Reply to: Examining microbe-metabolite correlations by linear methods

James T Morton^{1

2}, Daniel McDonald^{1

3}, Alexander A Aksenov^{4

5}, Louis Felix Nothias^{4

5}, James R Foulds⁶, Robert A Quinn⁷, Michelle H Badri⁸, Tami L Swenson⁹, Marc W Van Goethem⁹, Trent R Northen^{9

10}, Yoshiki Vazquez-Baeza^{3

11}, Mingxun Wang^{4

5}, Nicholas A Bokulich^{12

13}, Aaron Watters¹⁴, Se Jin Song^{1

3}, Richard Bonneau^{8

14

15

16}, Pieter C Dorrestein^{4

5}, Rob Knight^{17

18

19

20}

Affiliations

¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴ Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Information Systems, University of Maryland-Baltimore County, Baltimore, MD, USA.
⁷ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
⁸ Department of Biology, New York University, New York, NY, USA.
⁹ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁰ DOE Joint Genome Institute, Walnut Creek, CA, USA.
¹¹ Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA.
¹² The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
¹³ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
¹⁴ Flatiron Institute, Simons Foundation, New York, NY, USA.
¹⁵ Department of Computer Science, Courant Institute, New York, NY, USA.
¹⁶ Center for Data Science, New York University, New York, NY, USA.
¹⁷ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
¹⁸ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
¹⁹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
²⁰ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.

PMID: 33398188
DOI: 10.1038/s41592-020-01007-0

Comment

Reply to: Examining microbe-metabolite correlations by linear methods

James T Morton et al. Nat Methods. 2021 Jan.

. 2021 Jan;18(1):40-41.

doi: 10.1038/s41592-020-01007-0. Epub 2021 Jan 4.

Authors

Affiliations

¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
² Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
³ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
⁴ Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA.
⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
⁶ Department of Information Systems, University of Maryland-Baltimore County, Baltimore, MD, USA.
⁷ Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
⁸ Department of Biology, New York University, New York, NY, USA.
⁹ Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁰ DOE Joint Genome Institute, Walnut Creek, CA, USA.
¹¹ Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA.
¹² The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
¹³ Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
¹⁴ Flatiron Institute, Simons Foundation, New York, NY, USA.
¹⁵ Department of Computer Science, Courant Institute, New York, NY, USA.
¹⁶ Center for Data Science, New York University, New York, NY, USA.
¹⁷ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
¹⁸ Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
¹⁹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.
²⁰ Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA. rknight@ucsd.edu.

PMID: 33398188
DOI: 10.1038/s41592-020-01007-0

No abstract available

PubMed Disclaimer

Comment on

Learning representations of microbe-metabolite interactions.
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. Morton JT, et al. Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4. Nat Methods. 2019. PMID: 31686038 Free PMC article.
Examining microbe-metabolite correlations by linear methods.
Quinn TP, Erb I. Quinn TP, et al. Nat Methods. 2021 Jan;18(1):37-39. doi: 10.1038/s41592-020-01006-1. Epub 2021 Jan 4. Nat Methods. 2021. PMID: 33398187 No abstract available.

References

1. Quinn, T. P. & Erb, I. Examining microbe–metabolite correlations by linear methods. Nat. Methods https://doi.org/10.1038/s41592-020-01006-1 (2020).
1. Aitchison, J. A concise guide to compositional data analysis. http://www.leg.ufpr.br/lib/exe/fetch.php/pessoais:abtmartins:a_concise_g... (2003).
1. Filzmoser, P. & Hron, K. Correlation analysis for compositional data. Math. Geosci. 41, 905 (2009). - DOI
1. Friedman, J. & Alm, E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012). - DOI
1. Morton, J. T. et al. Establishing microbial composition measurement standards with reference frames. Nat. Commun. 10, 2719 (2019). - DOI

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Reply to: Examining microbe-metabolite correlations by linear methods

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Reply to: Examining microbe-metabolite correlations by linear methods

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