Strategies to improve reference databases for soil microbiomes

ISME Journal

Volumn 11, Issue 4, 2017, Pages 829-834

  Choi, Jinlyung ^a   Yang, Fan ^a   Stepanauskas, Ramunas ^b   Cardenas, Erick ^c   Garoutte, Aaron ^d   Williams, Ryan ^a   Flater, Jared ^a   Tiedje, James M ^d   Hofmockel, Kirsten S ^e,f   Gelder, Brian ^a   Howe, Adina ^a  

^a Iowa State University   (United States)

^b BIGELOW LABORATORY FOR OCEAN SCIENCES   (United States)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d MICHIGAN STATE UNIVERSITY   (United States)

^e PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^f IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIODIVERSITY; DATABASE; GENETIC ANALYSIS; GENOME; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; PHYLOGENETICS; REFERENCE SAMPLE; SOIL MICROORGANISM;

EID: 85004168862     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2016.168     Document Type: Article

References (20)

1. Buffie CG, Pamer EG. (2013). Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 13: 790-801.
2. Delmont TO, Prestat E, Keegan KP, Faubladier M, Robe P, Clark IM et al. (2012). Structure, fluctuation and magnitude of a natural grassland soil metagenome. ISME J 6: 1677-1687.
3. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS et al. (2013). Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science 342: 621-624.
4. Fierer N, Leff JW, Adams BJ, Nielsen UN, Bates ST, Lauber CL et al. (2012). Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc Natl Acad Sci USA 109: 21390-21395.
5. Gawad C, Koh W, Quake SR. (2016). Single-cell genome sequencing: current state of the science. Nat Rev Genet 17: 175-188.
6. Gilbert JA, Jansson JK, Knight R. (2014). The Earthmicrobiome project: successes and aspirations. BMC Biol 12: 69.
7. Hultman J, Waldrop MP, Mackelprang R, David MM, McFarland J, Blazewicz SJ et al. (2015). Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes. Nature 521: 208-212.
8. Huttenhower C, Gevers D, Knight R, Abubucker S, Badger JH, Chinwalla AT et al. (2012). Structure, function and diversity of the healthy human microbiome. Nature 486: 207-214.
9. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. (2002). Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 68: 2391-2396.
10. Kashtan N, Roggensack SE, Rodrigue S, Thompson JW, Biller SJ, Coe A et al. (2014). Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus. Science 344: 416-420.
11. Nunes da Rocha U, Van Overbeek L, Van Elsas JD. (2009). Exploration of hitherto-uncultured bacteria from the rhizosphere. FEMS Microbiol Ecol 69: 313-328.
12. Rideout JR, He Y, Navas-Molina JA, Walters WA, Ursell LK, Gibbons SM et al. (2014). Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences. PeerJ 2: e545-25.
13. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng J-F et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499: 431-437.
14. Rupnik M, Wilcox MH, Gerding DN. (2009). Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Micro 7: 526-536.
15. Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. (2012). Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Meth 9: 811-814.
16. Stepanauskas R. (2012). Single cell genomics: an individual look at microbes. Curr Opin Microbiol 15: 613-620.
17. Swan BK, Martinez-Garcia M, Preston CM, Sczyrba A, Woyke T, Lamy D et al. (2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333: 1296-1300.
18. Van Pham HT, Kim J. (2012). Cultivation of unculturable soil bacteria. Trends Biotechnol 30: 475-484.
19. Wang Q, Garrity GM, Tiedje JM, Cole JR. (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-5267.
20. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN et al. (2009). A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 462: 1056-1060.