The results demonstrated that at an error rate of 0.1%, all LY2874455 nmr indices including the richness estimates and Shannon index were hardly influenced (One Way ANOVA on ranks, P < 0.05, Dunn’s test for pair-wise comparisons between 0% error rate and 0.1% error rate, P > 0.05), but raising the error rate to 1% inflated the species
richness estimates significantly (One Way ANOVA on ranks, P < 0.05, Dunn’s test for pair-wise comparisons between 0% error rate and 1% error rate: ACE, 546 vs. 2435, P < 0.05; Chao1, 886 vs. 3680, P < 0.05; observed species, 285 vs. 577, P < 0.05). By comparison, although the Shannon index was also inflated (5.37 vs. 5.90, P < 0.05), the extent of inflation was much smaller than that of the species richness estimators, and no significant differences were observed between the two datasets (Additional file 1: Figure S3). The explanation for this result is that Shannon diversity index depends more on highly abundant OTUs compared to species richness estimates [20], is consequently less sensitive to sequencing errors and was therefore able to produce similar values for both of the datasets in the present study. In support of this theory, we found in a recent study [20] that Shannon diversity index of freshwater and marine sediments were
comparable across multiple studies. PCA using the Jaccard distances We next compared the two datasets in terms of β-diversity obtained using Principal RAD001 solubility dmso Component Analysis (PCA) with Jaccard distances (Figure 2a, b). The rationale for using the Jaccard, rather than the click here phylogenetic-based UniFrac, distances is that the V6
tag is very short with high variability, leading to a relatively lower resolution of the UniFrac distance after alignment and filtering of unmatched sequences. Procrustes analysis illustrates two PCA analyses in one plot, transforming one of the coordinate sets by rotating, scaling, and translating it to minimize the distances between two corresponding points of the same sample. The results of the two datasets (the V6 fragment extracted from two different PCR and sequencing runs) were Farnesyltransferase in accordance with each other based on the abundance-weighted and binary Jaccard distances (p = 0.000), with obvious clustering of samples from each individual. Figure 2 Principal component analysis of binary and abundance-weighted Jaccard distances between samples. (a and b) Procrustes analysis of PCA results based on binary (a) or abundance-weighted (b) Jaccard distances of the two datasets. Points linked with bars were obtained from the same individual but from two different datasets. (c) and (d) Two datasets were combined for meta-analysis based on binary (c) or abundance-weighted (d) Jaccard distance. Subsequently, we combined all sequences from these two datasets to simulate a meta-analysis (Figure 2c, d).
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