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. 2021 Jul 14;22:209. doi: 10.1186/s13059-021-02427-7

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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. 3 — The CRISPR-Cas system of Akkermansia candidate species and their viral targets. A CRISPR locus type composition of Akkermansia candidate species. All candidate species possess CRISPR locus type I-C, with the exception of A. muciniphila in which type II-C is present in more than 30% of the genomes. B Representative locus organization of CRISPR loci over Akkermansia candidate species. Some type I-C loci contain only one CRISPR array. Gene and CRISPR array lengths are scaled to correspond to the median length over all loci. C Phylogenetic tree of A. muciniphila subspecies colored by type II-C presence. D The total number of spacer sequences for the genomes in each Akkermansia candidate species. Type II-C loci were only found in A. muciniphila. Numbers above the boxplots correspond to the fraction of type I-C loci with two CRISPR arrays. E Logo plots of predicted PAM sequences in putative (phage) Viral Clusters (VCs, see the “Methods” section) upstream of sequences with perfect matches against CRISPR spacer sequences from type I-C loci. F Proportion of CRISPR spacers within candidate species genomes with a near-perfect match (at most 2 mismatched nucleotides) for four VCs. The number above the box plots corresponds to the fraction of genomes with at least one spacer hit against a given VC (see the “Methods” section). G Mapping of spacers from Akkermansia genomes against two representative VCs, visualized with a sliding window of 150 nt. See Additional file 2: Figure S8 for the remaining VCs. H Distribution of the relative abundances of the Akkermansia candidate species based on the presence or absence of each cognate VC in the metagenome (Additional file 1: Table S2, see the “Methods” section). P-values for differential abundance were determined via two-sided Wilcoxon rank-sum tests. P-values of <0.01 were considered significant. The numbers above the box plots correspond to the generalized fold change, with negative numbers indicating a higher bacterial abundance when a VC is detected [60]