For instance, Brand B is comprised of the family

Incertae Sedis XII (96%) within the order Bacillales (100%), which is not surprising since this brand is almost entirely dominated by a single classification (Exiguobacterium) at the genus level that falls within the Liver X Receptor agonist family Incertae Sedis XII. Similar to Brand B, Brand C is also dominated by Incertae Sedix XII (45%) and Bacillales (59%), as well as Exiguobacterium (46%) at the genus level. Brand A is dominated by Clostridiaceae (67%) at the Cell Cycle inhibitor family level, which falls within the order Clostridiales noted in Brand A at 67% abundance. Clostridiaceae dominates Brand A at the genus level with 68%, which falls within the Clostridiaceae family. The diversity and uniqueness of Brand A cheese is partially explained by a replicate within Brand A, replicate Brand A_rep1, that

appears to have more diversity at the class level than the other 3 replicates, with the presence of Alphaproteobacteria, Actinobacteria, and Betaproteobacteria, of which only Alphaproteobacteria is shared by Brand A_rep3 in very low abundance. This diversity is evident at the genus level as well (Figures 1 and 2), with Brand A_rep1 containing 4 operational taxonomic units (OTUs) not found in any other Brand A replicates, nor in any samples from the other cheese brands, using a 95% identity threshold for clustering sequences. In addition, Brand A_rep1 contains 13 OTUs total that occurred at a ≥ 1% abundance in the sample at the genus level, while the other Brand A replicates as well as all replicates from the other cheese brands contain no more than 7 OTUs per sample. Figure 1 Genus Ro 61-8048 research buy level abundance profiles using 16S rRNA sequence classifications. Taxa represented occurred at ≥ 1% abundance in that sample. Figure

2 Hierarchical clustering of samples using Genus level distributions. Displayed Exoribonuclease values are log transformed relative abundances within each sample, (e.g. 0.10 ~ −1; 0.01 ~ −2). Visualized using skiff in CloVR. Diversity analysis using operational taxonomic units Rarefaction curves of all enriched cheese samples (Figure 3), also support the observation that Brand A samples supported the greatest diversity among the three cheeses. The greater diversity of Brand A cheese sample Brand A_rep1 is displayed, rising dramatically above all other samples. This is confirmed with the UniFrac metric, which shows the replicate samples of each brand distinctly clustered together by brand except for Brand A_rep1. Brand C replicates cluster together rather tightly, more so than the Brand B replicates. Figure 3 Rarefaction curves of OTUs in all 4 replicates of each cheese brand. CloVR analysis Using the automated 16S rRNA pipelines provided by the CloVR software package ( http://​clovr.​org). Replicates within each cheese type clustered as expected at the genus level except for the Brand A_ rep1 (Figure 2).