Fig 1.
The proportion of amplicon sequence variants (ASVs) assigned at a given taxonomic rank using the SILVA database v138.
Fig 2.
A: β-diversity of faecal (WF), milk (WM) and blood (WB) samples shown with Principal Coordinate Analysis (PCoA) based on weighted UniFrac metric, calculated using normalized data. The letter W denotes the sampling area, Waaihoek while the letters F, W and B denote sample type. Each point represents a sample pool. B: β-diversity shown with Non-Metric Dimensional Scaling plot (stress = 0.113) using Bray dissimilarity metric between sample groups. The sample groups are color coded. Significant differences: P = 0.01, F = 4.599, PERMANOVA.
Fig 3.
Stacked bar-plot with proportions of bacterial phyla detected from the three sample groups.
Relative abundance graphed along the y-axis and sample type along the x-axis.
Fig 4.
Distribution of the 15 most abundant genus-level taxa across faecal, milk and blood samples.
Relative abundance graphed along the y-axis and sample type along the x-axis.
Fig 5.
A. Distribution of the top 15 genus-level taxa averaged between the faecal samples. Relative abundance graphed along the y-axis and sample type along the x-axis. B: Distribution of the top 15 genus-level taxa averaged between the milk samples. Relative abundance graphed along the y-axis and sample type along the x-axis. C: Distribution of the top 15 genus-level taxa averaged between the blood samples. Relative abundance graphed along the y-axis and sample type along the x-axis.
Table 1.
Core microbiota present in ≥ 75% of samples per group at ≥ 0,1% relative abundance including average and range across cow samples.
Fig 6.
Gel electrophoresis of Anaplasma PCR targeting the 16S rRNA gene from blood samples.
A: Lane 1 = 1 kb DNA ladder; 2–10 = Anaplasma positive samples; 11 = nuclease free H2O (-ve) control; 12 = A. marginale (+ve) control.
Fig 7.
UpSetR intersection plot showing number of unique and shared ASVs at genus level between faeces, milk and blood groups.
Fig 8.
A: Differentially abundant genus-level taxa (Padj < 0,01) between blood and faeces. Positive log2-fold change indicates increased abundance in blood compared to faeces, negative log2-fold change indicates decreased abundance. The dots are ASVs representing genera. B: Differentially abundant genus-level taxa (Padj < 0,01) between bovine blood and milk. Positive log2-fold change indicates increased abundance in blood compared to milk, negative log2-fold change indicates decreased abundance. The dots are ASVs representing genera. C: Differentially abundant genus-level taxa (Padj < 0,01) between bovine faeces and milk. Positive log2-fold change indicates increased abundance of the genera in faeces compared to milk. The dots are ASVs representing genera.