a) Diversities of the cultured microbiota and the original fecal sample (Fecal 7
mix). Data represents Shannon alpha diversity indexes at family level based on
16S rRNA profiling of V4 region. AMP/antibiotic (AB) treatments are
colour-coded. Untreated samples were grown in the absence of any AMP or AB. **
indicates a significant difference from two-sided Mann-Whitney U test,
p=0.005 for Untreated vs ABs,
p=3*10-4 for AMPs vs ABs. Sample sizes were 5,
15 and 15 for Untreated, AMPs and ABs, respectively. Central horizontal bars
represent median values. b) A PCoA (principal coordinate analysis)
plot based on unweighted UniFrac distances34 separates the AMP- and antibiotic-resistant, and the untreated
microbial communities (p=0.001, PERMANOVA test,
n=36). c) Differential abundance analyses
between the untreated and the AMP- and antibiotic-resistant microbiota at the
family level (see Methods). Brackets
depict a significant increase (red) or decrease (black) in abundance of a given
family as a consequence of AMP or antibiotic (AB) treatment based on pairwise
two-sided negative binomial tests (see Methods). Sample sizes were 5 and 3-3 for Untreated and AMPs and
ABs, respectively. The phylogenetic tree is based on the assignment of the NCBI
Taxonomy database and created by using ete3 toolkit37. d) Phylum-level distributions of resistant
gut bacteria and resistance DNA contigs originating from them. Compared to their
relative frequencies in the drug-treated cultured microbiota (based on colony
numbers), the phylogenetically close Proteobacteria contributed
disproportionally more AMP- (red bars) than antibiotic-resistance contigs (AB,
blue bars), whereas the opposite pattern was seen for the distantly related
Firmicutes. Asterisks indicate significant interaction terms in logistic
regression models, p=0.018 (*) and p=0.003
(**) for Proteobacteria and Firmicutes, respectively (for more details see Methods and Supplementary Table 11).
Sample sizes were 22651 and 24336 for the total colony number of AMP-resistant
and AB-resistant microbiota, respectively,and 33 and 54 for the number of
transferred AMP-resistant and AB-resistant contigs, respectively.