Fig 1.
Overview over samples and sampling time points in regard to parturition and birth in cow-calf pairs.
Fig 2.
(A) Species richness (Chao1), (B) Shannon and (C) Simpson diversity index and (D) number of observed OTUs in calf faeces during the five sampling time points.
Data are visualized as box-and-whisker plots showing the median and the interquartile (midspread) range (boxes containing 50% of all values), the whiskers (representing the 25 and 75 percentiles) and the extreme data points. Numbers above boxes indicate significant differences to the time points.
Fig 3.
The 50 most abundant OTUs in calf faecal samples and time-related abundance shifts.
The dendrogram was built based on Euclidean measures and was used to define the abundance clusters ‘stable’ (stable abundance), ‘enrichment’ (abundance increase over time) and ‘depletion’ (abundance decrease over time). TP = time point, TP 1 = 0.5 hours post natum (p.n.), TP 2 = 6 hours p.n., TP 3 = 12 hours p.n., TP 4 = 24 hours p.n., TP 5 = 48 hours p.n.
Table 1.
Results of qPCR for calf faecal samples (along the time line).
Table 2.
Copy number results of qPCR for cow faeces, cow colostrum, cow vagina, and calf mouth samples.
Fig 4.
Principal Coordinate Analysis (PCoA) of 16S rRNA gene OTUs based on Weighted UniFrac distances.
Dots are colored regarding the sample type. TP = time point, TP 1 = 0.5 hours post natum (p.n.), TP 2 = 6 hours p.n., TP 3 = 12 hours p.n., TP 4 = 24 hours p.n., TP 5 = 48 hours p.n.
Fig 5.
Light-yellow circular nodes represent the different OTUs (more abundant than 0.01% overall) and the size of each node is proportional to their relative abundance. The diamond shaped nodes represent the samples and are colored regarding the different types of samples. OTUs and the samples they belong to are connected by colored lines corresponding to the type of the sample. TP = time point, TP 1 = 0.5 hours post natum (p.n.), TP 2 = 6 hours p.n., TP 3 = 12 hours p.n., TP 4 = 24 hours p.n., TP 5 = 48 hours p.n.