The Human Oral Microbiome in Health and Disease: From Sequences to Ecosystems

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

(2019) Muneer Ahmad Malla et al.   Frontiers in Immunology

Porphyromonas gingivalis in Alzheimer’s disease brains: Evidence for disease causation and treatment with small-molecule inhibitors

(2019) Stephen S. Dominy et al.   Science Advances

Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls

(2019) Haifeng Lu et al.   Journal of Oral Microbiology

Comparison of Subgingival and Buccal Mucosa Microbiome in Chronic and Aggressive Periodontitis: A Pilot Study

(2019) Yiping Wei et al.   Frontiers in Cellular and Infection Microbiology

rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing

(2019) Jean-Claude Ogier et al.   BMC MICROBIOLOGY

metaQuantome: An integrated, quantitative metaproteomics approach reveals connections between taxonomy and protein function in complex microbiomes

(2019) Caleb W. Easterly et al.   MOLECULAR & CELLULAR PROTEOMICS

A Review and Tutorial of Machine Learning Methods for Microbiome Host Trait Prediction

(2019) Yi-Hui Zhou et al.   Frontiers in Genetics

Association between Alzheimer’s Disease and Oral and Gut Microbiota: Are Pore Forming Proteins the Missing Link?

(2018) Sebastian Aguayo et al.   JOURNAL OF ALZHEIMERS DISEASE

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Biodiversity of the human oral mycobiome in health and disease

(2018) Herath Mudiyansalage Herath Nihal Bandara et al.   ORAL DISEASES

Comparison of the oral microbiome in mouthwash and whole saliva samples

(2018) Xiaozhou Fan et al.   PLoS One

The analysis of the oral DNA virome reveals which viruses are widespread and rare among healthy young adults in Valencia (Spain)

(2018) Vicente Pérez-Brocal et al.   PLoS One

Identification of fungi in shotgun metagenomics datasets

(2018) Paul D. Donovan et al.   PLoS One

OUP accepted manuscript

(2018)   RHEUMATOLOGY

Tissue-Specific Immunity at the Oral Mucosal Barrier

(2018) Niki M. Moutsopoulos et al.   TRENDS IN IMMUNOLOGY

Deciphering the Human Virome with Single-Virus Genomics and Metagenomics

(2018) Maria de la Cruz Peña et al.   Viruses-Basel

Correcting for 16S rRNA gene copy numbers in microbiome surveys remains an unsolved problem

(2018) Stilianos Louca et al.   Microbiome

The short-term impact of probiotic consumption on the oral cavity microbiome

(2018) Erik Dassi et al.   Scientific Reports

The Performance of an Oral Microbiome Biomarker Panel in Predicting Oral Cavity and Oropharyngeal Cancers

(2018) Yenkai Lim et al.   Frontiers in Cellular and Infection Microbiology

Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults

(2018) Mikari Asakawa et al.   mSphere

The palatine tonsil bacteriome, but not the mycobiome, is altered in HIV infection

(2018) Yuto Fukui et al.   BMC MICROBIOLOGY

Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition

(2018) Jesse R. Willis et al.   Microbiome

New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract

(2018) Isabel F. Escapa et al.   mSystems

Periodontal Disease, Tooth Loss, and Cancer Risk

(2017) Dominique S Michaud et al.   EPIDEMIOLOGIC REVIEWS

The oral microbiota in colorectal cancer is distinctive and predictive

(2017) Burkhardt Flemer et al.   GUT

A tale of two risks: smoking, diabetes and the subgingival microbiome

(2017) Sukirth M Ganesan et al.   ISME Journal

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

On the ecosystemic network of saliva in healthy young adults

(2017) Egija Zaura et al.   ISME Journal

Challenges and perspectives of metaproteomic data analysis

(2017) Robert Heyer et al.   JOURNAL OF BIOTECHNOLOGY

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

(2017) Florent Lassalle et al.   MOLECULAR ECOLOGY

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Ecology of the Oral Microbiome: Beyond Bacteria

(2017) Jonathon L. Baker et al.   TRENDS IN MICROBIOLOGY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Breast tissue, oral and urinary microbiomes in breast cancer

(2017) Hannah Wang et al.   Oncotarget

Health-Associated Niche Inhabitants as Oral Probiotics: The Case of Streptococcus dentisani

(2017) Arantxa López-López et al.   Frontiers in Microbiology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Enterotypes in the landscape of gut microbial community composition

