PICRUSt2 for prediction of metagenome functions

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Fig. 1: PICRUSt2 algorithm.
Fig. 2: PICRUSt2 performance characteristics.
Fig. 3: PICRUSt2 accurately predicts MetaCyc pathways and phenotypes for characterizing overall environments.

Data availability

The repository at https://github.com/gavinmdouglas/picrust2_manuscript includes the processed data files that can be used to re-generate the figures and findings in this paper. The accession codes for all sequencing data used in this study are listed in the Supplementary Methods.

Code availability

PICRUSt2 is available at https://github.com/picrust/picrust2. The Python and R code used for the analyses and database construction described in this paper are available online at https://github.com/gavinmdouglas/picrust2_manuscript.

References

  1. 1.

    Langille, M. G. I. et al. Nat. Biotechnol. 31, 814–821 (2013).

    CAS  Article  Google Scholar 

  2. 2.

    Iwai, S. et al. PLoS One 11, e0166104 (2016).

    Article  Google Scholar 

  3. 3.

    Jun, S. R. et al. BMC Res. Notes 8, 479 (2015).

    Article  Google Scholar 

  4. 4.

    Aßhauer, K. P., Wemheuer, B., Daniel, R. & Meinicke, P. Bioinformatics 31, 2882–2884 (2015).

    Article  Google Scholar 

  5. 5.

    Wemheuer, F. et al. Preprint at bioRxiv https://doi.org/10.1101/490037 (2018).

  6. 6.

    DeSantis, T. Z. et al. Appl. Environ. Microbiol. 72, 5069–5072 (2006).

    CAS  Article  Google Scholar 

  7. 7.

    Markowitz, V. M. et al. Nucleic Acids Res. 40 (D1), D115–D122 (2012).

    CAS  Article  Google Scholar 

  8. 8.

    Barbera, P. et al. Syst. Biol. 68, 365–369 (2019).

    Article  Google Scholar 

  9. 9.

    Czech, L. & Stamatakis, A. PLoS One 14, e0217050 (2019).

    CAS  Article  Google Scholar 

  10. 10.

    Louca, S. & Doebeli, M. Bioinformatics 34, 1053–1055 (2018).

    CAS  Article  Google Scholar 

  11. 11.

    Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. Nucleic Acids Res. 40 (D1), D109–D114 (2012).

    CAS  Article  Google Scholar 

  12. 12.

    Narayan, N. R. et al. BMC Genomics 21, 56 (2020).

    CAS  Article  Google Scholar 

  13. 13.

    Caspi, R. et al. Nucleic Acids Res. 44 (D1), D471–D480 (2016).

    CAS  Article  Google Scholar 

  14. 14.

    Franzosa, E. A. et al. Nat. Methods 15, 962–968 (2018).

    CAS  Article  Google Scholar 

  15. 15.

    Chen, I.-M. A. et al. PLoS One 8, e54859 (2013).

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank Zhenjiang Xu and Amy Chen for providing us access to data files used for testing and the default reference database. We also thank Heather McIntosh for help designing the pipeline flowchart. G.M.D. is funded by an NSERC CGS-D scholarship. V.J.M. is funded by an NIH/NIAAA Ruth L. Kirschstein National Research Service Award (F30 AA026527). J.R.Z. is supported by NSF IOS CAREER grant 1942647. S.Y.N. is funded by an NSERC Discovery Grant. C.H. is funded in part by NIH NIDDK grants U54DK102557 and R24DK110499. M.G.I.L. is funded by an NSERC Discovery Grant and an NSERC Collaborative Research Development with co-funding from GlaxoSmithKline to M.G.I.L. and J.R.B.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Morgan G. I. Langille.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Editorial note: This article has been peer reviewed.

Supplementary information

Supplementary Information

Description: Supplementary Methods, Supplementary Results, Supplementary Figs. 117 and Supplementary Tables 1–4

Supplementary Data

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Douglas, G.M., Maffei, V.J., Zaneveld, J.R. et al. PICRUSt2 for prediction of metagenome functions. Nat Biotechnol 38, 685–688 (2020). https://doi.org/10.1038/s41587-020-0548-6

Download citation

Further reading