Metatranscriptomic analyses of the oral microbiome

The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease

(2019) Alex M. Valm   JOURNAL OF MOLECULAR BIOLOGY

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

(2019) Jessica L. Mark Welch et al.   Annual Review of Microbiology

Metatranscriptome of the Oral Microbiome in Health and Disease

(2018) J. Solbiati et al.   JOURNAL OF DENTAL RESEARCH

Periodontitis in US Adults

(2018) Paul I. Eke et al.   JOURNAL OF THE AMERICAN DENTAL ASSOCIATION

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis

(2018) Emily M. Nowicki et al.   mBio

Functional profiles of coronal and dentin caries in children

(2018) Christine A Kressirer et al.   Journal of Oral Microbiology

Genomics of the Uncultivated, Periodontitis-Associated Bacterium Tannerella sp. BU045 (Oral Taxon 808)

(2018) Clifford J. Beall et al.   mSystems

The contribution of Tannerella forsythia dipeptidyl aminopeptidase IV in the breakdown of collagen

(2018) Susan Yost et al.   Molecular Oral Microbiology

The oral microbiota: dynamic communities and host interactions

(2018) Richard J. Lamont et al.   NATURE REVIEWS MICROBIOLOGY

Report of the National Heart, Lung, and Blood Institute Working Group on the Role of Microbiota in Blood Pressure Regulation

(2017) Mohan K. Raizada et al.   HYPERTENSION

Global, Regional, and National Prevalence, Incidence, and Disability-Adjusted Life Years for Oral Conditions for 195 Countries, 1990–2015: A Systematic Analysis for the Global Burden of Diseases, Injuries, and Risk Factors

(2017) N.J. Kassebaum et al.   JOURNAL OF DENTAL RESEARCH

Molecular basis for immunohistochemical and inflammatory changes during progression of gingivitis to periodontitis

(2017) Sivge Kurgan et al.   PERIODONTOLOGY 2000

Potassium is a key signal in host-microbiome dysbiosis in periodontitis

(2017) Susan Yost et al.   PLoS Pathogens

The oral microbiome – an update for oral healthcare professionals

(2016) M. Kilian et al.   BRITISH DENTAL JOURNAL

First Cultivation of Health-Associated Tannerella sp. HOT-286 (BU063)

(2016) S.R. Vartoukian et al.   JOURNAL OF DENTAL RESEARCH

Biogeography of a human oral microbiome at the micron scale

(2016) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis

(2016) Shareef M. Dabdoub et al.   Scientific Reports

Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression

(2015) Ana E. Duran-Pinedo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sucrose- and Fructose-Specific Effects on the Transcriptome of Streptococcus mutans, as Determined by RNA Sequencing

(2015) Lin Zeng et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

metaModules identifies key functional subnetworks in microbiome-related disease

(2015) Ali May et al.   BIOINFORMATICS

Genetic variants of dental plaque Methanobrevibacter oralis

(2015) H. T. T. Huynh et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Binding of the Fap2 Protein of Fusobacterium nucleatum to Human Inhibitory Receptor TIGIT Protects Tumors from Immune Cell Attack

(2015) Chamutal Gur et al.   IMMUNITY

Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism

(2015) Anna Edlund et al.   ISME Journal

Binding of Cyclic Di-AMP to the Staphylococcus aureus Sensor Kinase KdpD Occurs via the Universal Stress Protein Domain and Downregulates the Expression of the Kdp Potassium Transporter

(2015) Joana A. Moscoso et al.   JOURNAL OF BACTERIOLOGY

The Microbiome in Populations with a Low and High Prevalence of Caries

(2015) I. Johansson et al.   JOURNAL OF DENTAL RESEARCH

Intermicrobial Interactions as a Driver for Community Composition and Stratification of Oral Biofilms

(2015) Nicholas S. Jakubovics   JOURNAL OF MOLECULAR BIOLOGY

Solving the etiology of dental caries

(2015) Aurea Simón-Soro et al.   TRENDS IN MICROBIOLOGY

Functional signatures of oral dysbiosis during periodontitis progression revealed by microbial metatranscriptome analysis

(2015) Susan Yost et al.   Genome Medicine

Mouthguards: does the indigenous microbiome play a role in maintaining oral health?