(2017) Paul I. Costea et al.   Nature Microbiology

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

The saliva microbiome profiles are minimally affected by collection method or DNA extraction protocols

(2017) Yenkai Lim et al.   Scientific Reports

A Highly Arginolytic Streptococcus Species That Potently Antagonizes Streptococcus mutans

(2016) Xuelian Huang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Temporal Stability of the Human Skin Microbiome

(2016) Julia Oh et al.   CELL

Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis

(2016) Vanessa Aguiar-Pulido et al.   Evolutionary Bioinformatics

Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study

(2016) Xiaozhou Fan et al.   GUT

Bacterial Amyloid and DNA are Important Constituents of Senile Plaques: Further Evidence of the Spirochetal and Biofilm Nature of Senile Plaques

(2016) Judith Miklossy   JOURNAL OF ALZHEIMERS DISEASE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

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

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

(2016) Edoardo Pasolli et al.   PLoS Computational Biology

Linkages between oral commensal bacteria and atherosclerotic plaques in coronary artery disease patients

(2016) Jyoti Chhibber-Goel et al.   npj Biofilms and Microbiomes

Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study

(2016) Toru Takeshita et al.   Scientific Reports

Effect of Bdellovibrio bacteriovorus HD100 on multispecies oral communities

(2015) Gitte Loozen et al.   ANAEROBE

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

TLR9 ligation in pancreatic stellate cells promotes tumorigenesis

(2015) Constantinos P. Zambirinis et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Extended evolution: A conceptual framework for integrating regulatory networks and niche construction

(2015) Manfred D. Laubichler et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

Influence of saliva on the oral microbiota

(2015) Philip D. Marsh et al.   PERIODONTOLOGY 2000

Environment and Colonisation Sequence Are Key Parameters Driving Cooperation and Competition between Pseudomonas aeruginosa Cystic Fibrosis Strains and Oral Commensal Streptococci

(2015) Robert A. Whiley et al.   PLoS One

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin

(2015) Guangxi Wu et al.   PLoS Genetics

Characterization of the salivary microbiome in patients with pancreatic cancer

(2015) Pedro J. Torres et al.   PeerJ

Modulation of host responses by oral commensal bacteria

(2015) Deirdre A Devine et al.   Journal of Oral Microbiology

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

Defining the role ofPorphyromonas gingivalispeptidylarginine deiminase (PPAD) in rheumatoid arthritis through the study of PPAD biology

(2014) Maximilian F Konig et al.   ANNALS OF THE RHEUMATIC DISEASES

Periodontal bacteria in human carotid atherothrombosis as a potential trigger for neutrophil activation

(2014) Hélène Rangé et al.   ATHEROSCLEROSIS

Gingipains from Porphyromonas gingivalis play a significant role in induction and regulation of CXCL8 in THP-1 cells

(2014) Kartheyaene Jayaprakash et al.   BMC MICROBIOLOGY

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

The Oral Microbiome and Oral Cancer

(2014) Laura Wang et al.   CLINICS IN LABORATORY MEDICINE

Oral cavity contains distinct niches with dynamic microbial communities

(2014) Xin Xu et al.   ENVIRONMENTAL MICROBIOLOGY

Candida albicans and Streptococcus mutans: a potential synergistic alliance to cause virulent tooth decay in children

(2014) Hyun Koo et al.   Future Microbiology

The oral microbiome and the immunobiology of periodontal disease and caries

(2014) Massimo Costalonga et al.   IMMUNOLOGY LETTERS

Subgingival microbiome in smokers and non-smokers in Korean chronic periodontitis patients

(2014) J.-H. Moon et al.   Molecular Oral Microbiology

Porphyromonas gingivalisgingipain is involved in the detachment and aggregation ofAggregatibacter actinomycetemcomitansbiofilm

(2014) A. Haraguchi et al.   Molecular Oral Microbiology

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Redefining the Human Oral Mycobiome with Improved Practices in Amplicon-based Taxonomy: Discovery of Malassezia as a Prominent Commensal

(2014) Amanda K. Dupuy et al.   PLoS One

The Same Microbiota and a Potentially Discriminant Metabolome in the Saliva of Omnivore, Ovo-Lacto-Vegetarian and Vegan Individuals

(2014) Francesca De Filippis et al.   PLoS One

PNAS Plus: From the Cover: Oligotyping analysis of the human oral microbiome

(2014) A. M. Eren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metatranscriptomics of the Human Oral Microbiome during Health and Disease

(2014) P. Jorth et al.   mBio

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity

(2013) Samuel B. Brusca et al.   CURRENT OPINION IN RHEUMATOLOGY

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

(2013) Loreto Abusleme et al.   ISME Journal

Subgingival microbiome in smokers and non-smokers in periodontitis: an exploratory study using traditional targeted techniques and a next-generation sequencing

(2013) Sergio Bizzarro et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Fungal systematics: is a new age of enlightenment at hand?

