Chapter 9 Does the antibiotic administration deplete the gut microbiota?

9.1 DNA extraction

Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: dna_extraction ~ time_point.x + (1 | individual)
   Data: dna_extraction_df

REML criterion at convergence: 232.6

Scaled residuals: 
    Min      1Q  Median      3Q     Max 
-1.0148 -0.4947 -0.2085  0.2941  3.4251 

Random effects:
 Groups     Name        Variance Std.Dev.
 individual (Intercept) 1.254    1.120   
 Residual               6.835    2.614   
Number of obs: 48, groups:  individual, 27

Fixed effects:
                        Estimate Std. Error      df t value Pr(>|t|)    
(Intercept)               3.0236     0.5575 44.3763   5.423  2.3e-06 ***
time_point.xAntibiotics  -1.9883     0.7647 15.7132  -2.600   0.0195 *  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation of Fixed Effects:
            (Intr)
tm_pnt.xAnt -0.621

9.2 Bacterial fraction change

Linear mixed model fit by REML. t-tests use Satterthwaite's method ['lmerModLmerTest']
Formula: value ~ time_point + (1 | individual)
   Data: mag_fragtion_accli_antib

REML criterion at convergence: -32.1

Scaled residuals: 
     Min       1Q   Median       3Q      Max 
-2.83330 -0.50215  0.02912  0.42721  2.64670 

Random effects:
 Groups     Name        Variance Std.Dev.
 individual (Intercept) 0.005276 0.07264 
 Residual               0.021003 0.14492 
Number of obs: 49, groups:  individual, 27

Fixed effects:
                      Estimate Std. Error       df t value Pr(>|t|)    
(Intercept)            0.59143    0.03177 45.81661   18.62  < 2e-16 ***
time_pointAntibiotics -0.32188    0.04191 26.03436   -7.68 3.74e-08 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Correlation of Fixed Effects:
            (Intr)
tm_pntAntbt -0.612