Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain

We thank C. Stringer and R. Kruszynski of the Natural History Museum, London; S. Schiffels; D. Sayer; Oxford Archaeology East; M. Farrell of the Royal College of Surgeons of England; J. Pearson of the Inverness Museum; and all of the museums for access to samples. We also thank the Museum of London for allowing us to collect and destructively analyse archaeological dental calculus samples from their collections from London, particularly J. Bekvalac and R. Redfern. We would also like to acknowledge J. VanderBerg at EnDev Geographic for producing the map used in Fig. 1. A.C., C.A. and L.W. thank the Australian Research Council for research funding (DP110105038) and Laureate (FL140100260). The work was also supported by an Australian Research Council Future Fellowship Award to L.S.W. (FT180100407). This material is also based on work supported by the National Science Foundation Graduate Research Fellowship Program awarded to A.S.G. under Grant No. DGE1255832. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.Peer reviewedPostprintPostprintPostprin

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution

Studies on the growth and metabolism of Eikenella corrodens / Neville Gully.

Copies of author's previously published articles inserted.Bibliography: leaves 175-194.xiii, 195 leaves : ill. ; 30 cm.Eikenella corrodens, a Gram-negative rod, is a normal inhabitant of the human oral cavity. It is one of the most commonly detected cultivable bacteria from sub- and supra-gingival plaque and is often isolated in elevated proportions from sites exhibiting destructive periodontal disease compared with healthy sites. The primary aim of this study was to investigate the metabolism of E. corrodons, with particular reference to energy generation, and to determine the effect of physical environmental parameters on its growth.Thesis (Ph.D.)--University of Adelaide, Dept. of Dentistry, 200

Strong genetic control of emergence of human primary incisors

Our understanding of tooth eruption in humans remains incomplete. We hypothesized that genetic factors contribute significantly to phenotypic variation in the emergence of primary incisors. We applied model-fitting to data from Australian twins to quantify contributions of genetic and environmental factors to variation in timing of the emergence of human primary incisors. There were no significant differences in incisor emergence times between zygosity groups or sexes. Emergence times of maxillary central incisors and mandibular lateral incisors were less variable than those of maxillary lateral incisors and mandibular central incisors. Maxillary lateral incisors displayed significant directional asymmetry, the left side emerging earlier than the right. Variation in timing of the emergence of the primary incisors was under strong genetic control, with a small but significant contribution from the external environment. Estimates of narrow-sense heritability ranged from 82 to 94% in males and 71 to 96% in females

Probiotic Lactobacillus Rhamnosus GG Protects Against P. Gingivalis And F. Nucleatum Gut Dysbiosis.

OBJECTIVES: This study investigated changes induced by Porphyromonas gingivalis and on gastrointestinal histology and gut microbiome in a mouse model of experimental periodontitis. The effect of probiotic Lactobacillus rhamnosus GG (LGG) in altering these changes was also investigated. METHODS: IThirty-six mice were allocated into six groups. Experimental alveolar bone loss was induced by oral inoculation with P. gingivalis and F. nucleatum. LGG was orally inoculated or orally gavaged. Gastrointestinal tissue changes were assessed using histological analysis and immunohistochemistry. Caecal microbiome was analysed by sequencing 16S rRNA genes of caecal content. RESULTS: Inoculation with P. gingivalis and F. nucleatum induced inflammation throughout gastrointestinal tract (p less than 0.05), increased expression of IL-6 in ileum (p = 0.052) and altered composition of caecal microbiome (p less than 0.05) in experimental mice compared to controls. Mice treated with LGG had reduced tissue inflammation in duodenum (p = 0.044) and lowered levels of IL-6 in ileum (p = 0.048) when compared with disease. LGG therapy influenced gut microbiome changes. CONCLUSION: P. gingivalis and F. nucleatum inoculation induced significant changes in intestinal inflammation and caecal microbiome. Oral gavage with LGG exerted a protective effect against intestinal inflammation and limited gut microbiome changes associated with P. gingivalis and F. nucleatum

Micro CT appearance and analysis of bone erosion in front paw radio-carpal joint.

<p>A. Micro CT appearance of paw for CMC control group at day 63. B. Micro CT appearance of paw for ECR527 & EA group at day 63. C. Micro CT appearance of paw for W50 & EA group at day 63. D. The front paws (left and right combined), were processed to determine bone loss/growth between the two scanned time points in the radio-carpal joint. Data represent mean (± SEM). The number of animals in each group was 6 and measurements were performed in duplicate. Statistical analysis was done by one way ANOVA and Bonferroni multiple comparisons. <i>Abbreviations:</i> CMC = carboxymethyl cellulose; ECR527 = PAD-deficient <i>P. gingivalis</i>; W50 = wild type <i>P. Gingivalis</i>; EA = experimental arthritis</p

Oligonucleotide primers used in this study.

a<p>Underlined sequence of SOE primers indicates the part of the primer that is not complementary to the target sequence, but provides complementarity with a second PCR product for splicing.</p

Visual appearance and scoring of paw swelling.

<p>A. Appearance of front and rear paws for CMC control group at day 7 post EA induction. B. Appearance of front and rear paws for ECR527 & EA group at day 7 post EA induction. C. Appearance of front and rear paws for W50 & EA group at day 7 post EA induction. D. Total paw score grade out of a 60 including front and back paws. Data represent mean (± SEM). The number of animals in each group was 6 and measurements were performed once daily per animal Statistical analysis was done by two way ANOVA and Tukey multiple comparisons. Raw data for data points are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100838#pone.0100838.s001" target="_blank">Figure S1</a>. <i>Abbreviations:</i> CMC = carboxymethyl cellulose; ECR527 = PAD-deficient <i>P. gingivalis</i>; W50 = wild type <i>P. Gingivalis</i>; EA = experimental arthritis</p

Histological analysis of maxillary periodontal tissues.

<p>A. Histology of mouse jaw for CMC control group at day 63. B. Histology of mouse jaw for ECR527 & EA group at day 63. C. Histology of mouse jaw for W50 & EA group at day 63. Arrow indicates increased inflammatory reaction in supra-crestal alveolar bone gingival tissue. D. Histological scores (mean ± SEM) for the presence of osteoclasts and evidence of bone erosion around the first and second upper molars for all groups in the study. Original magnification of A–C = 100X. The number of animals in each group was 6 and measurements were performed in triplicate. Statistical analysis was done by one way ANOVA and Tukey multiple comparisons. <i>Abbreviations:</i> CMC = carboxymethyl cellulose; ECR527 = PAD-deficient <i>P. gingivalis</i>; W50 = wild type <i>P. Gingivalis</i>; EA = experimental arthritis.</p

Serum anti-CCP antibody levels.

<p>The mean (± SEM) titre of anti-CCP antibodies detected in the sera of mice at week 9 from each of the 6 treatment groups. Raw data for data points are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100838#pone.0100838.s002" target="_blank">Figure S2</a>. The number in each group was 6 and measurements were performed in duplicate. Statistical analysis was done by one way ANOVA and Tukey multiple comparisons. <i>Abbreviations:</i> CMC = carboxymethyl cellulose; ECR527 = PAD-deficient <i>P. gingivalis</i>; W50 = wild type <i>P. Gingivalis</i>; EA = experimental arthritis</p