(2013) David S. Hibbett et al.   NATURE REVIEWS MICROBIOLOGY

Fusobacterium Is Associated with Colorectal Adenomas

(2013) Amber N. McCoy et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets

(2013) Omry Koren et al.   PLoS Computational Biology

Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis

(2012) Jose U. Scher et al.   ARTHRITIS AND RHEUMATISM

Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma

(2012) Smruti Pushalkar et al.   BMC MICROBIOLOGY

Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large European prospective cohort study

(2012) Dominique S Michaud et al.   GUT

Effects of the UK Biobank collection protocol on potential biomarkers in saliva

(2012) Rashida Pramanik et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Subgingival biodiversity in subjects with uncontrolled type-2 diabetes and chronic periodontitis

(2012) R. C. V. Casarin et al.   JOURNAL OF PERIODONTAL RESEARCH

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Categorization of the gut microbiota: enterotypes or gradients?

(2012) Ian B. Jeffery et al.   NATURE REVIEWS MICROBIOLOGY

Defining the human microbiome

(2012) Luke K Ursell et al.   NUTRITION REVIEWS

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

A Comparison of rpoB and 16S rRNA as Markers in Pyrosequencing Studies of Bacterial Diversity

(2012) Michiel Vos et al.   PLoS One

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

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging view of the human virome

(2012) Kristine M. Wylie et al.   Translational Research

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

Malassezia Fungi Are Specialized to Live on Skin and Associated with Dandruff, Eczema, and Other Skin Diseases

(2012) Charles W. Saunders et al.   PLoS Pathogens

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

Autoimmune responses in periodontal diseases

(2011) Javed Ali et al.   AUTOIMMUNITY REVIEWS

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

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

Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects

(2011) Flavia Matarazzo et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Mechanisms involved in the association between peridontal diseases and cardiovascular disease

(2011) R Teles et al.   ORAL DISEASES

Single Virus Genomics: A New Tool for Virus Discovery

(2011) Lisa Zeigler Allen et al.   PLoS One

The highly leukotoxic JP2 clone of Aggregatibacter actinomycetemcomitans: evolutionary aspects, epidemiology and etiological role in aggressive periodontitis

(2010) DORTE HAUBEK   APMIS

The weirdest people in the world?

(2010) Joseph Henrich et al.   BEHAVIORAL AND BRAIN 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

Association of Periodontitis With Rheumatoid Arthritis: A Pilot Study

(2010) Addie Dissick et al.   JOURNAL OF PERIODONTOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Oral microbiota and cancer

(2010) Jukka H. Meurman   Journal of Oral Microbiology

Diversity and Morphology of Members of the Phylum "Synergistetes" in Periodontal Health and Disease

(2009) S. R. Vartoukian et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The association between periodontal disease and cancer: A review of the literature

(2009) Sarah G. Fitzpatrick et al.   JOURNAL OF DENTISTRY

Individual Human Phenotypes in Metabolic Space and Time

(2009) Patrizia Bernini et al.   JOURNAL OF PROTEOME RESEARCH

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Metagenomic Analysis of Respiratory Tract DNA Viral Communities in Cystic Fibrosis and Non-Cystic Fibrosis Individuals

(2009) Dana Willner et al.   PLoS One

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Expression of Receptor for Advanced Glycation End Products (RAGE) is Related to Prognosis in Patients with Esophageal Squamous Cell Carcinoma

(2008) Taro Tateno et al.   ANNALS OF SURGICAL ONCOLOGY

EBV and CMV in chronic periodontitis: a prevalence study

(2008) Maryam Chalabi et al.   ARCHIVES OF VIROLOGY

Probiotic Formulations and Applications, the Current Probiotics Market, and Changes in the Marketplace: A European Perspective

(2008) Maija Saxelin   CLINICAL INFECTIOUS DISEASES

Advantages of multilocus sequence analysis for taxonomic studies: a case study using 10 housekeeping genes in the genus Ensifer (including former Sinorhizobium)

(2008) M. Martens et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY