Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analyzed the largest cohort and set of distinct, clinically relevant body habitats to date. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families, and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology, and translational applications of the human microbiome.

A variety of microbial communities and their genes (microbiome) exist throughout the human body, playing fundamental roles in human health and disease. The NIH funded Human Microbiome Project (HMP) Consortium has established a population-scale framework which catalyzed significant development of metagenomic protocols resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 to 18 body sites up to three times, which to date, have generated 5,177 microbial taxonomic profiles from 16S rRNA genes and over 3.5 Tb of metagenomic sequence. In parallel, approximately 800 human-associated reference genomes have been sequenced. Collectively, these data represent the largest resource to date describing the abundance and variety of the human microbiome, while providing a platform for current and future studies.

The Human Microbiome Project used rigorous good clinical practice standards to complete comprehensive body site sampling in healthy 18- to 40-yr-old adults, creating an unparalleled reference set of microbiome specimens. To ensure that specimens represented minimally perturbed microbiomes, we first screened potential participants using exclusion criteria based on health history, including the presence of systemic diseases (e.g., hypertension, cancer, or immunodeficiency or autoimmune disorders), use of potential immunomodulators, and recent use of antibiotics or probiotics. Subsequent physical examinations excluded individuals based on body mass index (BMI), cutaneous lesions, and oral health. We screened 554 individuals to enroll 300 (149 men and 151 women, mean age 26 yr, mean BMI 24 kg/m, 20.0% racial minority, and 10.7% Hispanic). We obtained specimens from the oral cavity, nares, skin, gastrointestinal tract, and vagina (15 specimens from men and 18 from women). The study evaluated longitudinal changes in an individual's microbiome by sampling 279 participants twice (mean 212 d after the first sampling; range 30-359 d) and 100 individuals 3 times (mean 72 d after the second sampling; range 30-224 d). This sampling strategy yielded 11,174 primary specimens, from which 12,479 DNA samples were submitted to 4 centers for metagenomic sequencing. Our clinical design and well-defined reference cohort has laid a foundation for microbiome research.

Background We previously reported in a cross-sectional study that patients who were in periodontal maintenance programs and were taking vitamin D and calcium supplementation had a trend for better periodontal health compared with patients not taking supplementation. The objective of the present study was to determine, for the same group of subjects, whether there was a difference in periodontal health over a one–year period. Methods Fifty-one patients enrolled in maintenance programs from two dental clinics were recruited. Twenty-three were taking vitamin D (≥400 international units/day) and calcium (≥1000mg/day) supplementation, and twenty-eight were not taking supplementation. All subjects had ≥2 interproximal sites with ≥3 mm clinical attachment loss. For mandibular-posterior teeth, these clinical parameters were recorded: gingival index, plaque index, probing depth, attachment loss, bleeding upon probing, calculus index and furcation involvement. Photostimulable-phosphor, posterior bitewing radiographs were taken to assess alveolar bone. Daily vitamin D and calcium intakes were estimated by nutritional analysis. Data were collected at baseline, 6 months, and 12 months. Results Clinical parameters improved with time in both groups (p<0.01). When clinical measures were considered collectively, the results were borderline significant at baseline (p=0.061), significant at 6 months (p=0.049) but not significant at 12 months (p=0.114). After adjusting for covariates, the effect of supplements was significant at baseline (p=0.037), borderline at 6 months (p=0.058) and not significant at 12 months (p=0.142) Conclusion Calcium and vitamin D supplementation has a modest positive effect on periodontal health, and consistent dental care improves clinical parameters of periodontal disease regardless of such supplements. Calcium and vitamin D supplementation has a modest positive effect on periodontal health, and consistent dental care improves clinical parameters of periodontal disease regardless of such supplements. Our findings raise the possibility that vitamin D, perhaps at higher doses, may positively impact on periodontal disease severity.

Background Low dietary intakes of vitamin D and calcium hasten bone loss and osteoporosis. Because vitamin D metabolites may also alter the inflammatory response and have anti-microbial effects, we studied whether use of vitamin D and calcium supplements affects periodontal disease status. Methods A cohort of 51 subjects receiving periodontal maintenance therapy was recruited from 2 dental clinics. Of these, 23 were taking vitamin D (≥400 international units/day) and calcium (≥1000mg/day) supplementation, and 28 were not taking such supplementation. All subjects had ≥2 interproximal sites with ≥3 mm clinical attachment loss. Daily calcium and vitamin D intakes (from food and supplements) were estimated by nutritional analysis. The following clinical parameters of periodontal disease were recorded for the mandibular posterior teeth: gingival index, probing depth, cementoenamel junction-gingival margin distance (attachment loss), bleeding upon probing, and furcation involvement. Posterior photostimulable-phosphor bitewing radiographs were taken to determine cementoenamel-junction-alveolar-crest distances (alveolar crest height loss). Data were analyzed with a repeated-measures, multivariate analysis of variance. Results Relative to subjects who did not take vitamin D and calcium supplementation, supplement takers had shallower probing depths, fewer bleeding sites, lower gingival index values, fewer furcation involvements, less attachment loss and less alveolar crest height loss. The repeated-measures analysis indicated that collectively these differences for clinical parameters were borderline significant (P=0.08). Conclusion In these subjects receiving periodontal maintenance therapy, there was a trend for better periodontal health with intake of vitamin D and calcium supplementation. More expanded longitudinal studies are required to determine the potential of this relationship.

