Abstract
To quantitatively measure the beta diversities between microbiomes, Microbiome Search Engine (MSE) (1) calculates phylogeny similarity using operational taxonomy unit (OTU) profiles; for both query and database samples, all 16S rRNA gene sequences are mapped to the Greengenes database (version 13-8) (2) for reference-based OTU picking with a 97% cutoff. Thus, in MSE, the comparison between query and database samples is approximately at the species level (3), although the actual taxonomic resolution varies according to taxon, due to differences in the evolutionary rates of the 16S rRNAs. Moreover, in MSE, both the relative abundance (with 16S rRNA gene copy number normalization [4]) and the phylogenetic structures of OTUs are utilized for similarity calculation (as in UniFrac [5, 6]), yet the speed is optimized by nonrecursive computing to enable real-time responses (7). By comparing the query sample (i.e., dust from university dormitories) provided by Sun …
Highlights
To quantitatively measure the beta diversities between microbiomes, Microbiome Search Engine (MSE) [1] calculates phylogeny similarity using operational taxonomy unit (OTU) profiles; for both query and database samples, all 16S rRNA gene sequences are mapped to the Greengenes database [2] for reference-based OTU picking with a 97% cutoff
In MSE, both the relative abundance and the phylogenetic structures of OTUs are utilized for similarity calculation, yet the speed is optimized by nonrecursive computing to enable real-time responses [7]
By comparing the query sample provided by Sun et al [8] and the MSE top-hit samples, which are from mosquito tissues, we found that abundant sequences of the two samples are distributed among different OTUs within the Pseudomonas genus, they are still very close in the common OTU-based phylogenetic tree (Fig. 1a), resulting in a high similarity of 0.916
Summary
To Sun et al, “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy”. By comparing the query sample (i.e., dust from university dormitories) provided by Sun et al [8] and the MSE top-hit samples, which are from mosquito tissues, we found that abundant sequences of the two (query and the top-hit) samples are distributed among different OTUs (species) within the Pseudomonas genus, they are still very close in the common OTU-based phylogenetic tree (extracted from the Greengenes tree) (Fig. 1a), resulting in a high similarity of 0.916 To test whether this match is significant, we ranked this value in pairwise similarity calculation among all microbiomes (n ϭ 177,022) in MSE [in total, (n · n – 1)/2 ϭ 15,668,305,731 times). The similarities between the query and each of the top 10 hits [10,11,12,13]
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