(2015) Purnima S. Kumar et al.   Frontiers in Cellular and Infection Microbiology

The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome

(2015) DeAnna E. Beasley et al.   PLoS One

High-Resolution Taxonomic Profiling of the Subgingival Microbiome for Biomarker Discovery and Periodontitis Diagnosis

(2014) Szymon P. Szafranski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbiota diversity and gene expression dynamics in human oral biofilms

(2014) Alfonso Benítez-Páez et al.   BMC GENOMICS

Altered Bacterial Profiles in Saliva from Adults with Caries Lesions: A Case-Cohort Study

(2014) D. Belstrøm et al.   CARIES RESEARCH

Cytokines and chemokines are differentially expressed in patients with periodontitis: Possible role for TGF-β1 as a marker for disease progression

(2014) Hazem Khalaf et al.   CYTOKINE

Oral cavity contains distinct niches with dynamic microbial communities

(2014) Xin Xu et al.   ENVIRONMENTAL MICROBIOLOGY

The Periodontal Pathogen Porphyromonas gingivalis Induces Expression of Transposases and Cell Death of Streptococcus mitis in a Biofilm Model

(2014) Ana E. Duran-Pinedo et al.   INFECTION AND IMMUNITY

Human oral viruses are personal, persistent and gender-consistent

(2014) Shira R Abeles et al.   ISME Journal

Community-wide transcriptome of the oral microbiome in subjects with and without periodontitis

(2014) Ana E Duran-Pinedo et al.   ISME Journal

Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

(2014) Chen-Hsun Tsai et al.   JOURNAL OF BACTERIOLOGY

The microbial basis of inflammatory bowel diseases

(2014) Sushila R. Dalal et al.   JOURNAL OF CLINICAL INVESTIGATION

Physiological roles of small RNA molecules

(2014) C. Michaux et al.   MICROBIOLOGY-SGM

Single Cell Genomics of Uncultured, Health-Associated Tannerella BU063 (Oral Taxon 286) and Comparison to the Closely Related Pathogen Tannerella forsythia

(2014) Clifford J. Beall et al.   PLoS One

Metagenomic Analysis of Nitrate-Reducing Bacteria in the Oral Cavity: Implications for Nitric Oxide Homeostasis

(2014) Embriette R. Hyde et al.   PLoS One

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

(2014) Laurens Kraal et al.   PLoS One

Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

(2014) Xuesong He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Power analysis and sample size estimation for RNA-Seq differential expression

(2014) Travers Ching et al.   RNA

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

Insights into the distribution and abundance of the ubiquitous Candidatus Saccharibacteria phylum following tag pyrosequencing

(2014) Belinda Ferrari et al.   Scientific Reports

Functional expression of dental plaque microbiota

(2014) Scott N. Peterson et al.   Frontiers in Cellular and Infection Microbiology

Metatranscriptomics reveals overall active bacterial composition in caries lesions

(2014) Aurea Simón-Soro et al.   Journal of Oral Microbiology

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

A Tissue-Dependent Hypothesis of Dental Caries

(2013) Á. Simón-Soro et al.   CARIES RESEARCH

Bacterial markers vs. clinical markers to predict progression of chronic periodontitis: a 2-yr prospective observational study

(2013) Georgios Charalampakis et al.   EUROPEAN JOURNAL OF ORAL SCIENCES

Expression ofPorphyromonas gingivalissmall RNA in response to hemin availability identified using microarray and RNA-seq analysis

