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. 2021 May 26;9:112. doi: 10.1186/s40168-021-01044-7

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Inferred species- and strain-level growth rates showed geographically specific profiles. GRiD and SMEG were respectively applied to infer the a species- and b strain-level growth rates. GRiD was shown for species-level taxa with indices detected in greater than 10% of samples in the dataset. Samples with coverage below the default threshold for each species could not have their growth rates inferred and are indicated as white spaces on the plots