Fig. 6
From: Vertical transmission of gut bacteria in commercial chickens is limited
Analysis of interventions aimed at disrupting vertical transmission. A Number of observed ASVs in treated and untreated hen samples. Box plots are presented (centerline, median; box limits, upper and lower quartiles; whiskers, min and max values). Two-tailed Mann–Whitney test of each antibiotic-treated vs. untreated samples of the same type; hens’ feces n = 24, treated hens’ feces n = 4, hens’ cecum n = 4, treated hens’ cecum n = 4, hens’ jejunum n = 4, treated hens’ jejunum n = 5; *p < 0.05, ***p ≤ 0.001. B Number of observed ASVs in treated and untreated chick samples. Box plots are presented (centerline, median; box limits, upper and lower quartiles; whiskers, min and max values). Kruskal–Wallis test of each treated group vs. the untreated group; untreated d2 n = 87, egg disinfection d2 n = 22, antibiotics d2 n = 20; untreated d7 n = 89, egg disinfection d7 n = 20, antibiotics d7 n = 19; untreated d14 n = 86, egg disinfection d14 n = 22, antibiotics d14 n = 20; *p < 0.05, **p ≤ 0.01. C, D Treatment effect on the transmission of specific phylogenetic groups. C-disinfection. D-antibiotic cocktail. For both C and D, occurrences in chicks’ fecal samples of ASVs (either shared with hens’ feces or absent from hens’ samples) from each phylogenetic group were summed for treated and untreated chick samples and normalized to the number of samples in each treatment group (C-untreated n = 74, treated n = 64; D-untreated n = 69, treated n = 59). Log2 transformation of the fold change (treated:untreated) ratio is presented. Phylogenetic groups with at least 60 occurrences are presented. The number of occurrences in each phylogenetic group is indicated above the bar. To infer significance, 1,000 random permutations were generated by shuffling the treatment labels and recalculating the ratios. A ratio was considered significant if it was more than two standard deviations from the mean of the random permutations. E Presence of live bacterial cells of the top three transmitted ASVs in adult hens’ reproductive tract and on eggshells. For shell gland, magnum and infundibulum n = 10 each; for eggshell n = 9