Oral Microbiome Profiles: 16S rRNA Pyrosequencing and Microarray Assay Comparison

Columbia University, United States of America
PLoS ONE (Impact Factor: 3.23). 07/2011; 6(7):e22788. DOI: 10.1371/journal.pone.0022788
Source: PubMed


The human oral microbiome is potentially related to diverse health conditions and high-throughput technology provides the possibility of surveying microbial community structure at high resolution. We compared two oral microbiome survey methods: broad-based microbiome identification by 16S rRNA gene sequencing and targeted characterization of microbes by custom DNA microarray.
Oral wash samples were collected from 20 individuals at Memorial Sloan-Kettering Cancer Center. 16S rRNA gene survey was performed by 454 pyrosequencing of the V3-V5 region (450 bp). Targeted identification by DNA microarray was carried out with the Human Oral Microbe Identification Microarray (HOMIM). Correlations and relative abundance were compared at phylum and genus level, between 16S rRNA sequence read ratio and HOMIM hybridization intensity.
The major phyla, Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria were identified with high correlation by the two methods (r = 0.70∼0.86). 16S rRNA gene pyrosequencing identified 77 genera and HOMIM identified 49, with 37 genera detected by both methods; more than 98% of classified bacteria were assigned in these 37 genera. Concordance by the two assays (presence/absence) and correlations were high for common genera (Streptococcus, Veillonella, Leptotrichia, Prevotella, and Haemophilus; Correlation = 0.70-0.84).
Microbiome community profiles assessed by 16S rRNA pyrosequencing and HOMIM were highly correlated at the phylum level and, when comparing the more commonly detected taxa, also at the genus level. Both methods are currently suitable for high-throughput epidemiologic investigations relating identified and more common oral microbial taxa to disease risk; yet, pyrosequencing may provide a broader spectrum of taxa identification, a distinct sequence-read record, and greater detection sensitivity.

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Available from: Zhiheng Pei, Jul 07, 2014
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    • "Although, the compatibility of the fragment length should be according with sequencing platform read length capacity. There are many studies that target different regions of the 16S rRNA gene, for example V3–V5 [29], V1–V2 [30], V1–V3 [26], V4–V5 [31], and V8–V9 [32]. There is an active discussion about the hypervariable region that should be sequenced to perform a microbial diversity analysis. "
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    • "The microarray approach is potentially cheaper and more rapid for identifying microbial causative than sequencing-based methods, although detection is limited to the probes printed on the microarray (DeSantis et al., 2007; Hamady and Knight, 2009). In a direct comparison of a 16S rRNA gene microarray with pyrosequencing for oral microbiome characterization, both methods excelled at highthroughput characterization of common microbial taxa; for less common genera, pyrosequencing provided broader and more sensitive detection (Ahn et al., 2011). Improved microarray designs could circumvent these drawbacks, and meanwhile, the current designs present a compromise between cost/time and diagnostic sensitivity. "
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    • "Hundreds of microbial species inhabit the human nasal, oral and pharyngeal cavities, including 25–40 families of bacteria, archaea, ameba and fungi, according to ample evidence from laboratory cultures [4]. The number of newly discovered species has considerably increased owing to the recent advances in metagenomic (Box 1) research techniques, especially highthroughput sequencing technology, that enable the discovery of non-culturable species [5] [6] [7]. In the pharynx, five major bacterial phyla have been identified thus far according to data released by the Human Microbiome Project (HMP): Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria (Figure 1A). "
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