Fig. 4: Reduced in vivo fitness of co-diversified LGM strains compared to WGM relatives.

a Principal coordinates plot shows beta-diversity (Jaccard) dissimilarities among microbiota profiles based on laboratory mouse– and wildling-derived ASVs within co-diversified taxa. Plot shows data from the Wildling/Jackson co-housing experiments. Shapes and colors denote host of origin as indicated in the key. Samples from ex-germ-free mice (n = 6) are colored according to the day of sample collection. Arrows connect longitudinal samples from the same germ-free mouse. b Line plots show that ex-germ-free mice (n = 6) sampled on days 2–17 harbored a greater fraction of wildling-derived ASVs from co-diversified taxa than laboratory mouse–derived ASVs from co-diversified taxa. The y-axis displays the microbiota similarity (1 minus Jaccard dissimilarity) of ex-germ-free mouse samples to their wildling cage mates minus the similarity of the ex-germ-free mouse samples to their laboratory-mouse cage mates. Colors of lines denote whether they are based on ASV profiles within co-diversifying taxa or other taxa, as indicated by the key. Datapoints are jittered along the x-axis. Asterisks indicate significant differences between the analyses conducted using ASVs from co-diversified taxa and the analyses conducted using all other ASVs; Wilcoxon Test, p-value = ns not significant, * < 0.05, ** < 0.01. c Box plots show the normalized read counts (log₁₀[read count + 1]) of all laboratory mouse–specific or wildling-specific ASVs from co-diversified genera in the laboratory and wildling mice sampled at day 0 (before co-housing) (n = 6). For boxplots, the middle line represents the median value, the lower and upper hinges correspond to the first and third quartiles, respectively, and the upper and lower whiskers extend to the largest and smallest values, respectively, within 1.5 times the inter-quartile range. Significant differences in mean abundance are shown (Wilcoxon Test, p-value = ns not significant, * < 0.05, ** < 0.01). d Line plots show higher relative abundance in ex-germ-free mice of wildling-derived ASVs from bacterial genera showing evidence of co-diversification (yellow) compared to laboratory mouse–derived ASVs from the same genera (blue). Each line indicates the normalized relative abundance (log₁₀[read count + 1]) within individual ex-germ-free mice (n = 6) sampled between days 1 and 17 of wildling-derived (yellow) or laboratory mouse–derived (blue) ASVs from a co-diversified genus. Significant differences in mean were assessed with modified Wilcoxon rank sum tests for zero-inflated data, *p-value < 0.05, ****p-value < 0.0001. Results from experiments with Taconic mice are presented in Supplementary Fig. 9. Raw data and metadata used for these analyses are presented in Supplementary Data 14 and Supplementary Data 16. Source data are provided as a Source Data file. P-values are provided in Supplementary Data 15.