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. 2017 Apr;11(4):829-834.
doi: 10.1038/ismej.2016.168. Epub 2016 Dec 9.

Strategies to improve reference databases for soil microbiomes

Jinlyung Choi  1 , Fan Yang  1 , Ramunas Stepanauskas  2 , Erick Cardenas  3 , Aaron Garoutte  4 , Ryan Williams  1 , Jared Flater  1 , James M Tiedje  4 , Kirsten S Hofmockel  5   6 , Brian Gelder  1 , Adina Howe  1
Affiliations

Strategies to improve reference databases for soil microbiomes

Jinlyung Choi et al. ISME J. 2017 Apr.
No abstract available

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree of EMP OTUs clustered by taxonomy. Ring I (green) represents the cumulative log-scaled abundance of OTUs in EMP soil samples. Ring II (red) represents EMP OTUs that share >97% gene similarity (to RefSoil 16S rRNA genes; ring III (blue) indicates that these 16S rRNA genes shared similarity to sorted cells that were selected for single-cell genomics. A: Acidobacteria, B: Actinobacteria, C: Aquificae, D: Armatimonadetes, E: Bacteroidetes, F: Chlamydiae, G: Chlorobi, H: Chloroflexi, I: Crenarchaeota, K: Deferribacteres, L: Deinococcus-Thermus, M: Euryarchaeota, N: Firmicutes, O: Fusobacteria, P: Gemmatimonadetes, Q: Nitrospirae, R: Planctomycetes, S: Proteobacteria, T: Spirochaetes, U: Synergistetes, V: Tenericutes, W: Thermotogae, X: Verrucomicrobia, Y: Cyanobacteria/Chloroplast.
See this image and copyright information in PMC

References

    1. Buffie CG, Pamer EG. (2013). Microbiota-mediated colonization resistance against intestinal pathogens. Nat Rev Immunol 13: 790–801. - PMC - PubMed
    1. 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. - PMC - PubMed
    1. 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. - PubMed
    1. 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. - PMC - PubMed
    1. Gawad C, Koh W, Quake SR. (2016). Single-cell genome sequencing: current state of the science. Nat Rev Genet 17: 175–188. - PubMed