruben ;

Alam, Intikhab ;

Cusack, Michael ;

Duarte, Carlos M. .

SCIENTIFIC REPORTS, 2019, 9 (1)

[2] Characterization of vesicular stomatitis virus populations by tunable resistive pulse sensing [J].

Akpinar, Fulya ;

Yin, John .

JOURNAL OF VIROLOGICAL METHODS, 2015, 218 :71-76

[3] Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system [J].

Anantharaman, Karthik ;

Brown, Christopher T. ;

Hug, Laura A. ;

Sharon, Itai ;

Castelle, Cindy J. ;

Probst, Alexander J. ;

Thomas, Brian C. ;

Singh, Andrea ;

Wilkins, Michael J. ;

Karaoz, Ulas ;

Brodie, Eoin L. ;

Williams, Kenneth H. ;

Hubbard, Susan S. ;

Banfield, Jillian F. .

NATURE COMMUNICATIONS, 2016, 7

[4] Environmental conditions shape the nature of a minimal bacterial genome [J].

Antczak, Magdalena ;

Michaelis, Martin ;

Wass, Mark N. .

NATURE COMMUNICATIONS, 2019, 10 (1)

[5] KBase: The United States Department of Energy Systems Biology Knowledgebase [J].

Arkin, Adam P. ;

Cottingham, Robert W. ;

Henry, Christopher S. ;

Harris, Nomi L. ;

Stevens, Rick L. ;

Maslov, Sergei ;

Dehal, Paramvir ;

Ware, Doreen ;

Perez, Fernando ;

Canon, Shane ;

Sneddon, Michael W. ;

Henderson, Matthew L. ;

Riehl, William J. ;

Murphy-Olson, Dan ;

Chan, Stephen Y. ;

Kamimura, Roy T. ;

Kumari, Sunita ;

Drake, Meghan M. ;

Brettin, Thomas S. ;

Glass, Elizabeth M. ;

Chivian, Dylan ;

Gunter, Dan ;

Weston, David J. ;

Allen, Benjamin H. ;

Baumohl, Jason ;

Best, Aaron A. ;

Bowen, Ben ;

Brenner, Steven E. ;

Bun, Christopher C. ;

Chandonia, John-Marc ;

Chia, Jer-Ming ;

Colasanti, Ric ;

Conrad, Neal ;

Davis, James J. ;

Davison, Brian H. ;

DeJongh, Matthew ;

Devoid, Scott ;

Dietrich, Emily ;

Dubchak, Inna ;

Edirisinghe, Janaka N. ;

Fang, Gang ;

Faria, Jose P. ;

Frybarger, Paul M. ;

Gerlach, Wolfgang ;

Gerstein, Mark ;

Greiner, Annette ;

Gurtowski, James ;

Haun, Holly L. ;

He, Fei ;

Jain, Rashmi .

NATURE BIOTECHNOLOGY, 2018, 36 (07) :566-569

[6]

Bhargava P., 2019, Plant Microbe Interface, P271, DOI [10.1007/978-3-030-19831-212, DOI 10.1007/978-3-030-19831-212]

[7] Long-Read Sequencing - A Powerful Toll in Viral Transcriptome Research [J].

Boldogkoi, Zsolt ;

Moldovan, Norbert ;

Balazs, Zsolt ;

Snyder, Michael ;

Tombacz, Ddra .

TRENDS IN MICROBIOLOGY, 2019, 27 (07) :578-592

[8] Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea [J].

Bowers, Robert M. ;

Kyrpides, Nikos C. ;

Stepanauskas, Ramunas ;

Harmon-Smith, Miranda ;

Doud, Devin ;

Reddy, T. B. K. ;

Schulz, Frederik ;

Jarett, Jessica ;

Rivers, Adam R. ;

Eloe-Fadrosh, Emiley A. ;

Tringe, Susannah G. ;

Ivanova, Natalia N. ;

Copeland, Alex ;

Clum, Alicia ;

Becraft, Eric D. ;

Malmstrom, Rex R. ;

Birren, Bruce ;

Podar, Mircea ;

Bork, Peer ;

Weinstock, George M. ;

Garrity, George M. ;

Dodsworth, Jeremy A. ;

Yooseph, Shibu ;

Sutton, Granger ;

Gloeckner, Frank O. ;

Gilbert, Jack A. ;

Nelson, William C. ;

Hallam, Steven J. ;

Jungbluth, Sean P. ;

Ettema, Thijs J. G. ;

Tighe, Scott ;

Konstantinidis, Konstantinos T. ;

Liu, Wen-Tso ;

Baker, Brett J. ;

Rattei, Thomas ;

Eisen, Jonathan A. ;

Hedlund, Brian ;

McMahon, Katherine D. ;

Fierer, Noah ;

Knight, Rob ;

Finn, Rob ;

Cochrane, Guy ;

Karsch-Mizrachi, Ilene ;

Tyson, Gene W. ;

Rinke, Christian ;

Lapidus, Alla ;

Meyer, Folker ;

Yilmaz, Pelin ;

Parks, Donovan H. ;

Eren, A. M. .

NATURE BIOTECHNOLOGY, 2017, 35 (08) :725-731

[9] Unusual biology across a group comprising more than 15% of domain Bacteria [J].

Brown, Christopher T. ;

Hug, Laura A. ;

Thomas, Brian C. ;

Sharon, Itai ;

Castelle, Cindy J. ;

Singh, Andrea ;

Wilkins, Michael J. ;

Wrighton, Kelly C. ;

Williams, Kenneth H. ;

Banfield, Jillian F. .

NATURE, 2015, 523 (7559) :208-U173

[10] New CRISPR-Cas systems from uncultivated microbes [J].

Burstein, David ;

Harrington, Lucas B. ;

Strutt, Steven C. ;

Probst, Alexander J. ;

Anantharaman, Karthik ;

Thomas, Brian C. ;

Doudna, Jennifer A. ;

Banfield, Jillian F. .

NATURE, 2017, 542 (7640) :237-241

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