Changes in Abundance of Oral Microbiota Associated with Oral Cancer

Schmidt, Brian L.; Kuczynski, Justin; Bhattacharya, Aditi; Huey, Bing; Corby, Patricia; Queiroz, Erica; Nightingale, K Florence; Kerr, Alexander Ross; DeLacure, Mark D.; Veeramachaneni, Ratna; Olshen, Adam B.; Albertson, Donna G.; Teh, Muy-Teck

doi:10.1371/journal.pone.0098741

Cited by 313 publications

(368 citation statements)

References 55 publications

(75 reference statements)

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“…Bacterial cell lysis, the first step in DNA extraction, could be accomplished by several methods on the basis of either enzymatic, chemical or mechanical protocols and a combination of these methods (Huang et al, 2011, Jiang et al, 2014, Niwa et al, 2005, Said et al, 2014, Schmidt et al, 2014. A number of workers have compared different commercial kits and non-commercial protocols using either human samples or a laboratory created bacterial community (Claassen et al, 2013, Kennedy et al, 2014, McOrist et al, 2002, Wagner Mackenzie et al, 2015, Yuan et al, 2012.…”

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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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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“…Its open-ended character allows for the discovery of new taxa potentially related to disease, and its culture-independent nature does not exclude species and phylotypes that are difficult to grow or currently uncultivated but that might have a role in disease initiation. The most recent studies of the association between the oral microbiome and OSCC have used 454 pyrosequencing (Schmidt et al 2014;Guerrero-Preston et al 2016). However, this form of sequencing has recently been outperformed by MiSeq Illumina sequencing (Caporaso et al 2012), which has a lower error rate and generates over 10 times more reads (Nelson et al 2014) and has thus become the leading sequencing platform for human microbiome studies (Amarasekara et al 2015).…”

Section: Introductionmentioning

confidence: 99%

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

et al. 2016

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Fanconi anemia (FA) is a rare genetic disease characterized by chromosomal instability and impaired DNA damage repair. FA patients develop oral squamous cell carcinoma (OSCC) earlier and more frequently than the general population, especially after hematopoietic stem cell transplantation (HSCT). Although evidence of an etiological role of the local microbiome and carcinogenesis has been mounting, no information exists regarding the oral microbiome of FA patients. The aim of this study was to explore the salivary microbiome of 61 FA patients regarding their oral health status and OSCC risk factors. After answering a questionnaire and receiving clinical examination, saliva samples were collected and analyzed using 16S rRNA sequencing of the V3-V4 hypervariable region. The microbial profiles associated with medical and clinical parameters were analyzed using general linear models. Patients were young (mean age, 22 y) and most had received HSCT (n = 53). The most abundant phyla were Firmicutes [mean relative abundance (SD), 42.1% (10.1%)] and Bacteroidetes [(25.4% (11.4%)]. A history of graft-versus-host disease (GVHD) (n = 27) was associated with higher proportions of Firmicutes (43.8% × 38.5%, P = 0.05). High levels of gingival bleeding were associated with the genera Prevotella (22.25% × 20%), Streptococcus (19.83% × 17.61%), Porphyromonas (3.63% × 1.42%, P = 0.03), Treponema (1.02% × 0.28%, P = 0.009), Parvimonas (0.28% × 0.07%, P = 0.02) and Dialister (0.27% × 0.10%, P = 0.04). Finally, participants transplanted over 11 y ago showed the highest levels of Streptococcus (18.4%), Haemophilus (12.7%) and Neisseria (6.8%). In conclusion, FA patients that showed poor oral hygiene harbored higher proportions of the genera of bacteria compatible with gingival disease. Specific microbial differences were associated with a history of oral GVHD and a history of oral mucositis.

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“…Other predominant genera such as Rothia, Prevotella, Capnocytophaga and Neisseria, might be involved in the susceptibility of an individual to periodontal disease (Ling et al 2010). In contrast Schmidt et al (2014) reported that in the cancer tissue samples Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal tissue samples from the same patient. In another study Devi and Singh (2014), reported that after standard radiotherapy, there was a profound shift in the oral microflora to predominance of acidogenic microbes, primarily Streptococcus mutans and Lactobacilli coincident with a decrease in salivary flora and an increase in caries risk.…”

Section: Changes In Oral Cavity Microflora After Radiotherapymentioning

confidence: 83%

Effect of Radiotherapy on Oral Microflora of Patients with Head and Neck Malignancies

2017

IJSR

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Globally cancer is a big threat to life of human beings and scientists are researching mechanisms to get rid from this deadly disease. After Human Genome Project now scientists are moving towards the microbiome studies of individuals. The head and neck cancers for which radiotherapy is an effective treatment has resulted in harmful effects of radiation on oral mucosa, dentition, salivary glands, masticatory musculature and most importantly the oral microflora. Basic and clinical data suggest that patients´oral microflora alter after radiotherapy induces diseases like candidasis, dental or radiation caries, mucositis, hyposalivation and xerostomia. The imbalance of natural oral microflora can play an important role in the pathogenesis of head and neck malignancies after radiotherapy. Therefore this review has been written to elaborate the effects of radiation on oral microflora of patients after radiotherapy, so that timely treatment planning and preventive measures are undertaken to avoid complications.

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Changes in Abundance of Oral Microbiota Associated with Oral Cancer

Cited by 313 publications

References 55 publications

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

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

The Salivary Microbiome and Oral Cancer Risk: A Pilot Study in Fanconi Anemia

Effect of Radiotherapy on Oral Microflora of Patients with Head and Neck Malignancies

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