Human Oral Microbiome

Key papers on the human oral microbiome. List probably not complete, but I tried. Updated September 2016.

Research papers

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology – June 2016

Using 16S rRNA gene amplification and next-generation sequencing, we generated microbial taxonomic inventories for 37 individuals representing five towns within the C&A tribes. For comparison, we performed the same laboratory techniques on saliva samples from 20 non-native individuals (NNI) from Norman, Oklahoma.

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome – Niklas Grassl – Genome Medicine – April 2016

Standard clinical cotton swabs were used to collect saliva form eight healthy individuals at two different time points, allowing us to study inter-individual differences and interday changes of the saliva proteome.

Cigarette smoking and the oral microbiome in a large study of American adults
Jing Wu – The ISME Journal – March 2016

In a study of 1204 US adults, we assessed the relationship of cigarette smoking with the oral microbiome. 16S rRNA gene sequencing was performed on DNA from oral wash samples, sequences were clustered into operational taxonomic units (OTUs) using QIIME and metagenomic content was inferred using PICRUSt.

Biogeography of a human oral microbiome at the micron scale – Jessica L. Mark Welch – PNAS – January 2016

Using spectral imaging fluorescence in situ hybridization as guided by metagenomic sequence analysis, we have discovered a distinctive, multigenus consortium in the microbiome of supragingival dental plaque. The consortium consists of a radially arranged, nine-taxon structure organized around cells of filamentous corynebacteria.

The human oral metaproteome reveals potential biomarkers for caries disease – Pedro Belda-Ferre – Proteomics – 2015

A total of 7771 bacterial and 853 human proteins were identified in 17 individuals, which provide the first available protein repertoire of human dental plaque.

Oligotyping analysis of the human oral microbiome – A. Murat Eren – PNAS USA – June 2014

Using Human Microbiome Project 16S rRNA gene sequence data for the nine sites in the oral cavity, we identified 493 oligotypes from the V1-V3 data and 360 oligotypes from the V3-V5 data.

The Impact of Various Time Intervals on the Supragingival Plaque Dynamic Core Microbiome – Wen-xin Jiang – PLOS ONE – May 2015

The aim of this study was to examine the influence of various time intervals on the composition of the supragingival plaque microbiome, especially the dynamic core microbiome, and to find a suitable observation interval for further studies on oral microbiota.

Dynamics of tongue microbial communities with single-nucleotide resolution using oligotyping – Jessica L. Mark Welch – Frontiers in Microbiology – November 2014

We employed oligotyping to analyze, with single-nucleotide resolution, oral microbial 16S ribosomal RNA (rRNA) gene sequence data from a time course sampled from the tongue of two individuals, and we interpret our results in the context of oligotypes that we previously identified in the oral data from the Human Microbiome Project.

Host lifestyle affects human microbiota on daily timescales – LA David, AC Materna, J Friedman, I Baptista, MC Blackburn, A Perrotta, SE Erdman, EJ Alm. – Genome Biology – July 2014

Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months.

Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples – Nicola Segata – Genome Biology – June 2012

We describe the bacterial community composition of ten digestive tract sites from more than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically determined metabolic potentials of four representative sites.

Moving pictures of the human microbiome – J Gregory Caporaso – Genome Biology – May 2011

Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints.

Bacterial diversity in the oral cavity of ten healthy individuals – Elisabeth M Bik (that’s me!) – ISME Journal – 2010

The composition of the oral microbiota from 10 individuals with healthy oral tissues was determined using culture-independent techniques. From each individual, 26 specimens, each from different oral sites at a single point in time, were collected and pooled. Near full length 16S rRNA gene sequences (n=11,368).

The Human Oral Microbiome – Floyd E. Dewhirst – Journal of Bacteriology – 2010

Analysis of 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa, description of HOMD database (see also below)

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing – Vladimir Lazarevic – Journal of Microbiological Methods – 2009

We amplified samples from the oral cavity of three healthy individuals using primers covering an ~ 82-base segment of the V5 loop, and sequenced using the Illumina technology in a single orientation. We identified 135 genera or higher taxonomic ranks from the resulting 1,373,824 sequences.


Influence of saliva microbes on releasing smells:

Ability of human oral microbiota to produce wine odorant aglycones from odourless grape glycosidic aroma precursors – Carolina Muñoz-González – Food Chemistry, November 2015

Understanding the role of saliva on aroma release from wine by using static and dynamic headspace conditions – Carolina Muñoz-González – Journal of Agricultural and Food Chemistry – July 2014

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
Paola Piombino – PLOS ONE – January 2014

Simulation of retronasal aroma of white and red wine in a model mouth system. Investigating the influence of saliva on volatile compound concentrations
Alessandro Genovese – Food Chemistry, May 2009


Review papers on oral microbiome composition

The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000 – August 2016

Book Chapter: The Oral Microbiota – Nicole B. Arweiler – Microbiota of the Human Body 2016

The oral microbiome diversity and its relation to human diseases – Jinzhi He – Folia Microbiologica – 2015

The oral microbiome in health and disease – William G. Wade – Pharmacological Research – 2013

Molecular analysis of human oral microbiota – Mitsuo Sakamoto – Journal of Periodontal Research – 2005

Reviews on relationship between oral health and systemic health

The microbiome–systemic diseases connection – TA van der Meulen – Oral Diseases 2016

Immune dysregulation mediated by the oral microbiome: potential link to chronic inflammation and atherosclerosis – C. Slocum – Journal of Internal Medicine – 2016

From focal sepsis to periodontal medicine: a century of exploring the role of the oral microbiome in systemic disease – Purnima S. Kumar – The Journal of Physiology 2016

From the acta prize lecture 2014: the periodontal-systemic connection seen from a microbiological standpoint – Ingar Olsen – Acta Odontologica Scandinavica – 2015

The oral microbiome: Its role in health and in oral and systemic infections – Frank A. Scannapieco – Clinical Microbiology Newsletter 2013

Oral microbiota and systemic disease – Purnima S. Kumar – Anaerobe – 2013

Popular Press and other links

The Oral Microbiota Affects More Than Just the Mouth – Lily Berrin – PLOS Blogs – March 2015

For World Oral Health Day, Lily Berrin, daughter of a periodontist and dental hygienist, highlights recent PLOS Pathogens content to remind us that oral pathogens do more than just cause cavities.

HOMD: The Human Oral Microbiome Database

The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with comprehensive information o­n the approximately 700 prokaryote species that are present in the human oral cavity. Approximately 49% are officially named, 17% unnamed (but cultivated) and 34% are known o­nly as uncultivated phylotypes.

Does That Wine Smell Good? Bacteria in Your Saliva Deserve Some of the Credit
Study shows some wine aromatics aren’t released until they meet the bacteria in our mouths – Kasay Carpenter – Wine Spectator – December 2015

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