Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals

Ghannoum, Mahmoud A.; Jurevic, Richard J.; Mukherjee, Pranab K.; Fan, Chun‐An; Sikaroodi, Masoumeh; Naqvi, Ammar S.; Gillevet, Patrick M.

doi:10.1371/journal.ppat.1000713

Cited by 958 publications

(962 citation statements)

References 36 publications

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“…No rRNA reads were identified from Candida or other fungi that are regular inhabitants of the oral cavity, indicating that although these organisms are frequently detected by PCR amplification (Ghannoum et al, 2010), they are probably present at low proportions. In sample CA-04, significant hits to the rRNA ITS region of the protozoan Trichomonas tenax were found.…”

Section: Estimating Diversity In the Oral Metagenomementioning

confidence: 98%

The oral metagenome in health and disease

Belda-Ferre¹,

Alcaraz²,

et al. 2011

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The oral cavity of humans is inhabited by hundreds of bacterial species and some of them have a key role in the development of oral diseases, mainly dental caries and periodontitis. We describe for the first time the metagenome of the human oral cavity under health and diseased conditions, with a focus on supragingival dental plaque and cavities. Direct pyrosequencing of eight samples with different oral-health status produced 1 Gbp of sequence without the biases imposed by PCR or cloning. These data show that cavities are not dominated by Streptococcus mutans (the species originally identified as the ethiological agent of dental caries) but are in fact a complex community formed by tens of bacterial species, in agreement with the view that caries is a polymicrobial disease. The analysis of the reads indicated that the oral cavity is functionally a different environment from the gut, with many functional categories enriched in one of the two environments and depleted in the other. Individuals who had never suffered from dental caries showed an overrepresentation of several functional categories, like genes for antimicrobial peptides and quorum sensing. In addition, they did not have mutans streptococci but displayed high recruitment of other species. Several isolates belonging to these dominant bacteria in healthy individuals were cultured and shown to inhibit the growth of cariogenic bacteria, suggesting the use of these commensal bacterial strains as probiotics to promote oral health and prevent dental caries.

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Section: Estimating Diversity In the Oral Metagenomementioning

confidence: 98%

The oral metagenome in health and disease

Belda-Ferre¹,

Alcaraz²,

et al. 2011

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“…A standardized oral rinse is a widely used, non-invasive collection method for evaluating the human oral microbiome in culture-independent studies (Ahn et al, 2011, Bassis et al, 2015, Ghannoum et al, 2010, Twigg III et al, 2014. Although wide varieties of DNA extraction methods have been used by researchers for the purpose of human oral microbiome profiling, no consistent method has emerged as a bench mark for such investigations.…”

Section: Accepted M Manuscriptmentioning

confidence: 99%

The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology

Sohrabi

Nair

Samaranayake

et al. 2016

Journal of Microbiological Methods

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Q., The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology, Journal of Microbiological Methods (2016Methods ( ), doi: 10.1016Methods ( /j.mimet.2016 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. A C C E P T E DM A N U S C R I P T ACCEPTED MANUSCRIPT A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT Highlights Lysozyme-achromopeptidase cell lysis yielded the highest gDNA level  Lysozyme-zirconium beads cell lysis extracted the highest level of bacterial DNA  Lysozyme-zirconium beads cell lysis yielded the highest level of Firmicutes A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT ABSTRACTRecent culture-independent studies have enabled detailed mapping of human microbiome that has not been hitherto achievable by culture-based methods. DNA extraction is a key element of bacterial culture-independent studies that critically impacts on the outcome of the detected microbial profile. Despite the variations in DNA extraction methods described in the literature, no standardized technique is available for the purpose of microbiome profiling.Hence, standardization of DNA extraction methods is urgently needed to yield comparable data from different studies. We examined the effect of eight different cell lysis protocols on the yield and quality of the extracted DNA from oral rinse samples. These samples were exposed to cell lysis techniques based on enzymatic, mechanical, and a combination of enzymatic-mechanical methods. The outcome measures evaluated were total bacterial population, Firmicutes levels and human DNA contamination (in terms of surrogate GAPDH levels). We noted that all three parameters were significantly affected by the method of cell lysis employed. Although the highest yield of gDNA was obtained using lysozymeachromopeptidase method, the lysozyme-zirconium beads method yielded the peak quantity of total bacterial DNA and Firmicutes with a lower degree of GAPDH contamination compared with the other methods. Taken together our data clearly points to an urgent need for a consensus, standardized DNA extraction technique to evaluate the oral microbiome using oral rinse samples. Further, if Firmicutes levels are the focus of investigation in oral rinse microbiome analyses then the lysozyme-zirconium bead method would be the method of choice in preference to others.

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“…Although the C. parapsilosis complex has been recognized as comprising distinct species, little is known about the transmission and infectivity of the two more rare species present within the complex, C. orthopsilosis and C. metapsilosis, while C. parapsilosis has now been recognized as a major human fungal pathogen, ranking as the second or third most frequently occurring cause of bloodstream infection in Europe, Canada and Latin America (Almirante et al, 2006;Pemán et al, 2005;Pfaller et al, 2008). Data on the frequency of isolation of C. orthopsilosis and C. metapsilosis have just started to be released (Odds et al, 2007;Tavanti et al, 2007;Kocsubé et al, 2007;Gomez-Lopez et al, 2008;Lockhart et al, 2008;Hensgens et al, 2009;Silva et al, 2009;Gonçalves et al, 2010;Ghannoum et al, 2010;Bonfietti et al, 2012). These retrospective epidemiological studies have been undertaken to screen for C. orthopsilosis and C. metapsilosis among isolates previously identified as C. parapsilosis, showing that a small proportion of isolates actually belong to the species C. orthopsilosis or C. metapsilosis, with significant geographical variation.…”

Section: Introductionmentioning

confidence: 99%