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Reply to: Erroneous predictions of auxotrophies by CarveMe

Nature Ecology & Evolution volume 7, pages 196–197 (2023)Cite this article

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The Original Article was published on 05 December 2022

replying to: M. Price Nature Ecology & Evolution https://doi.org/10.1038/s41559-022-01936-3 (2022).

In our article1, we used genome-scale metabolic models to analyse the interaction potential of higher-order co-occurring communities on a global scale (using sequencing data from the Earth Microbiome Project2). The analysis revealed two distinct types of co-occurring communities that we classified as cooperative and competitive based on predicted differences in their metabolic interaction potential. This observation is supported in our study by distinct patterns of genome sizes, relative abundances, stability and habitat preferences. In a recent communication, Price3: (1) questions amino acid auxotrophy predictions made by CarveMe, the tool used to build the models in our work, for a small group of bacteria from a limited habitat range; and (2) postulates that most of the auxotrophy predictions in our work are incorrect. We address these points below.

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Authors and Affiliations

  1. Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway

    Daniel Machado

  2. MRC Toxicology Unit, University of Cambridge, Cambridge, UK

    Kiran R. Patil

Authors
  1. Daniel Machado
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  2. Kiran R. Patil
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Contributions

D.M. and K.R.P. wrote the article.

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Correspondence to Kiran R. Patil.

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The authors declare no competing interests.

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Nature Ecology & Evolution thanks Joshua Goldford and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Machado, D., Patil, K.R. Reply to: Erroneous predictions of auxotrophies by CarveMe. Nat Ecol Evol 7, 196–197 (2023). https://doi.org/10.1038/s41559-022-01939-0

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