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      Changes in Abundance of Oral Microbiota Associated with Oral Cancer

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          Abstract

          Individual bacteria and shifts in the composition of the microbiome have been associated with human diseases including cancer. To investigate changes in the microbiome associated with oral cancers, we profiled cancers and anatomically matched contralateral normal tissue from the same patient by sequencing 16S rDNA hypervariable region amplicons. In cancer samples from both a discovery and a subsequent confirmation cohort, abundance of Firmicutes (especially Streptococcus) and Actinobacteria (especially Rothia) was significantly decreased relative to contralateral normal samples from the same patient. Significant decreases in abundance of these phyla were observed for pre-cancers, but not when comparing samples from contralateral sites (tongue and floor of mouth) from healthy individuals. Weighted UniFrac principal coordinates analysis based on 12 taxa separated most cancers from other samples with greatest separation of node positive cases. These studies begin to develop a framework for exploiting the oral microbiome for monitoring oral cancer development, progression and recurrence.

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          Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

          The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.
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            Defining the healthy "core microbiome" of oral microbial communities

            Background Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing). Results We sampled and sequenced microbiomes from several intraoral niches (dental surfaces, cheek, hard palate, tongue and saliva) in three healthy individuals. Within an individual oral cavity, we found over 3600 unique sequences, over 500 different OTUs or "species-level" phylotypes (sequences that clustered at 3% genetic difference) and 88 - 104 higher taxa (genus or more inclusive taxon). The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas) and Fusobacteria (genus Fusobacterium). Each individual sample harboured on average 266 "species-level" phylotypes (SD 67; range 123 - 326) with cheek samples being the least diverse and the dental samples from approximal surfaces showing the highest diversity. Principal component analysis discriminated the profiles of the samples originating from shedding surfaces (mucosa of tongue, cheek and palate) from the samples that were obtained from solid surfaces (teeth). There was a large overlap in the higher taxa, "species-level" phylotypes and unique sequences among the three microbiomes: 84% of the higher taxa, 75% of the OTUs and 65% of the unique sequences were present in at least two of the three microbiomes. The three individuals shared 1660 of 6315 unique sequences. These 1660 sequences (the "core microbiome") contributed 66% of the reads. The overlapping OTUs contributed to 94% of the reads, while nearly all reads (99.8%) belonged to the shared higher taxa. Conclusions We obtained the first insight into the diversity and uniqueness of individual oral microbiomes at a resolution of next-generation sequencing. We showed that a major proportion of bacterial sequences of unrelated healthy individuals is identical, supporting the concept of a core microbiome at health.
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              Examining the global distribution of dominant archaeal populations in soil.

              Archaea, primarily Crenarchaeota, are common in soil; however, the structure of soil archaeal communities and the factors regulating their diversity and abundance remain poorly understood. Here, we used barcoded pyrosequencing to comprehensively survey archaeal and bacterial communities in 146 soils, representing a multitude of soil and ecosystem types from across the globe. Relative archaeal abundance, the percentage of all 16S rRNA gene sequences recovered that were archaeal, averaged 2% across all soils and ranged from 0% to >10% in individual soils. Soil C:N ratio was the only factor consistently correlated with archaeal relative abundances, being higher in soils with lower C:N ratios. Soil archaea communities were dominated by just two phylotypes from a constrained clade within the Crenarchaeota, which together accounted for >70% of all archaeal sequences obtained in the survey. As one of these phylotypes was closely related to a previously identified putative ammonia oxidizer, we sampled from two long-term nitrogen (N) addition experiments to determine if this taxon responds to experimental manipulations of N availability. Contrary to expectations, the abundance of this dominant taxon, as well as archaea overall, tended to decline with increasing N. This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups.
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                Author and article information

                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                2 June 2014
                : 9
                : 6
                : e98741
                Affiliations
                [1 ]Bluestone Center for Clinical Research, New York University College of Dentistry, New York, New York, United States of America
                [2 ]Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
                [3 ]Bioinformatics Department, Second Genome, San Bruno, California, United States of America
                [4 ]Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
                [5 ]Department of Oral and Maxillofacial Pathology, Radiology and Medicine, New York University College of Dentistry, New York, New York, United States of America
                [6 ]Departments of Otolaryngology and Plastic Surgery, New York University, New York, New York, United States of America
                Barts & The London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom
                Author notes

                Competing Interests: The receipt of an award for sequencing from Roche, a commercial funder, does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. Dr. Justin Kuczynski is an employee of Second Genome, Inc. His employment does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials.

                Conceived and designed the experiments: BLS DGA. Performed the experiments: AB BH RV KN. Analyzed the data: JK ABO DGA. Contributed reagents/materials/analysis tools: BLS PMC ELSQ KN ARK MDD. Wrote the paper: BLS JK. Enrolled patients: BLS PC ELSQ KN ARK MDD. Collected patient samples: BLS ARK.

                [¤a]

                Current address: Department of Diagnostic Sciences Texas A&M HSC Baylor College of Dentistry, Dallas, Texas, United States of America

                [¤b]

                Current address: Bluestone Center for Clinical Research and Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America

                Article
                PONE-D-13-34607
                10.1371/journal.pone.0098741
                4041887
                24887397
                9867f778-cf45-4a58-967f-4c3a30691e03
                Copyright @ 2014

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 21 August 2013
                : 7 May 2014
                Page count
                Pages: 12
                Funding
                This work was supported in part by an award of a GS Junior 454 Sequencing run from Roche, the National Center for Research Resources, the National Center for Advancing Translational Sciences, and the Office of the Director, National Institutes of Health, through University of San Francisco (UCSF)-­-CTSI grant number UL1 RR024129, and individual investigator awards from the National Cancer Institute grant (R01 CA131286, R21 CA 941186215) and the National Institute of Dental and Craniofacial Research (R01 DE019796). Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Biomarkers
                Biotechnology
                Applied Microbiology
                Ecology
                Microbial Ecology
                Genetics
                Genomics
                Metagenomics
                Microbiology
                Medical Microbiology
                Medicine and Health Sciences
                Dermatology
                Skin Neoplasms
                Skin Tumors
                Oral Mucosal Cancers
                Diagnostic Medicine
                Oncology
                Cancers and Neoplasms
                Carcinomas
                Squamous Cell Carcinomas
                Head and Neck Squamous Cell Carcinoma
                Head and Neck Tumors
                Oral Leukoplakia
                Basic Cancer Research
                Cancer Detection and Diagnosis
                Otorhinolaryngology
                Head and Neck Cancers
                Pathology and Laboratory Medicine

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                Uncategorized

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