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Erroneous predictions of auxotrophies by CarveMe

Nature Ecology & Evolution volume 7, pages 194–195 (2023)Cite this article

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Matters Arising to this article was published on 05 December 2022

The Original Article was published on 04 January 2021

arising from: D. Machado et al. Nature Ecology & Evolution https://doi.org/10.1038/s41559-020-01353-4 (2021)

In their paper, D. Machado et al. claim to identify ‘cooperative’ communities with many amino acid auxotrophies1. A related paper, with many of the same authors, claims that 26% of bacteria from free-living communities are amino acid auxotrophs2. The putative amino acid auxotrophies were derived from genome sequences via the metabolic models of CarveMe3 but were not validated in any way. I checked the predictions of CarveMe for prototrophic bacteria and found a high rate of spurious auxotrophies.

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Data availability

CarveMe’s auxotrophy predictions are available for 127 of the initial list of 140 bacteria that grow in defined media without any amino acids4 (these were identified from a database of media-isolate combinations9 and from a compilation of nitrogen-fixing microbes10). CarveMe’s auxotrophy predictions can be obtained by using the download.sh script in https://github.com/cdanielmachado/cooccurrence (after download, the predictions are in the tab delimited files in the ancestrality subdirectory). CarveMe’s models can be downloaded from https://github.com/cdanielmachado/embl_gems. A list of the 127 bacteria, as well as a table comparing the spurious CarveMe “auxotrophies” to the GapMind annotations for those pathways and genomes, is available from figshare (https://doi.org/10.6084/m9.figshare.20993512.v1). The GapMind annotations for the 127 prototrophic bacteria (as well as some other bacteria and archaea) are available from https://doi.org/10.6084/m9.figshare.9693689.v1 and can be viewed at https://papers.genomics.lbl.gov/cgi-bin/gapView.cgi?set=aa&orgs=orgsDef_150. (GapMind has been updated since the original publication, so the two analyses are not always identical.)

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Acknowledgements

This material by ENIGMA, Ecosystems and Networks Integrated with Genes and Molecular Assemblies (http://enigma.lbl.gov), a Science Focus Area programme at Lawrence Berkeley National Laboratory is based on work supported by the US Department of Energy, Office of Science, Office of Biological & Environmental Research under contract number DE-AC02-05CH11231.

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  1. Environmental Genomics and Systems Biology, Lawrence Berkeley National Lab, Berkeley, CA, USA

    Morgan Price

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Correspondence to Morgan Price.

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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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Price, M. Erroneous predictions of auxotrophies by CarveMe. Nat Ecol Evol 7, 194–195 (2023). https://doi.org/10.1038/s41559-022-01936-3

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