Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections
Background The microbiome of built environment surfaces is impacted by the presence of humans. In this study, we tested the hypothesis that analysis of surface swabs from clinic toilet/bathroom yields results correlated with sexually transmitted infection (STI) notifications from corresponding human populations. We extended a previously reported study in which surfaces in toilet/bathroom facilities in primary health clinics in the Australian Northern Territory (NT) were swabbed then tested for nucleic acid from the STI agents Chlamydia trachomatis, Neisseria gonorrhoeae and Trichomonas vaginalis. This was in the context of assessing the potential for such nucleic acid to contaminate specimens collected in such facilities. STIs are notifiable in the NT, thus allowing comparison of swab and notification data. Methods An assumption in the design was that while absolute built environment loads of STI nucleic acids will be a function of patient traffic density and facility cleaning protocols, the relative loads of STI nucleic acids from different species will be largely unaffected by these processes. Another assumption was that the proportion of swabs testing positive for STIs provides a measure of surface contamination. Accordingly, “STI profiles” were calculated. These were the proportions that each of the three STIs of interest contributed to the summed STI positive swabs or notifications. Three comparisons were performed, using swab data from clinics in remote Indigenous communities, clinics in small-medium towns, and a single urban sexual health clinic. These data were compared with time and place-matched STI notifications. Results There were significant correlations between swab and notifications data for the both the remote Indigenous and regional data. For the remote Indigenous clinics the p values ranged from 0.041 to 0.0089, depending on data transformation and p value inference method. Further, the swab data appeared to strongly indicate known higher relative prevalence of gonorrhoeae in central Australia than in northern Australia. Similarly, the regional clinics yielded p values from 0.0088–0.0022. In contrast, swab and notifications data from the sexual health clinic were not correlated. Discussion Strong correlations between swab and notifications were observed. However, there was evidence for limitations of this approach. Despite the correlation observed with the regional clinics data, one clinic yielded zero positive swabs for C. trachomatis, although this STI constituted 25.1% of the corresponding notifications. This could be ascribed to stochastic effects. The lack of correlation observed for sexual health clinic data was also likely due to stochastic effects. It was concluded that toilet/bathroom surface swab sampling has considerable potential for public health surveillance. The approach may be applicable in situations other than primary health clinics, and for targets other than STIs.
Giffard et al. (2017) Primary health clinic toilet/bathroom surface swab sampling can indicate community profile of sexually transmitted infections. PeerJ 5:e3487 https://doi.org/10.7717/peerj.3487
Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments
Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible and used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. This freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.
Yim et al. (2017) Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments. PeerJ 5:e3486 https://doi.org/10.7717/peerj.3486
Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project
Obtaining human population level estimates of the prevalence of foodborne pathogens is critical for understanding outbreaks and ameliorating such threats to public health. Estimates are difficult to obtain due to logistic and financial constraints, but citizen science initiatives like that of the American Gut Project (AGP) represent a potential source of information concerning enteric pathogens. With an emphasis on genera Listeria and Salmonella, we sought to document the prevalence of those two taxa within the AGP samples. The results provided by AGP suggest a surprising 14% and 2% of samples contained Salmonella and Listeria, respectively. However, a reanalysis of those AGP sequences described here indicated that results depend greatly on the algorithm for assigning taxonomy and differences persisted across both a range of parameter settings and different reference databases (i.e., Greengenes and HITdb). These results are perhaps to be expected given that AGP sequenced the V4 region of 16S rRNA gene, which may not provide good resolution at the lower taxonomic levels (e.g., species), but it was surprising how often methods differ in classifying reads—even at higher taxonomic ranks (e.g., family). This highlights the misleading conclusions that can be reached when relying on a single method that is not a gold standard; this is the essence of Segal’s Law: an individual with one watch knows what time it is but an individual with two is never sure. Our results point to the need for an appropriate molecular marker for the taxonomic resolution of interest, and calls for the development of more conservative classification methods that are fit for purpose. Thus, with 16S rRNA gene datasets, one must be cautious regarding the detection of taxonomic groups of public health interest (e.g., culture independent identification of foodborne pathogens or taxa associated with a given phenotype).
