kine expression) as response, and c) colonization levels measured in log(CFU) as response. These models were used to evaluate a) impact of antibiotics on specific microbiota and the immune response, b) influence of specific microbiota on cytokine mRNA expression c) the role of specific microbiota and cytokine mRNA expression on the level of *C. albicans* colonization. In each model, antibiotic treatment (PSG, vancomycin), exposure to *C. albicans* (+/− *C. albicans* gavage), and time-points of sampling (Day 7, 21) were included as indicator variables. Mice in control groups served as the reference baseline. Each bacterial model was estimated from 30 mice, 10 in each treatment group (controls, vancomycin and PSG). Each fungal model was estimated from 36 mice, 12 in each treatment group. All data analyses were performed in the R language for statistical computing[@b60].

Data and code availability
--------------------------

Sequencing data, experimental data and associated documentation are available on the accompanying website for our project[@b47]. Source code for our analysis is available at GitHub[@b30].

Author Contributions
====================

J.S. and S.G.F. interpreted the analyses and wrote the manuscript. J.S. designed and implemented the statistical analysis. N.V.S. and H.L. conducted the mouse experiments and DNA/RNA extractions. S.M. conducted the sequencing experiments. S.S. designed and implemented the bioinformatics workflow. S.G.F., W.C.N., N.V.S., S.M. and L.L. designed the study. All authors reviewed the manuscript.

Supplementary Material {#s1}
======================

###### Supplementary Information

Supplementary Information

We thank the authors of *BoomSpikeSlab*, *scales*, *ggplot2*, *plyr*, *reshape2*, *data.table*, *Hmisc*, *RcolorBrewer*, *R Studio* and the R Core Development Team for their statistical packages. We thank Benjamin Rosen for his constructive comments and Reed Shabman for contributing "*Reed*\'*s mouse*" to our manuscript. We gratefully acknowledge the collaborative pl