(2013) Priscilla Phillips et al.   FEMS MICROBIOLOGY LETTERS

The social structure of microbial community involved in colonization resistance

(2013) Xuesong He et al.   ISME Journal

The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation

(2013) Loreto Abusleme et al.   ISME Journal

Differences in bacterial saliva profile between periodontitis patients and a control cohort

(2013) Daniel Belstrøm et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Calculating Sample Size Estimates for RNA Sequencing Data

(2013) Steven N. Hart et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Microbial Geography of the Oral Cavity

(2013) Á. Simón-Soro et al.   JOURNAL OF DENTAL RESEARCH

Investigating Acid Production by Streptococcus mutans with a Surface-Displayed pH-Sensitive Green Fluorescent Protein

(2013) Lihong Guo et al.   PLoS One

The Dental Plaque Microbiome in Health and Disease

(2013) Scott N. Peterson et al.   PLoS One

Bacterial Community Development in Experimental Gingivitis

(2013) James O. Kistler et al.   PLoS One

Genome-Wide Identification of Regulatory RNAs in the Human Pathogen Clostridium difficile

(2013) Olga A. Soutourina et al.   PLoS Genetics

Biogeography of the ecosystems of the healthy human body

(2013) Yanjiao Zhou et al.   GENOME BIOLOGY

Murine Gut Microbiota and Transcriptome Are Diet Dependent

(2012) Erica M. Carlisle et al.   ANNALS OF SURGERY

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Effect of Periodontal Pathogens on the Metatranscriptome of a Healthy Multispecies Biofilm Model

(2012) J. Frias-Lopez et al.   JOURNAL OF BACTERIOLOGY

The Small RNA RteR Inhibits Transfer of the Bacteroides Conjugative Transposon CTnDOT

(2012) J. L. Waters et al.   JOURNAL OF BACTERIOLOGY

Using high throughput sequencing to explore the biodiversity in oral bacterial communities

(2012) P.I. Diaz et al.   Molecular Oral Microbiology

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

(2012) Bo Liu et al.   PLoS One

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

(2012) Xuejian Xiong et al.   PLoS One

Non-coding sRNAs regulate virulence in the bacterial pathogen Vibrio cholerae

(2012) J. Patrick Bardill et al.   RNA Biology

Compartmentalized Control of Skin Immunity by Resident Commensals

(2012) S. Naik et al.   SCIENCE

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

(2012) Georgia Giannoukos et al.   GENOME BIOLOGY

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples

(2012) Nicola Segata et al.   GENOME BIOLOGY

Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation

(2011) Shinnosuke Murakami et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Association between genetic risk score and periodontitis onset and progression: A pilot study

(2011) M. Ricci et al.   ARCHIVES OF ORAL BIOLOGY

Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement

(2011) George Hajishengallis et al.   Cell Host & Microbe

Pathobionts of the gastrointestinal microbiota and inflammatory disease

(2011) Janet Chow et al.   CURRENT OPINION IN IMMUNOLOGY

Beyond the oral microbiome

(2011) Howard F. Jenkinson   ENVIRONMENTAL MICROBIOLOGY

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

(2011) A. D. Kostic et al.   GENOME RESEARCH

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing

(2011) Ann L Griffen et al.   ISME Journal

Cultivable Anaerobic Microbiota of Severe Early Childhood Caries

(2011) A. C. R. Tanner et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Microbiota of Severe Early Childhood Caries before and after Therapy

(2011) A.C.R. Tanner et al.   JOURNAL OF DENTAL RESEARCH

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

In-vivo-induced antigenic determinants of Fusobacterium nucleatum subsp. nucleatum

(2011) H.-R. Lee et al.   Molecular Oral Microbiology

Linear amplification for deep sequencing

(2011) Wieteke A M Hoeijmakers et al.   Nature Protocols

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia-specific small, noncoding RNAs required for virulence

(2011) J. T. Koo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Salmonella Small Non-Coding RNA Facilitates Bacterial Invasion and Intracellular Replication by Modulating the Expression of Virulence Factors

