Fig 1.
(A) 4 days equilibration period (yellow), 3 days steady-state period (orange) and 8 days experimental period (red). (B) Three non-infected fermenters from the steady-state- and experimental period are depicted in A-C and three C. perfringens infected fermenters in D-F. S = RUSITEC effluent sampling, yellow “x” = C. perfringens inoculation. The red boxes indicate C. perfringens-spiked fermenters.
Table 1.
The 50 most abundant OTUs are shown with the respective relative abundance in the RUSITEC samples, sequence similarity to Greengenes hits, match length and accession number.
Fig 2.
UniFrac distances of amplicon sequencing data depicted as PCoA Plot with sampling days shown in different colors.
The percent variation explained by each principal coordinate is indicated by the axes. A: weighted and B: unweighted UniFrac with only non-infected fermenters (Fig 1B, fermenters A-C). C: weighted and D: unweighted UniFrac with fermenters used for the C. perfringens spiking experiment (Fig 1B, fermenters D-F). Only fermenters at days 10, 12, and 15 are spiked with C. perfringens. Native rumen fluid samples of donor animals are included in each panel (Native rumen fluid).
Table 2.
Statistical analysis of OTU richness and diversity of non-infected fermenters A-C with regard to sampling day.
Fig 3.
Phylotypes which were statistically significantly enriched at a certain time point were highlighted in color in the cladogram. To investigate shifts along the time line only the non-infected fermenters A-C were used.
Table 3.
Metabolite concentrations, redox potential and pH of non-infected fermenters A-C with regard to sampling time points.
Table 4.
Total bacteria qPCR results of the control fermenters (fermenter A-C).
Fig 4.
Phylotypes which are statistically significantly enriched in the non-infected vessels or in the C. perfringens infected vessels were highlighted in color in the cladogram. A = day 10, B = day 12, and C = day 15.
Table 5.
Metabolite concentration between non-infected (A-C) and infected fermenters (D-F).