Pettengill et al. (2017) Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project. PeerJ 5:e3480 https://doi.org/10.7717/peerj.3480
Phytochemical-rich medicinal plant extracts suppress bacterial antigens-induced inflammation in human tonsil epithelial cells
Background Pharyngitis is an inflammatory condition of the pharynx and associated structures commonly caused by the Group A streptococci (GAS). There is a growing interest in discovering plant-based anti-inflammatory compounds as potential alternatives to conventional drugs. This study evaluated anti-inflammatory activity of phytochemical-rich extracts prepared from 12 herbal plants using human tonsil epithelial cells (HTonEpiC) in vitro. Methods The HTonEpiC were induced by a mixture of lipoteichoic acid (LTA) and peptidoglycan (PGN) (10 µg/mL; bacterial antigens) for 4 h and then exposed to ethanol extracts (EE) or aqueous extracts (AE) for 20 h. The secretion of four pro-inflammatory cytokines was measured using enzyme-linked immunosorbent assays (ELISA). Total phenolic and total flavonoid contents of the extracts were determined using spectrophotometric methods. Results The herbal plant extracts (≤5 µg/mL) were not cytotoxic to HTonEpiC. The extracts exhibited a broad range of reduction (1.2%–92.6%) of secretion of interleukin-8 (IL-8), human beta defensin-2 (hBD-2), epithelial-derived neutrophil activating protein-78 (ENA-78), and granulocyte chemotactic protein-2 (GCP-2). Both EE and AE of clove, ginger, and echinacea flower and EE from danshen root significantly inhibited the pro-inflammatory cytokine production as induced by LTA and PGN in HTonEpiCs at the concentrations of 1 and 5 µg/mL. Discussion Our observations indicate that danshen root, clove, ginger, and echinacea flower extracts exhibit an anti-inflammatory effect in HTonEpiCs. The most efficacious extracts from danshen root, clove, ginger and echinacea flowers have potential to be used as natural sources for developing phytotherapeutic products in the management of painful inflammation due to streptococcal pharyngitis.
Wijesundara et al. (2017) Phytochemical-rich medicinal plant extracts suppress bacterial antigens-induced inflammation in human tonsil epithelial cells. PeerJ 5:e3469 https://doi.org/10.7717/peerj.3469
Climate, soil or both? Which variables are better predictors of the distributions of Australian shrub species?
Background Shrubs play a key role in biogeochemical cycles, prevent soil and water erosion, provide forage for livestock, and are a source of food, wood and non-wood products. However, despite their ecological and societal importance, the influence of different environmental variables on shrub distributions remains unclear. We evaluated the influence of climate and soil characteristics, and whether including soil variables improved the performance of a species distribution model (SDM), Maxent. Methods This study assessed variation in predictions of environmental suitability for 29 Australian shrub species (representing dominant members of six shrubland classes) due to the use of alternative sets of predictor variables. Models were calibrated with (1) climate variables only, (2) climate and soil variables, and (3) soil variables only. Results The predictive power of SDMs differed substantially across species, but generally models calibrated with both climate and soil data performed better than those calibrated only with climate variables. Models calibrated solely with soil variables were the least accurate. We found regional differences in potential shrub species richness across Australia due to the use of different sets of variables. Conclusions Our study provides evidence that predicted patterns of species richness may be sensitive to the choice of predictor set when multiple, plausible alternatives exist, and demonstrates the importance of considering soil properties when modeling availability of habitat for plants.
