Table 1.
Comparison of OTU-binning methods.
Figure 1.
Distribution of bacterial phyla in fecal samples from cattle.
The distribution of phyla is based on the relative abundance of 16S rRNA pyrotags from 22 fecal samples from cattle. The taxonomic affiliations were predicted using the RDP classifier with a bootstrap cutoff of 80. Pyrotags that could not be assigned at the phylum rank were classified as “Unknown”. Sample names listed on the x-axis were from E. coli O157:H7 negative steers (NS - red) or super-shedders (SS - blue).
Figure 2.
Alpha diversity in cattle fecal samples from super-shedder (SS) and non-shedder steers (NS) as represented by rarefaction curves (A), and boxplots for Good's coverage (B), Richness (C) and Shannon Diversity Index (D) using the Esprit-tree OTU matrix.
The number of OTUs was used as a measure of the richness in Fig C. In Fig B, C and D, each box plot summarizes the distribution of the data set. Lower, mid, and upper horizontal lines denote the first quartile, median and the third quartile, respectively. Vertical lines reach the 1.5 interquartile range from the respective quartiles or reach the extreme value, whichever is closer. The remaining clustering methods gave similar results.
Figure 3.
Non-metric multidimensional scaling plots of the distances for 22 fecal samples based on the different OTU matrices.
Mothur, Esprit-Tree, CROP, UPARSE and Otupipe were used to bin 16S pyrotags into OTUs. Otupipe2 and Otupipe4 matrices were generated with MinSize parameter set to 2 or 4, respectively. In addition, 16S pyrotags were mapped into against a full-length 16S reference dataset to generate OTU matrices at 97% (RefMap97) or 90% (RefMap90) identity. The plots contain data from super-shedders (SS) and non-shedders (NS). ANOISM was used to test for similarities between SS and NS steers, generating correlation (R) and significance (p) values.
Figure 4.
Heat map showing OTUs with a significant differential abundance (p<0.05) between super-shedder (SS; light grey axis labels) and non-shedder (NS; black axis labels) steers.
Bacterial taxonomic affiliations are indicated on the left of the heat map at the phylum and genus level except in cases where genus is unknown in which case taxa are summarized at higher ranks. The relative abundance of each OTU is coded as indicated by the scale on the right, with highest number of pyroseqs for each OTUs set as 1.
Figure 5.
The number of OTUs shared by fecal samples.