Fig 1.
Sample timepoints and treatments for monitoring the intestinal microbiota during and after drug clearance of T.muris infection.
Fig 2.
Impact of T.muris infection on microbial communities assessed by DGGE:
NMDS analysis of bacterial community profiling in stool samples by 16S rRNA gene DGGE comparing day 0 to day 41 (○ & ◻) in infected (red) and non infected (blue) individual mice. Demonstrating a significant shift as a result of time and infection (F1,16 = 9.05, p = 0.002). Axis represent scale for Euclidian distance between samples centred on zero, Stress indicates the quality of fit of data (>0.2 is a good fit).
Fig 3.
Time course monitoring of microbial communities by DGGE after antihelmintic treatment to clear infection:
NMDS plots of DGGE analysis of bacterial communities of the 16S RNA gene in stool samples. Monitoring the change over time as a result of prolonged infection and clearance by antihelmithic treatment at a) day 41, b) day 47, c) day 63, d) day 77, e) day 91, f) The pairwise comparisons of treatments for significant differences assessed by PERMANOVA with bonferroni corrected p values < 0.0083. Axis represent scale for Euclidian distance between samples centred on zero, Stress indicates the quality of fit of data (>0.2 is a good fit).
Fig 4.
Shannon diversity from 454 pyrosequencing of stool samples over time:
Microbial diversity was measured between treatments at each time point in individual stool samples from rarfied pyrosequecing OTU tables at 97% sequence similarity level. NA = naïve, NH naïve antihelminthic treated, IH = infected antihelminthic treated, IF = Infected. The labels a,b and c denoting samples significantly different tested by ANOVA (p = 0.05) with post hoc TukeyHSD tests as required.
Fig 5.
Shannon diversity of specific bacterial phyla in treatments from 454 pyrosequencing of stool samples:
Microbial diversity was assessed for a) Bacteroidetes, b) Firmicutes, and c) Proteobacteria between treatments at each time point in individual stool samples from rarefied pyrosequecing OTU tables at 97% sequence similarity level. NA = naïve, NH naïve antihelmintic treated, IH = infected antihelmintic treated, IF = Infected. The labels a,b and c denoting samples significantly different tested by ANOVA (p = 0.05) with TukeyHSD tests as required.
Fig 6.
NMDS analysis of bacterial communities in stool samples assessed by 454 pyrosequencing at individual time-points:
Comparisons were made between the groups Naïve, naïve antihelminthic treated, infected antihelminthic treated and Infected, in order of dark blue, light blue, orange, red. a) Day 0 there were no significant differences, b) day 28 & c) day 41, naïve and naïve antihelminthic treated were significantly different to infected and infected antihelminthic treated (p < 0.0083), D91 all significantly different (p < 0.0083). Axis represent scale for Euclidian distance between samples centred on zero, Stress indicates the quality of fit of data (>0.2 is a good fit).
Fig 7.
Impact of infection by T.muris on bacterial community composition:
Bacterial community proportions of Prevotella and Parabacteroides were identified as significantly altered as a result of treatment in relation to time, and a level of recovery as a result of antihelmintic treatment of Prevotella populations. NA = naïve, NH naïve antihelmintic treated, IH = infected antihelmintic treated, IF = Infected. The labels a and b denoting samples significantly different tested by ANOVA (p = 0.05) with post hoc TukeyHSD tests as required.
Fig 8.
Impact of T. muris infection of mouse growth:
At day 91 there is a treatment impact (F3,21 = 9.04, p <0.001) which TukeyHSD tests identified as naïve gaining more weight than infected and infected antihelmintic treated (p <0.001 and 0.01 respectively). Naive antihelmintic treated were not different to naïve, but significantly higher than infected (p = 0.03). NA = naïve, NH naïve antihelmintic treated, IH = infected antihelmintic treated, IF = Infected. Arrow indicates point of antihelmintic treatment.