(2011) Hao Gong et al.   PLoS Pathogens

Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

(2010) C. C. G. M. Booijink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Chitinolytic Activity of Listeria monocytogenes EGD Is Regulated by Carbohydrates but Also by the Virulence Regulator PrfA

(2010) M. H. Larsen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The struggle for iron - a metal at the host-pathogen interface

(2010) Manfred Nairz et al.   CELLULAR MICROBIOLOGY

Molecular epidemiology and spatial distribution of Selenomonas spp. in subgingival biofilms

(2010) Julia Drescher et al.   EUROPEAN JOURNAL OF ORAL SCIENCES

The Human Oral Microbiome

(2010) F. E. Dewhirst et al.   JOURNAL OF BACTERIOLOGY

Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth

(2010) E. L. Gross et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Periodontal bacteria and hypertension: the oral infections and vascular disease epidemiology study (INVEST)

(2010) Moïse Desvarieux et al.   JOURNAL OF HYPERTENSION

Identification of regulatory RNAs in Bacillus subtilis

(2010) Irnov Irnov et al.   NUCLEIC ACIDS RESEARCH

Contribution of Porphyromonas gingivalis lipopolysaccharide to periodontitis

(2010) Sumita Jain et al.   PERIODONTOLOGY 2000

Microbial shift and periodontitis

(2010) Alex B. Berezow et al.   PERIODONTOLOGY 2000

Dental plaque biofilms: communities, conflict and control

(2010) Philip D. Marsh et al.   PERIODONTOLOGY 2000

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes

(2010) Alexandra Sittka et al.   RNA Biology

Small RNA-mediated regulation at the level of transcript stability

(2010) Marie-Pier Caron et al.   RNA Biology

Fusobacterium nucleatum ATCC 10953 Requires Actinomyces naeslundii ATCC 43146 for Growth on Saliva in a Three-Species Community That Includes Streptococcus oralis 34

(2009) S. Periasamy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Regulatory RNAs in Bacteria

(2009) Lauren S. Waters et al.   CELL

Experimental approaches for the discovery and characterization of regulatory small RNA

(2009) Cynthia Mira Sharma et al.   CURRENT OPINION IN MICROBIOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Aggregatibacter actinomycetemcomitans Builds Mutualistic Biofilm Communities with Fusobacterium nucleatum and Veillonella Species in Saliva

(2009) S. Periasamy et al.   INFECTION AND IMMUNITY

Negative Correlation of Distributions of Streptococcus cristatus and Porphyromonas gingivalis in Subgingival Plaque

(2009) B.-y. Wang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Treponema denticola biofilm-induced expression of a bacteriophage, toxin-antitoxin systems and transposases

(2009) H. L. Mitchell et al.   MICROBIOLOGY-SGM

Metatranscriptomics reveals unique microbial small RNAs in the ocean’s water column

(2009) Yanmei Shi et al.   NATURE

Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

(2009) Jane M. Liu et al.   NUCLEIC ACIDS RESEARCH

Progression of chronic periodontitis can be predicted by the levels ofPorphyromonas gingivalisandTreponema denticolain subgingival plaque

(2009) S. J. Byrne et al.   Oral microbiology and immunology

Small RNA gene identification and mRNA target predictions in bacteria

(2008) C. Pichon et al.   BIOINFORMATICS

The Potassium Transporter Trk and External Potassium Modulate Salmonella enterica Protein Secretion and Virulence

(2008) J. Su et al.   INFECTION AND IMMUNITY

The nitrate–nitrite–nitric oxide pathway in physiology and therapeutics

(2008) Jon O. Lundberg et al.   NATURE REVIEWS DRUG DISCOVERY

Evolution of Streptococcus pneumoniae and Its Close Commensal Relatives

(2008) Mogens Kilian et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial complexes in supragingival plaque

(2008) A. D. Haffajee et al.   Oral microbiology and immunology