Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition

BACKGROUND

The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.

RESULTS

Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations.

CONCLUSIONS

We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.

Clinical evaluation of the Baska Mask laryngeal mask in adult patients in ambulatory surgery

OBJECTIVE

To evaluate the clinical performance of the Baska Mask, a new second-generation supraglottic airway device with a self-inflating cuff and two side suction channels for continuous aspiration.

MATERIAL AND METHODS

Eighty adult patients without difficult airways were prospectively included. Ease of insertion and number of attempts needed, quality of ventilation, airway seal pressure, fibreoptic view, ease of gastric access, and complications were assessed. Sizes 3, 4, 5 were analyzed and compared.

RESULTS

First attempt insertion success rate was 88% and the overall rate was 100%, although additional maneuvers were necessary in 44% of the cases. The ventilation was adequate in 96%, with 39% of them requiring adjusting maneuvers. Size 3 needed significantly less adjustments, and achieved a higher seal pressure than sizes 4 and 5 combined. The airway seal pressure was 33 ± 7 cm H2O. Complete or partial vocal cords were visible in 90% of the 66 cases assessed. Partial obstruction, caused by distortion of the cuff-free border, was seen in 5%, and no glottic structures were identified in 5%. Gastric access was easy in all cases. Complications were mild and transient.

CONCLUSIONS

The Baska Mask achieves a high seal pressure, effective ventilation, and a quick access to drain gastric contents. However, additional adjustment maneuvers are frequently required to insert the mask and to optimize ventilation.

MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae

MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due to its small size, its ability to grow in vitro, and the amount of data produced over the past decades, M. pneumoniae is an interesting model organisms for the development of systems biology approaches for unicellular organisms. Our database hosts a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses. These include data obtained from gene expression profiling experiments, gene essentiality studies, protein abundance profiling, protein complex analysis, metabolic reactions and network modeling, cell growth experiments, comparative genomics and 3D tomography. In addition, the intuitive web interface provides access to several visualization and analysis tools as well as to different data search options. The availability and—even more relevant—the accessibility of properly structured and organized data are of up-most importance when aiming to understand the biology of an organism on a global scale. Therefore, MyMpn constitutes a unique and valuable new resource for the large systems biology and microbiology community.

PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes our repository freely accessed and easily edited by any scientists. To this purpose, we encourage plant biologist experts to join our annotation effort and share their knowledge on resistance-gene biology with the rest of the scientific community.

Prediction of protein function improving sequence remote alignment search by a fuzzy logic algorithm

The functional annotation of the new protein sequences represents a major drawback for genomic science. The best way to suggest the function of a protein from its sequence is by finding a related one for which biological information is available. Current alignment algorithms display a list of protein sequence stretches presenting significant similarity to different protein targets, ordered by their respective mathematical scores. However, statistical and biological significance do not always coincide, therefore, the rearrangement of the program output according to more biological characteristics than the mathematical scoring would help functional annotation. A new method that predicts the putative function for the protein integrating the results from the PSI-BLAST program and a fuzzy logic algorithm is described. Several protein sequence characteristics have been checked in their ability to rearrange a PSI-BLAST profile according more to their biological functions. Four of them: amino acid content, matched segment length and hydropathic and flexibility profiles positively contributed, upon being integrated by a fuzzy logic algorithm into a program, BYPASS, to the accurate prediction of the function of a protein from its sequence.

ArchDB: automated protein loop classification as a tool for structural genomics

The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. A large body of evidence suggests that protein structural information is frequently encoded in local sequences, and that folds are mainly made up of a number of simple local units of super-secondary structural motifs, consisting of a few secondary structures and their connecting loops. Moreover, protein loops play an important role in protein function. Here we present ArchDB, a classification database of structural motifs, consisting of one loop plus its bracing secondary structures. ArchDB currently contains 12,665 super-secondary elements classified into 1496 motif subclasses. The database provides an easy way to retrieve functional information from protein structures sharing a common motif, to search motifs found in a given SCOP family, superfamily or fold, or to search by keywords on proteins with classified loops. The ArchDB database of loops is located at http://sbi.imim.es/archdb.

Post-pH effect in oral streptococci

OBJECTIVES

To study the post-pH effect (PpHE) in 11 strains of oral streptococci belonging to Streptococcus sanguis, S. mitis, S. gordonii, S. mutans and S. sobrinus by using the BacT/Alert microbial detection system.

METHODS

The bacterial cultures were exposed to a different pH (3.6, 4.0, 4.6, 5.0, 5.6, 7.0, 7.5, 8.0 and 8.6) for 1 h, and then returned to a neutral medium. The automated BacT/Alert system determined resumed microbial growth by measuring CO2 generation. The PpHE expresses the time difference between resumed growth (after pH shock) and optimal growth (pH 7.0 used as the control).

RESULTS

PpHE was found to be minimal for alkaline pH values, and to be strain and species dependent.

CONCLUSIONS

The PpHE may be useful as an ecological determinant or as an indicator of the cariogenicity of oral streptococci.