Comparing the Bacterial Diversity of Acute and Chronic Dental Root Canal Infections

This study performed barcoded multiplex pyrosequencing with a 454 FLX instrument to compare the microbiota of dental root canal infections associated with acute (symptomatic) or chronic (asymptomatic) apical periodontitis. Analysis of samples from 9 acute abscesses and 8 chronic infections yielded partial 16S rRNA gene sequences that were taxonomically classified into 916 bacterial species-level operational taxonomic units (OTUs) (at 3% divergence) belonging to 67 genera and 13 phyla. The most abundant phyla in acute infections were Firmicutes (52%), Fusobacteria (17%) and Bacteroidetes (13%), while in chronic infections the dominant were Firmicutes (59%), Bacteroidetes (14%) and Actinobacteria (10%). Members of Fusobacteria were much more prevalent in acute (89%) than in chronic cases (50%). The most abundant/prevalent genera in acute infections were Fusobacterium and Parvimonas. Twenty genera were exclusively detected in acute infections and 18 in chronic infections. Only 18% (n = 165) of the OTUs at 3% divergence were shared by acute and chronic infections. Diversity and richness estimators revealed that acute infections were significantly more diverse than chronic infections. Although a high interindividual variation in bacterial communities was observed, many samples tended to group together according to the type of infection (acute or chronic). This study is one of the most comprehensive in-deep comparisons of the microbiota associated with acute and chronic dental root canal infections and highlights the role of diverse polymicrobial communities as the unit of pathogenicity in acute infections. The overall diversity of endodontic infections as revealed by the pyrosequencing technique was much higher than previously reported for endodontic infections

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol to generate millions of overlapping reads. Combinatorial sequence tagging can be used to examine hundreds of samples with far fewer primers than is required when sequence tags are incorporated at only a single end. The number of reads generated permitted saturating or near-saturating analysis of samples of the vaginal microbiome. The large number of reads al- lowed an in-depth analysis of errors, and we found that PCR-induced errors composed the vast majority of non-organism derived species variants, an ob- servation that has significant implications for sequence clustering of similar high-throughput data. We show that the short reads are sufficient to assign organisms to the genus or species level in most cases. We suggest that this method will be useful for the deep sequencing of any short nucleotide region that is taxonomically informative; these include the V3, V5 regions of the bac- terial 16S rRNA genes and the eukaryotic V9 region that is gaining popularity for sampling protist diversity.Comment: 28 pages, 13 figure

Stochastic population growth in spatially heterogeneous environments

Classical ecological theory predicts that environmental stochasticity increases extinction risk by reducing the average per-capita growth rate of populations. To understand the interactive effects of environmental stochasticity, spatial heterogeneity, and dispersal on population growth, we study the following model for population abundances in $n$ patches: the conditional law of $X_{t+dt}$ given $X_t=x$ is such that when $dt$ is small the conditional mean of $X_{t+dt}^i-X_t^i$ is approximately $[x^i\mu_i+\sum_j(x^j D_{ji}-x^i D_{ij})]dt$, where $X_t^i$ and $\mu_i$ are the abundance and per capita growth rate in the $i$-th patch respectivly, and $D_{ij}$ is the dispersal rate from the $i$-th to the $j$-th patch, and the conditional covariance of $X_{t+dt}^i-X_t^i$ and $X_{t+dt}^j-X_t^j$ is approximately $x^i x^j \sigma_{ij}dt$. We show for such a spatially extended population that if $S_t=(X_t^1+...+X_t^n)$ is the total population abundance, then $Y_t=X_t/S_t$, the vector of patch proportions, converges in law to a random vector $Y_\infty$ as $t\to\infty$, and the stochastic growth rate $\lim_{t\to\infty}t^{-1}\log S_t$ equals the space-time average per-capita growth rate \sum_i\mu_i\E[Y_\infty^i] experienced by the population minus half of the space-time average temporal variation \E[\sum_{i,j}\sigma_{ij}Y_\infty^i Y_\infty^j] experienced by the population. We derive analytic results for the law of $Y_\infty$, find which choice of the dispersal mechanism $D$ produces an optimal stochastic growth rate for a freely dispersing population, and investigate the effect on the stochastic growth rate of constraints on dispersal rates. Our results provide fundamental insights into "ideal free" movement in the face of uncertainty, the persistence of coupled sink populations, the evolution of dispersal rates, and the single large or several small (SLOSS) debate in conservation biology.Comment: 47 pages, 4 figure

BRST Quantization of Unimodular Gravity

We study the quantization of two versions of unimodular gravity, namely fully diffeomorphism-invariant unimodular gravity and unimodular gravity with fixed metric determinant, utilizing standard path integral approach. We derive the BRST symmetry of effective actions corresponding to several relevant gauge conditions. We observe that for some gauge conditions, the restricted gauge structure may complicate the formulation and effective actions, in particular, if the chosen gauge conditions involve the canonical momentum conjugate to the induced metric on the spatial hypersurface. The BRST symmetry is extended further to the finite field-dependent BRST transformation, in order to establish the mapping between different gauge conditions in each of the two versions of unimodular gravity.Peer reviewe

Effects of Trophic Skewing of Species Richness on Ecosystem Functioning in a Diverse Marine Community

Widespread overharvesting of top consumers of the world’s ecosystems has “skewed” food webs, in terms of biomass and species richness, towards a generally greater domination at lower trophic levels. This skewing is exacerbated in locations where exotic species are predominantly low-trophic level consumers such as benthic macrophytes, detritivores, and filter feeders. However, in some systems where numerous exotic predators have been added, sometimes purposefully as in many freshwater systems, food webs are skewed in the opposite direction toward consumer dominance. Little is known about how such modifications to food web topology, e.g., changes in the ratio of predator to prey species richness, affect ecosystem functioning. We experimentally measured the effects of trophic skew on production in an estuarine food web by manipulating ratios of species richness across three trophic levels in experimental mesocosms. After 24 days, increasing macroalgal richness promoted both plant biomass and grazer abundance, although the positive effect on plant biomass disappeared in the presence of grazers. The strongest trophic cascade on the experimentally stocked macroalgae emerged in communities with a greater ratio of prey to predator richness (bottom-rich food webs), while stronger cascades on the accumulation of naturally colonizing algae (primarily microalgae with some early successional macroalgae that recruited and grew in the mesocosms) generally emerged in communities with greater predator to prey richness (the more top-rich food webs). These results suggest that trophic skewing of species richness and overall changes in food web topology can influence marine community structure and food web dynamics in complex ways, emphasizing the need for multitrophic approaches to understand the consequences of marine extinctions and invasions

Disturbance Alters the Phylogenetic Composition and Structure of Plant Communities in an Old Field System

The changes in phylogenetic composition and structure of communities during succession following disturbance can give us insights into the forces that are shaping communities over time. In abandoned agricultural fields, community composition changes rapidly when a field is plowed, and is thought to reflect a relaxation of competition due to the elimination of dominant species which take time to re-establish. Competition can drive phylogenetic overdispersion, due to phylogenetic conservation of ‘niche’ traits that allow species to partition resources. Therefore, undisturbed old field communities should exhibit higher phylogenetic dispersion than recently disturbed systems, which should be relatively ‘clustered’ with respect to phylogenetic relationships. Several measures of phylogenetic structure between plant communities were measured in recently plowed areas and nearby ‘undisturbed’ sites. There was no difference in the absolute values of these measures between disturbed and ‘undisturbed’ sites. However, there was a difference in the ‘expected’ phylogenetic structure between habitats, leading to significantly lower than expected phylogenetic diversity in disturbed plots, and no difference from random expectation in ‘undisturbed’ plots. This suggests that plant species characteristic of each habitat are fairly evenly distributed on the shared species pool phylogeny, but that once the initial sorting of species into the two habitat types has occurred, the processes operating on them affect each habitat differently. These results were consistent with an analysis of correlation between phylogenetic distance and co-occurrence indices of species pairs in the two habitat types. This study supports the notion that disturbed plots are more clustered than expected, rather than ‘undisturbed’ plots being more overdispersed, suggesting that disturbed plant communities are being more strongly influenced by environmental filtering of conserved niche traits

Multi-level, cross-sectional study of workplace social capital and smoking among Japanese employees

<p>Abstract</p> <p>Background</p> <p>Social capital is hypothesized to be relevant to health promotion, and the association between community social capital and cigarette smoking has been examined. Individual-level social capital has been found to be associated with smoking cessation, but evidence remains sparse on the contextual effect of social capital and smoking. Further, evidence remains sparse on the association between smoking and social capital in the workplace, where people are spending an increasing portion of their daily lives. We examined the association between workplace social capital and smoking status among Japanese private sector employees.</p> <p>Methods</p> <p>We employed a two-stage stratified random sampling procedure. Of the total of 1,800 subjects in 60 companies, 1,171 (men/women; 834/337) employees (65.1%) were identified from 46 companies in Okayama in 2007. Workplace social capital was assessed in two dimensions; trust and reciprocity. Company-level social capital was based on inquiring about employee perceptions of trust and reciprocity among co-workers, and then aggregating their responses in order to calculate the proportion of workers reporting mistrust and lack of reciprocity. Multilevel logistic regression analysis was conducted using Markov Chain Monte Carlo methods to explore whether individual- and company-level social capital was associated with smoking. Odds ratios (ORs) and 95% credible intervals (CIs) for current smoking were obtained.</p> <p>Results</p> <p>Overall, 33.3% of the subjects smoked currently. There was no relationship between individual-level mistrust of others and smoking status. By contrast, one-standard deviation change in company-level mistrust was associated with higher odds of smoking (OR: 1.25, 95% CI: 1.06-1.46) even after controlling for individual-level mistrust, sex, age, occupation, educational attainment, alcohol use, physical activity, body mass index, and chronic diseases. No clear associations were found between lack of reciprocity and smoking both at the individual- and company-level.</p> <p>Conclusions</p> <p>Company-level mistrust is associated with higher likelihood of smoking among Japanese employees, while individual perceptions of mistrust were not associated. The link between lack of reciprocity and smoking was not supported either at the individual- or company-level. Further studies are warranted to examine the possible link between company-level trust and smoking cessation in the Japanese workplace.</p

Community Analysis of Chronic Wound Bacteria Using 16S rRNA Gene-Based Pyrosequencing: Impact of Diabetes and Antibiotics on Chronic Wound Microbiota

Background: Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. Methodology/Principal Findings: We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds-approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007) and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. Conclusions/Significance: The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure-reducing some bacteria while selecting for others

Psychometric evaluation of a short measure of social capital at work

BACKGROUND: Prior studies on social capital and health have assessed social capital in residential neighbourhoods and communities, but the question whether the concept should also be applicable in workplaces has been raised. The present study reports on the psychometric properties of an 8-item measure of social capital at work. METHODS: Data were derived from the Finnish Public Sector Study (N = 48,592) collected in 2000–2002. Based on face validity, an expert unfamiliar with the data selected 8 questionnaire items from the available items for a scale of social capital. Reliability analysis included tests of internal consistency, item-total correlations, and within-unit (interrater) agreement by r(wg )index. The associations with theoretically related and unrelated constructs were examined to assess convergent and divergent validity (construct validity). Criterion-related validity was explored with respect to self-rated health using multilevel logistic regression models. The effects of individual level and work unit level social capital were modelled on self-rated health. RESULTS: The internal consistency of the scale was good (Cronbach's alpha = 0.88). The r(wg )index was 0.88, which indicates a significant within-unit agreement. The scale was associated with, but not redundant to, conceptually close constructs such as procedural justice, job control, and effort-reward imbalance. Its associations with conceptually more distant concepts, such as trait anxiety and magnitude of change in work, were weaker. In multilevel models, significantly elevated age adjusted odds ratios (ORs) of poor self-rated health (OR = 2.42, 95% confidence interval (CI): 2.24–2.61 for the women and OR = 2.99, 95% CI: 2.56–3.50 for the men) were observed for the employees in the lowest vs. highest quartile of individual level social capital. In addition, low social capital at the work unit level was associated with a higher likelihood of poor self-rated health. CONCLUSION: Psychometric techniques show our 8-item measure of social capital to be a valid tool reflecting the construct and displaying the postulated links with other variables