Fig 1.
Illustration of sampling site.
Samples were taken from (A) healthy control skin at the fore udder attachment, (B) mild and (C) severe udder cleft dermatitis.
Fig 2.
Distribution of reads classified as Bacteria, Archaea, fungi, protozoa and virus within each sample (A) and sample type (B and C) based on samples from mild (M, n = 17) and severe (S, n = 19) udder cleft dermatitis (UCD) and samples from skin at the fore udder attachment from healthy controls (C, n = 13). The P-values from comparing the abundance between sample types are denoted in the margins of B and C by *** if P≤0.001, ** if P≤0.01 and * if P≤0.05. The exact P-values were for Bacteria: C/M P = 0.01, C/S P<0.0001, M/S P = 0.02, Archaea: C/M P = 0.0007, C/S P<0.0001, M/S P = 0.004, fungi: C/M P = 0.05, C/S P = 0.0007, protozoa: C/M P = 0.04, and viruses: C/M P = 0.2, C/S P = 0.002.
Fig 3.
Data dimensionality reduction with principal component analysis (PCA) performed on the bacterial phylum (A), genus (B) and species level (C) for 49 samples from mild (n = 17) and severe (n = 19) udder cleft dermatitis and samples from skin at the fore udder attachment from healthy controls (n = 13). The (%) given for each PCA axis indicates the variation explained by that specific axis. The fourth PCA axis on genus level separated a subgroup of control samples and is presented in S2 Fig.
Fig 4.
Distribution of bacterial phyla (A), genera (B) and species (C) representing ≥10% of the classified reads in at least one sample out of 49 samples from mild (n = 17) and severe (n = 19) udder cleft dermatitis (UCD) lesions and skin samples from healthy controls (n = 13) in a study of the microbiota of UCD in comparison to healthy skin using shotgun metagenomic sequencing. On the species level (C), the order of the samples was changed to highlight the major subgroups that were distinguishable, and the red colour indicates the percentage (0–15%) of the bacterial reads for each species within each sample.
Table 1.
Comparison of UCD samples and healthy skin.
Fig 5.
Box plot of the Shannon diversity index for bacterial genera (A) and species (B), in samples from mild (n = 17) and severe (n = 19) udder cleft dermatitis (UCD) and samples from skin at the fore udder attachment from healthy controls (n = 13).
Fig 6.
The archaeal proportion of all classified reads within each sample (A), the distribution of archaeal genera representing ≥5% of the archaeal reads in at least one sample (B) and a principal component analysis (C), based on samples from mild (n = 17) and severe (n = 19) udder cleft dermatitis (UCD) and samples from skin at the fore udder attachment from healthy controls (n = 13).
Fig 7.
Sankey visualization (obtained by the metagenomics tool Pavian) of the microbiota in a mild (A) and a severe (B) udder cleft dermatitis lesion in the same cow, sampled in December 2018 and six weeks later in January 2019. The flow diagram illustrates the proportion of bacterial reads assigned to a specific taxon at domain (D), kingdom (K), phylum (P), family (F), genera (G) and species level.
Fig 8.
Sankey visualization (obtained by the metagenomics tool Pavian) of the microbiota of a severe udder cleft dermatitis (UCD) lesion sampled at two different time points from the same cow, in October 2018 (A) and in January 2019 (B). The flow diagram illustrates the proportion of bacterial reads assigned to a specific taxon at domain (D), kingdom (K), phylum (P), family (F), genera (G) and species level.