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Reply to: Microbial dark matter could add uncertainties to metagenomic trait estimations

Nature Microbiology (2024)Cite this article

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The Original Article was published on 13 May 2024

replying to E. D. Osburn et al. Nature Microbiology https://doi.org/10.1038/s41564-024-01687-w (2024)

In a recent paper, we used soil metagenomes from global biomes to assess life history strategies across soil bacterial communities1. We compiled 102 traits in a multi-table coinertia analysis to characterize the life history strategies of soil bacteria. Although we only used annotated reads for the calculation of most traits, full metagenomes were used to quantify bacterial average genome size (AGS) and ribosomal RNA operon copy numbers. In response, Osburn and co-workers2 pointed out a potential bias in our method for estimating bacterial AGS. We acknowledge that estimating bacterial AGS for an environment as complex and unexplored as soil is non-trivial. Although we agree that our approach has a bias towards bacterial AGS overestimation, we show that the alternative calculation proposed by Osburn et al.2 appears to have an even stronger underestimation bias. Still, neither approach led to a different conclusion for our proposed life history strategies, demonstrating the robustness of our results.

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Fig. 1: AGS calculation using the metagenome.
Fig. 2: Biases of bacterial AGS estimation methods.

References

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Author information

Authors and Affiliations

  1. Department of Earth System Science, University of California, Irvine, Irvine, CA, USA

    Gabin Piton, Steven D. Allison & Adam C. Martiny

  2. Eco&Sols, INRAE–IRD–CIRAD–SupAgro, University of Montpellier, Montpellier, France

    Gabin Piton

  3. Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA

    Steven D. Allison, Jennifer B. H. Martiny, Kathleen K. Treseder & Adam C. Martiny

  4. Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden

    Mohammad Bahram

  5. Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia

    Mohammad Bahram

  6. Gut Microbes and Health, Quadram Institute Bioscience, Norwich, UK

    Falk Hildebrand

  7. Digital Biology, Earlham Institute, Norwich, UK

    Falk Hildebrand

Authors
  1. Gabin Piton
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  2. Steven D. Allison
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  3. Mohammad Bahram
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  4. Falk Hildebrand
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  5. Jennifer B. H. Martiny
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  6. Kathleen K. Treseder
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  7. Adam C. Martiny
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Contributions

This reply was written by G.P. with inputs from A.C.M., F.H., S.D.A. and J.B.H.M. Metagenome composition simulations were carried out by G.P. All authors read and approved the paper.

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Correspondence to Gabin Piton.

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The authors declare no competing interests.

Peer review

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Nature Microbiology thanks Kate Buckeridge and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Notes 1 and 2 and Figs. 1 and 2.

Supplementary Table

A table with simulations of bacterial AGS and associated biases when using the full metagenome or bacteria-annotated reads only. Scenarios corresponding to low- and high-pH soils are simulated.

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Piton, G., Allison, S.D., Bahram, M. et al. Reply to: Microbial dark matter could add uncertainties to metagenomic trait estimations. Nat Microbiol (2024). https://doi.org/10.1038/s41564-024-01688-9

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