Hageer et al. (2017) Climate, soil or both? Which variables are better predictors of the distributions of Australian shrub species?. PeerJ 5:e3446 https://doi.org/10.7717/peerj.3446
Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands
Symbiotic microalgae (Symbiodinium spp.) strongly influence the performance and stress-tolerance of their coral hosts, making the analysis of Symbiodinium communities in corals (and metacommunities on reefs) advantageous for many aspects of coral reef research. High-throughput sequencing of ITS2 nrDNA offers unprecedented scale in describing these communities, yet high intragenomic variability at this locus complicates the resolution of biologically meaningful diversity. Here, we demonstrate that generating operational taxonomic units by clustering ITS2 sequences at 97% similarity within, but not across, samples collapses sequence diversity that is more likely to be intragenomic, while preserving diversity that is more likely interspecific. We utilize this ‘within-sample clustering’ to analyze Symbiodinium from ten host taxa on shallow reefs on the north and south shores of St. John, US Virgin Islands. While Symbiodinium communities did not differ between shores, metacommunity network analysis of host-symbiont associations revealed Symbiodinium lineages occupying ‘dominant’ and ‘background’ niches, and coral hosts that are more ‘flexible’ or ‘specific’ in their associations with Symbiodinium. These methods shed new light on important questions in coral symbiosis ecology, and demonstrate how application-specific bioinformatic pipelines can improve the analysis of metabarcoding data in microbial metacommunity studies.
Cunning et al. (2017) Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands. PeerJ 5:e3472 https://doi.org/10.7717/peerj.3472
The biochronology and palaeobiogeography of Baru (Crocodylia: Mekosuchinae) based on new specimens from the Northern Territory and Queensland, Australia
New records of the Oligo–Miocene mekosuchine crocodylian, Baru, from Queensland and the Northern Territory are described. Baru wickeni and Baru darrowi are accepted as valid species in the genus and their diagnoses are revised. Both species are present in Queensland and the Northern Territory but are restricted in time, with B. wickeni known from the late Oligocene and B. darrowi from the middle Miocene. The broad geographic distributions and restricted time spans of these species indicate that this genus is useful for biochronology. The record of B. wickeni from the Pwerte Marnte Marnte Local Fauna in the Northern Territory establishes that the species inhabited the north-western margin of the Lake Eyre Basin (LEB) drainage system. More southerly Oligo–Miocene sites in the LEB contain only one crocodylian species, Australosuchus clarkae. The Pwerte Marnte Marnte occurrence of B. wickeni indicates that the separation of Baru and Australosuchus did not correspond with the boundaries of drainage basins and that palaeolatitude was a more likely segregating factor.
Yates (2017) The biochronology and palaeobiogeography of Baru (Crocodylia: Mekosuchinae) based on new specimens from the Northern Territory and Queensland, Australia. PeerJ 5:e3458 https://doi.org/10.7717/peerj.3458
Microbial bioenergetics of coral-algal interactions
Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time) and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify microbial impacts on reef health.
