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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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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 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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DOI: https://doi.org/10.1038/s41564-024-01688-9