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. 2021 Mar 29;9:77. doi: 10.1186/s40168-021-01033-w

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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. 6 — Relative abundance and OPR counts for strains in ex vivo-cultured murine faecal samples. Mean relative abundance (left panel) of each strain in murine faecal samples (n=6) after ex vivo culturing. The numbers within brackets denote the corresponding median per base sequence coverage of each strain. The dashed line represents the 1% relative abundance threshold. OPR counts (middle panel) over the genome of control (n=3, dark purple) and induced (n=3, red) samples, excluding OPRs at the beginning and end of the genome. The OPR counts of each sample were normalised per cell. OPR ratios (right panel) between induced and control samples. Strains, for which an active prophage was identified by ΔPtoH ratio and OPRs, are marked by an asterisk