Fig. 2: Temporal behavior of PEx types.

A Time evolution of representative community compositions in three PEx types (PAT, AN1, AN2). Sample compositions were encoded by ASV groups and classified by a Dirichlet multinomial mixture (DMM) model into six community classes. Three classes were dominated by strictly anaerobic taxa, two by classical CF pathogens and one by facultative anaerobes (color coding according to legend). Community classes were independent of time towards start of PEx treatment but differed between PEx types (\(n=789\) samples). B Time evolution of microbiome diversity towards start of PEx treatment (\(n=789\) samples). Microbiomes in all PEx types showed significant time dependency (LMM, \({{{{{{\rm{p}}}}}}}_{{{{{{\rm{PAT}}}}}}}=1.26{{{{{\rm{e}}}}}}-3,\,{{{{{{\rm{p}}}}}}}_{{{{{{\rm{AN}}}}}}1}=4.6{{{{{\rm{e}}}}}}-2,\,{{{{{{\rm{p}}}}}}}_{{{{{{\rm{AN}}}}}}2}=3.6{{{{{\rm{e}}}}}}-2\)) with Shannon diversity decreasing in pathogen-dominated and increasing in anaerobe-dominated PEx types towards treatment. C Time evolution of community richness towards PEx treatment (\(n=789\) samples). Chao1 richness changed significantly with time in pathogen-dominated and in one anaerobic PEx type (LMM, \({{{{{{\rm{p}}}}}}}_{{{{{{\rm{PAT}}}}}}}=\,4.19{{{{{\rm{e}}}}}}-5,\,{{{{{{\rm{p}}}}}}}_{{{{{{\rm{AN}}}}}}1}=2.45{{{{{\rm{e}}}}}}-2\)). Boxes in B, C depict the interquartile range; the horizontal line represents the median value. Whiskers extend to the minimum and maximum values, excluding outliers, defined as 1.5 times the interquartile range. D Community turnover \(T\) relative to the previous 20 days for three PEx types. Samples were grouped according to their relative collection term prior to PEx treatment and mean values are plotted (in blue, mean of samples collected <24 days before treatment; in green, 24–60 days). Aitchison distance from focal sample to \(n\) previously collected samples (sampling distance) was plotted, the slope of a linear fit was used to quantify \(T\). Linear fit was represented with 95% confidence intervals of estimates (gray). \(T\) was significantly reduced in pathogen-dominated microbiomes and significantly increased in anaerobe-dominated microbiomes in a 23-day-interval before PEX antibiotic treatment (one-sided ANCOVA for every PEX type, not shown in figure,\(\,{{{{{{\rm{p}}}}}}}_{{{{{{\rm{PAT}}}}}}}=\,2.07{{{{{\rm{e}}}}}}-8\); \({{{{{{\rm{p}}}}}}}_{{{{{{\rm{AN}}}}}}1}=9.75e-5\); \({{{{{{\rm{p}}}}}}}_{{{{{{\rm{AN}}}}}}2} < 2e-16\)). Source data for Fig. 2 are provided in the Source Data file.