Figure 1.
Relative abundance of the most predominant bacterial genera in the pinna of porcine ears at various time points in the absence of mites.
At week 0, Streptococcus was the most dominant genus, followed by Lactobacillus, Actinectobacter, Enhydrobacter, Aerococcus and Rothia in decreasing abundance. At week 7, Streptococcus was still the most dominant genus, followed by smaller abundance of Corynebacterium, Chryseobacterium, Rothia, Clostridium and Lactobacillus. Similarly at week 10, Streptococcus was the dominant genus, followed by Corynebacterium, Rothia, Kocouria, Clostridium and Lactobacillus. At week 21, Lactobacillus was the most dominant, followed by Streptococcus and Kocuria. Only genera, with a relative abundance of ≥10% in at least one sample are illustrated.
Figure 2.
(a) Composition of the microbial communities before, during and after scabies mite infection.
Microbial community structure was analysed by 454 pyrosequencing of the 16S rRNA gene of the total DNA, extracted from the skin scrapings of the pinna of pig ears. Samples were taken before the scabies infection from all cohorts at week 0. Cohorts M and MD were then challenged with an equal dosage of S. scabiei var. suis in both ears. Visible signs of scabies infection developed by week 7, which progressed to severe form of infection by week 10. Scabies infection was treated with an acaricide (Dectomax®) and skin was allowed to heal. Final skin scrapings were taken at week 21. Bubble volumes correlate with the abundance (%) of the each genus detected in the sample. (b) Effect of scabies mite infection on the microbial community diversity visualised by Shannon index for all samples from the cohorts C (i, mite free), M (ii, mite infested), MD (iii, mite infested and Dexamethasone treated). Community diversity is expressed as the mean Shannon index (OTU level). Paired t-test was carried out for pigs where both time points were available (M.10: n = 2, MD: n = 4, other: n = 5). Significant differences are annotated by *: p<0.05, **:p<0.01, ***: p<0.001.
Table 1.
Relative abundance of the bacterial genera at defined time points.
Figure 3.
(a) Phylogenetic tree of Staphylococcus indicating tentative species.
(b) Relative abundance of staphylococcal species in each sample. (a) A phylogenetic tree was constructed for OTUs assigned to the genus Staphylococcus using known reference 16S rRNA genes. The accession is noted in bracket for each reference species. The number in brackets following the OTU name indicates the read counts within the OTU. The tree was rooted with the outlier Bacillus subtilis. Several OTUs (1, 6, 8, 9, 14) are in close proximity to the 16S rRNA gene of S. chromogenes. (b) Bar chart demonstrating the relative abundance of each OTU in the pig cohorts over time. An extensive change of the OTUs is measured in the scabies infected cohort M and MD from week 7 onwards. The change was irreversible despite treatment. In particular, OTU1, OTU6, OTU8, OTU9, OTU14, all related to S. chromogenes, are dominating the skin microbiota.
Figure 4.
(a) Phylogenetic tree of Streptococcus indicating tentative species.
(b) Relative abundance of streptococcal species in each sample. (a) A phylogenetic tree was constructed for OTUs assigned to the genus Streptococcus using known reference 16S rRNA genes. The accession is noted in bracket for each reference species. The number in brackets following the OTU name indicates the read counts within the OTU. The tree was rooted with the outlier Lactococcus lactis. (b) Bar chart demonstrating the relative abundance of each OTU in the pig cohorts over time. The graph depicts that the OTUs are overall stable between the three cohorts within each week and over time, irrespective of the presence or absence of mites.
Figure 5.
Microbial composition of skin samples and isolated scabies mites collected from severely scabies infested crusted sites (week 10) and control animals.
Bubble plot of the taxonomic profile as calculated for the OTU level. Only OTUs with a relative abundance of ≥2% in at least one sample are shown. Each OTU is denoted with the taxonomic classification according to the RDP Classifier (confidence value ≥0.6). The taxonomic composition between the healthy skin and the mite containing skin as well as the washed mites is differing mainly based on the relative abundance of Corynebacteria.