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We are now beginning to consider how the in planta microbial community figures into pair-wise models of host and pathogen.
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They exhibit major differences in pH (∼3 8), dissolved oxygen, Fe, total dissolved sulfide, as well as predominant solid phases intimately associated with the microbial community (Figure 1, Table 1).
Bray-Curtis similarity indices calculated based on taxonomic clustering of sequences at 97% similarity from each sample revealed that different individuals of the same species harbor similar microbial communities (Figures 3 5).
Projection of the global metabolic profiles onto the KEGG pathways using the iPath tool [35] further demonstrated the overall similarity of the MF and FF the gut microbial communities (Figure 2b).
Although the three higher pH sites at Joseph's Coat (JCHS), Calcite (CS), and Mammoth Hot Springs (MHS) are all sulfidic and sub-oxic, they are geochemically distinct from one another and yield significantly different microbial communities (Figure 1).
Figure 5 Microbial community distribution and relative abundance in different biocathode materials packed MFCs.
(JPG 31 KB) 13568_2014_22_MOESM2_ESM.jpg Additional file 2: Figure S2.: Microbial community distribution based on the V3-V5 primer set in DPMM and DPME.
To visualize specific species and relative abundance within each electrode material, column chart was performed to illustrate the microbial community composition, as shown in Figure 6.
We used Principal Component Analysis (PCA) to assess similarity in microbial community structure across all samples (Figure 4).
10.7554/eLife.05477.013 Figure 8. Microbial community composition, community complexity, and an overview of binning for samples from infant #2.
Changes in the top 20 taxa during EEN are displayed in Figure 2. Microbial community structure at each EEN sample time point was independent of other concomitant treatment or whether this was the first or a subsequent EEN course suggesting that the observed changes were associated with EEN only.
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