Fig. 1

Diversity of phage defense systems in the genomes of cheese-associated bacterial species. A Core genome phylogeny of the 26 predominant species found in the cheese-associated communities and their corresponding color key used in B. B Species-level composition of cheese-associated communities (starter and non-starter) grouped by studies. Sample type and community profiling method (16S rRNA gene amplicon or shotgun metagenomics sequencing) is indicated. C Heatmap illustrating the fraction of genomes per species containing different innate and adaptive immunity mechanisms. The color scheme is indicated below D and E. D The absolute count and E relative fraction of core (> 90% of strains), accessory (90%< of strains > 10%), and cloud (< 10% of strains) defense systems. F Principal component analysis of all strains based on the abundance/presence of different defense systems (colored according to legend in A). G The number of different defense systems vs. average nucleotide identity between two genomes of the same species. Including only the most dominant species comparisons. The statistics of the regression lines are illustrated in Suppl. Fig. 4 and the colors corresponds to the legend in A