Roach et al. (2017) Microbial bioenergetics of coral-algal interactions. PeerJ 5:e3423 https://doi.org/10.7717/peerj.3423
Dietary and cardio-metabolic risk factors in patients with Obstructive Sleep Apnea: cross-sectional study
Background Little is known about the role of dietary intake in obstructive sleep apnea (OSA), which could prove important in improving clinical outcomes for people with obesity and/or cardiovascular disease within these populations. Reduction in energy intake typically results in weight loss, markedly improving metabolic parameters and ameliorating OSA severity. The aim of this study was to evaluate the association of dietary and cardio-metabolic risk factors with OSA severity. Methods This was a cross-sectional study. A total of 75 volunteers at risk of OSA were recruited from 153 patients suffering from sleep disturbance at the Department of Pulmonology, Allergology and Respiratory Oncology at the Poznan University of Medical Sciences. Polysomnography was used for OSA diagnosis. Sleep quality was assessed by the Pittsburgh Sleep Quality Index. Blood pressure, parameters of glucose (fasting glucose, glucose tolerance test) and lipid metabolism (TC, LDL-C, HDL-C, TG) were assessed using routine enzymatic methods. Dietary intake was evaluated by 24-hr dietary recalls and Food Frequency Questionnaire. Ordinal logistic regression models were used for association of background characteristics and dietary intake with OSA severity. All analyses were adjusted for age, sex, BMI, smoking and alcohol intake. Results A higher percentage of smokers were observed in patients with mild OSA, while alcohol intake was the highest in severe OSA patients. Approximately 60% of the studied patients were self-reported poor sleepers. Results from ordinal logistic regression models showed that higher intakes of alcohol intake were associated with increased odds of severe OSA; whereas higher HDL-C levels were associated with lower odds (OR 0.01; 95% CI [0.0003–0.55]). Significantly higher odds of high OSA severity were observed in patients with disturbed sleep stages and obstructive sleep apnea. Moreover, the investigation of nutrient intake in relation to OSA severity showed that a higher intake of dietary fiber was associated with decreased OSA severity (OR 0.84; 95% CI [0.71–0.98]). Conclusions The severity of OSA is related to higher alcohol consumption and disturbed sleep. The significantly lower dietary fiber intake in patients with severe OSA is of particular importance for dietary consulting in clinical practice, which may positively influence cardiometabolic outcomes.
Stelmach-Mardas et al. (2017) Dietary and cardio-metabolic risk factors in patients with Obstructive Sleep Apnea: cross-sectional study. PeerJ 5:e3259 https://doi.org/10.7717/peerj.3259
The Venice specimen of Ouranosaurus nigeriensis (Dinosauria, Ornithopoda)
Ouranosaurus nigeriensis is an iconic African dinosaur taxon that has been described on the basis of two nearly complete skeletons from the Lower Cretaceous Gadoufaoua locality of the Ténéré desert in Niger. The entire holotype and a few bones attributed to the paratype formed the basis of the original description by Taquet (1976). A mounted skeleton that appears to correspond to O. nigeriensis has been on public display since 1975, exhibited at the Natural History Museum of Venice. It was never explicitly reported whether the Venice specimen represents a paratype and therefore, the second nearly complete skeleton reported in literature or a third unreported skeleton. The purpose of this paper is to disentangle the complex history of the various skeletal remains that have been attributed to Ouranosaurus nigeriensis (aided by an unpublished field map of the paratype) and to describe in detail the osteology of the Venice skeleton. The latter includes the paratype material (found in 1970 and collected in 1972), with the exception of the left femur, the right coracoid and one manus ungual phalanx I, which were replaced with plaster copies, and (possibly) other manus phalanges. Some other elements (e.g., the first two chevrons, the right femur, the right tibia, two dorsal vertebrae and some pelvic bones) were likely added from other individual/s. The vertebral column of the paratype was articulated and provides a better reference for the vertebral count of this taxon than the holotype. Several anatomical differences are observed between the holotype and the Venice specimen. Most of them can be ascribed to intraspecific variability (individual or ontogenetic), but some are probably caused by mistakes in the preparation or assemblage of the skeletal elements in both specimens. The body length of the Venice skeleton is about 90% the linear size of the holotype. Osteohistological analysis (the first for this taxon) of some long bones, a rib and a dorsal neural spine reveals that the Venice specimen is a sub-adult; this conclusion is supported by somatic evidence of immaturity. The dorsal ‘sail’ formed by the elongated neural spines of the dorsal, sacral and proximal caudal vertebrae characterizes this taxon among ornithopods; a display role is considered to be the most probable function for this bizarre structure. Compared to the mid-1970s, new information from the Venice specimen and many iguanodontian taxa known today allowed for an improved diagnosis of O. nigeriensis.
Bertozzo et al. (2017) The Venice specimen of Ouranosaurus nigeriensis (Dinosauria, Ornithopoda). PeerJ 5:e3403 https://doi.org/10.7717/peerj.3403