A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

Dental calculus is not equivalent to bone collagen for isotope analysis: a comparison between carbon and nitrogen stable isotope analysis of bulk dental calculus, bone and dentine collagen from same individuals from the Medieval site of El Raval (Alicante, Spain)

(2014) D.C. Salazar-García et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Unlocking Ancient Protein Palimpsests

(2014) E. Cappellini et al.   SCIENCE

Metaproteomics: Harnessing the Power of High Performance Mass Spectrometry to Identify the Suite of Proteins That Control Metabolic Activities in Microbial Communities

(2013) Robert L. Hettich et al.   ANALYTICAL CHEMISTRY

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae

(2013) V. J. Schuenemann et al.   SCIENCE

Vaginal Microbiome: Rethinking Health and Disease

(2012) Bing Ma et al.   Annual Review of Microbiology

Insights into the virulence of oral biofilms: discoveries from proteomics

(2012) Masae Kuboniwa et al.   Expert Review of Proteomics

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Stable carbon and nitrogen isotopes of human dental calculus: a potentially new non-destructive proxy for paleodietary analysis

(2012) G. Richard Scott et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

New Insights into the Composition and Functions of the Acquired Enamel Pellicle

(2012) W.L. Siqueira et al.   JOURNAL OF DENTAL RESEARCH

DNA Binding to Hydroxyapatite: A Potential Mechanism for Preservation of Microbial DNA

(2012) Malin Brundin et al.   JOURNAL OF ENDODONTICS

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Making ubiquitin specific

(2012) Titia K. Sixma   Nature Chemical Biology

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus

(2012) Karen Hardy et al.   NATURWISSENSCHAFTEN

Variola Virus in a 300-Year-Old Siberian Mummy

(2012) Philippe Biagini et al.   NEW ENGLAND JOURNAL OF MEDICINE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

(2012) Sanqing Yuan et al.   PLoS One

Deep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease

(2012) Bo Liu et al.   PLoS One

Detecting the Immune System Response of a 500 Year-Old Inca Mummy

(2012) Angelique Corthals et al.   PLoS One

Genotype of a historic strain of Mycobacterium tuberculosis

(2012) A. S. Bouwman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Competence Is a Major Mechanism for Horizontal DNA Transfer in the Oral Pathogen Porphyromonas gingivalis

(2012) G. D. Tribble et al.   mBio

Atmosphere: A Source of Pathogenic or Beneficial Microbes?

(2012) Paraskevi N. Polymenakou   Atmosphere

Setting the stage – Building and working in an ancient DNA laboratory

(2011) Michael Knapp et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers

(2011) William A. Walters et al.   BIOINFORMATICS

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis

(2011) Matthew B. Scholz et al.   CURRENT OPINION IN BIOTECHNOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains

(2011) Hans R. Preus et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

(2011) Enrico Cappellini et al.   JOURNAL OF PROTEOME RESEARCH

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Transfer of antibiotic resistance by transformation with eDNA within oral biofilms

(2010) Saad Hannan et al.   FEMS IMMUNOLOGY AND MEDICAL MICROBIOLOGY

Survival and recovery of DNA from ancient teeth and bones

(2010) C.J. Adler et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Calculus removal and the prevention of its formation

(2010) Søren Jepsen et al.   PERIODONTOLOGY 2000

Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium)

(2010) A. G. Henry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One gram of soil: a microbial biochemical gene library

(2009) J. T. Trevors   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Evaluation of Different Methods for Extracting Extracellular DNA from the Biofilm Matrix

(2009) J. Wu 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

In the news

(2009)   NATURE REVIEWS MICROBIOLOGY

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Determination of the Genome Sequence of Porphyromonas gingivalis Strain ATCC 33277 and Genomic Comparison with Strain W83 Revealed Extensive Genome Rearrangements in P. gingivalis

(2008) M. Naito et al.   DNA RESEARCH

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Using plant microfossils from dental calculus to recover human diet: a case study from Tell al-Raqā'i, Syria

(2008) Amanda G. Henry et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Changes in starch grain morphologies from cooking

(2008) Amanda G. Henry et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Starch granules, dental calculus and new perspectives on ancient diet

(2008) Karen Hardy et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Microbial diversity and the genetic nature of microbial species

(2008) Mark Achtman et al.   NATURE REVIEWS MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

The perils of plenty: what are we going to do with all these genes?

(2008) A. Rodrigo et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Starch grains on human teeth reveal early broad crop diet in northern Peru

(2008) D. R. Piperno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of oral bacteria in cardiovascular specimens

(2008) K. Nakano et al.   Oral microbiology and immunology