16S amplicon pyrosequencing analysis of mouse caecum from niave, sham and brain injury mice. Bacterial species relative abundances from rarefied OTU data (1866 sequences) were used for NMDS analysis Samples are as follows: ○ = t 0; □ = t 72 h post treatment; white = naïve; grey = sham; black = brain injury. Axis represent scale for simularity distance scores between sample centered to (0,0). Pair-wise comparisons were undertaken to identify significant differences using PERMANOVA. Naïve vs. Sham (adonis: F.Model1,8 = 2.12, p = 0.008); Naïve vs. Brain Injury (adonis: F.Model1,8 = 2.24, p = 0.008); Sham vs. Brain injury, (adonis: F.Model1,8 = 1.02, p = 0.484).