Fig 1.
PCoA plot based on UniFrac distances of the gut microbial communities established in the luminal and mucosal phases for the ascending, transverse and descending regions over time.
After calculating the axes, the samples are faceted into their corresponding regions. The dashed ellipses represent samples in that facet 3 days after inoculation that fall within a 95% confidence interval. (A) Weighted UniFrac distance analysis, (B) Unweighted UniFrac distance analysis.
Fig 2.
Comparison of unweighted and weighted UniFrac measurements from each time point to the next for the luminal and mucosal phases of each colon region over time.
Fig 3.
Composition of the gut microbial communities at the class level.
Taxa with >1% relative abundance in samples are listed, while the rest of taxa are lumped into the “other” category. On the left of each figure, labeled 0, is the composition determined from the fecal homogenate used to inoculate the system. Communities from each region over time established in (A) SHIME 1, Luminal phase; (B) SHIME 2, Luminal phase; (C) SHIME 1, Mucosal phase.
Fig 4.
Comparison of relative abundance, at the family level, between the luminal phase of the AC, TC, and DC regions of each SHIME system after stabilization (Day10-Day 43).
Only families with a greater than .01% relative abundance in at least one region were considered. The error bars represent the standard deviation between the percent abundance at these time points. The P values based on a 2 tailed student t-test between regions are listed in the bottom chart. The P values were corrected for multiple comparisons. A green box indicates that p < 0.05.
Fig 5.
Comparison of relative abundance at the family level between the mucosal phase of the AC, TC, and DC regions of the SHIME 1 system.
The relative abundance at the family level for each region at each all time points after stabilization (Day10-Day 43) were averaged and plotted together. Only families with at least a .01% relative abundance in at least one region were considered. The error bars represent the standard deviation between the percent abundance at these time points. The P values based on a 2 tailed student t-test between regions are listed in the bottom chart. P values were corrected for multiple comparison. A green box indicates that the p value was less than 0.05.
Fig 6.
Alpha diversity measurements over time for the mucosal and luminal phase of the AC, TC, and DC regions.
The black dotted line represents the Shannon diversity of the fecal sample used to inoculate the system. (A) The number of OTUs identified (B) Shannon diversity index.
Table 1.
Percent relative abundance at the family level for the mucosal and luminal phases of each region after stabilization (greater than .01% abundance for one region).
M:L refers to the mucosal abundance divided by the luminal abundance. The green shading represents families with a significant increase in mucosal abundance and pink shading represents families with a significant decrease in mucosal abundance. A * indicates that p < .05 according to a 2 tailed, student t-test corrected for multiple comparison.
Fig 7.
Comparison of the combined communities for each SHIME system to the fecal inoculum.
SHIME 1 combined and SHIME 2 combined is the sum of the luminal phases for the AC, TC, and DC regions from day 10–43; SHIME 1 combined (M+L) is the sum of the luminal and mucosal phases of the AC, TC, and DC regions from day 10–43.
Fig 8.
SCFA analysis for the TWINSHIME system.
(A) Total SCFAs measured for each region over time (mmol/L). (B) Total average amount of SCFAs (mmol/L) and (C) Ratio of Acetic Acid: Propionic Acid Butyric Acid for each region over time. (D) Total average branched chain SCFAs (mmol/L) for each region after system stabilization (Day 17–43). The bar marked 0 is the amount of A:P:B for the original fecal inoculum. In the table underneath is the average ratio numbers for A:P:B for each region. A * indicates p< .05 and ** indicates p < .003 according to a 2-tailed student t test.