Article

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

Columbia University, United States of America
PLoS ONE (Impact Factor: 3.53). 07/2011; 6(7):e22788. DOI: 10.1371/journal.pone.0022788
Source: PubMed

ABSTRACT 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.

0 Followers
 · 
186 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: DNA microarray analysis is a computer based technology, that a reverse capture, which targets 10 periodontal bacteria (ParoCheck) is available for rapid semi-quantitative determination. The aim of this three-year retrospective study was to display the microarray analysis results for the subgingival biofilm samples taken from patient cases diagnosed with different forms of periodontitis.
    Anaerobe 01/2015; DOI:10.1016/j.anaerobe.2015.01.011 · 2.36 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Considerable evidence suggests that microbial biofilms play an important role in periprosthetic joint infection (PJI) pathogenesis. Compared to free-floating planktonic bacteria, biofilm bacteria are more difficult to culture and possess additional immune-evasive and antibiotic resistance mechanisms, making infections harder to detect and eradicate. This article reviews cutting-edge advances in biofilm-associated infection diagnosis and treatment in the context of current PJI guidelines and highlights emerging technologies that may improve the efficacy and reduce costs associated with PJI. Promising PJI diagnostic tools include culture-independent methods based on sequence comparisons of the bacterial 16S ribosomal RNA gene, which offer higher throughput and greater sensitivity than culture-based methods. For therapy, novel methods based on disrupting biofilm-specific properties include quorum quenchers, bacteriophages, and ultrasound/electrotherapy. Since biofilm infections are not easily detected or treated by conventional approaches, molecular diagnostic techniques and next-generation anti-biofilm treatments should be integrated into PJI clinical practice guidelines in the near future.
    Diagnostic Microbiology and Infectious Disease 11/2014; 81(3). DOI:10.1016/j.diagmicrobio.2014.08.018 · 2.57 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The compositions and abundance of the microbiota in the ecological niche of human throat and their possible relationship between the microbiota and laryngeal cancer are poorly understood. To obtain insight into this, we enrolled 27 laryngeal carcinoma patients and 28 subjects with vocal cord polyps as controls. For each subject, we simultaneously collected swab samples from the upper throat near epiglottis (site I) and tissue samples from the vestibulum laryngis to the subglottic region (site II). The microbiota of the throat were fully characterized by pyrosequencing of barcoded 16S rRNA genes. We found 14 phyla, 20 classes, 38 orders, 85 families, and 218 genera in the throat of enrolled subjects. The main phyla were Firmicutes (54.7%), Fusobacteria (14.8%), Bacteroidetes (12.7%), and Proteobacteria (10.6%). Streptococcus (37.3%), Fusobacterium (11.3%), and Prevotella (10.6%) were identified as the three most predominant genera in the throat. The relative abundances of 23 bacterial genera in the site I were significantly different compared with the site II (p < 0.05). The relative proportions of 12 genera largely varied between laryngeal cancer patients and control subjects (p < 0.05). Collectively, this study outlined the spatial structure of microbial communities in the human throat. The spatial structure of bacterial communities significantly varied in two anatomical sites of the throat. The bacterial profiles in the throat were strongly different between laryngeal cancer patients and control subjects, and several of these microorganisms may be related to laryngeal carcinoma.
    Applied and Environmental Microbiology 09/2014; 80(23). DOI:10.1128/AEM.02329-14 · 3.95 Impact Factor

Full-text (3 Sources)

Download
23 Downloads
Available from
Jul 7, 2014