AimThe goal of this study was to identify progressing periodontal sites by applying linear mixed models (LMM) to longitudinal measurements of clinical attachment loss (CAL).MethodsNinety‐three periodontally healthy and 236 periodontitis subjects had their CAL measured bi‐monthly for 12 months. The proportions of sites demonstrating increases in CAL from baseline above specified thresholds were calculated for each visit. The proportions of sites reversing from the progressing state were also computed. LMM were fitted for each tooth site and the predicted CAL levels used to categorize sites regarding progression or regression. The threshold for progression was established based on the model‐estimated error in predictions.ResultsOver 12 months, 21.2%, 2.8% and 0.3% of sites progressed, according to thresholds of 1, 2 and 3 mm of CAL increase. However, on average, 42.0%, 64.4% and 77.7% of progressing sites for the different thresholds reversed in subsequent visits. Conversely, 97.1%, 76.9% and 23.1% of sites classified as progressing using LMM had observed CAL increases above 1, 2 and 3 mm after 12 months, whereas mean rates of reversal were 10.6%, 30.2% and 53.0% respectively.Conclusion LMM accounted for several sources of error in longitudinal CAL measurement, providing an improved method for classifying progressing sites.

Aim: The goal of the present longitudinal cohort study was to examine patterns of periodontal disease progression at progressing sites and subjects defined based on linear mixed models (LMM) of clinical attachment loss (CAL). Materials and Methods:A total of 113 periodontally healthy and 302 periodontitis subjects had their CAL calculated bimonthly for 12 months. LMMs were fitted for each site and the predicted CAL levels used to categorize their progression state.Participants were grouped based on the number of progressing sites into unchanged, transitional and active subjects. Patterns of periodontal disease progression were explored using descriptive statistics. Results:Progression occurred primarily at molars (50% of progressing sites) and interproximal sites (72%), affected a higher proportion of deep than shallow sites (2.7% versus 0.7%), and pocketing was the main mode of progression (49%). We found a low level of agreement (47%) between the LMM and traditional approaches to determine progression such as change in CAL ≥3 mm. Fourteen per cent of subjects were classified as active and among those 93% had periodontitis. The annual mean rate of progression for the active subjects was 0.35 mm/year.

Objectives Determine the level of calcium and vitamin D oral supplementation in patients in periodontal disease maintenance programs. Design Convenience survey. Setting St. Louis Metropolitan region. Subjects and Methods Patients (n=228) in two university-based, periodontal-disease maintenance programs. Main Outcome Measures Reported amounts of oral calcium and vitamin D supplementation were tested for differences based on gender and race. Results The last published recommended daily intakes from the United States (U.S.) Food and Nutrition Board (FNB) for adults >50 years of age are 1200 mg calcium and 400 IU vitamin D (or 600 IU if over 70). The mean age of the 228 patients (125 females and 103 males) was 63.6±11.0 years (standard deviation). Of the 228 patients surveyed: (1) 204(89%) were >50 years of age, and of these, only 15(7%) met the U.S. FNB’s recommended intakes of calcium and vitamin D from supplementation, (2) 138(66%) reported that they took no oral supplementation, with significantly more males (n=82) than females (n=56) not taking supplementation (p=0.03), (3) 88(39%) took calcium supplementation, with females (947±511mg/day) taking significantly (p<0.001) more than males (632±907mg/day), and (4) 66(29%) took vitamin D supplementation, with females(420±227 IU/day) taking approximately the same amount as males (443±317 IU/day, p>0.05). The amounts of oral supplementation did not vary with race (p>0.05). Conclusion The use of calcium and vitamin D supplementation has been promoted for years; yet the numbers of adults taking supplements remains low and the level of supplementation varies greatly. Knowledge of the benefits of supplementation needs to be better disseminated and research needs to be conducted to determine optimal levels of calcium and vitamin D supplementation.