Table 3

Results of the linear mixed regression model applied to the longitudinal changes in relative abundance of Bifidobacterium and Gammaproteobacteria during the first 3 months of life

Differentially abundant taxa Bifidobacterium Gammaproteobacteria
 CovariatesEstimated meanSEP valueEstimated meanSEP value
(Intercept)−4.630.39<0.001−3.330.24<0.001
IBD maternal status−1.390.50 0.007 0.910.29 0.002
Time of sampling0.020.004 <0.001 −0.0010.0030.86
Born by C-section−0.180.500.720.240.290.41
Exposure to antibiotics−1.380.930.140.710.560.21
Feeding: formula exclusive−1.750.88 0.048 −0.780.540.15
Feeding: mixed−0.450.390.25−0.500.260.05
  • IBD status determines the composition of the adaptive immune system in GFM.

  • Repeated measurements included baby stool at 7, 14, 30, 60 and 90 days. Maternal IBD status, mode of delivery and time were treated as fixed effects, with a random intercept for each subject ID. Feeding behaviour and antibiotics exposure were entered as time-varying covariates. The model was fitted via restricted maximum likelihood approach with the correlation structure of autoregressive process of order 1.

  • C-section, caesarean section; GFM, germ-free mice.