A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop 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 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Genetic and Structural Analyses of Cytoplasmic Filaments of Wild-Type Treponema phagedenis and a Flagellar Filament-Deficient Mutant

Unique cytoplasmic filaments are found in the treponeme genus of spirochete bacteria. Their function is unknown, but their location underneath the periplasmic flagellar filaments (PFF) suggests a role in motility and/or cell structure. To better understand these unique structures, the gene coding for the cytoplasmic filaments, cfpA, was identified in various treponemal species. Treponema phagedenis cfpA was 2,037 nucleotides long, and the encoded polypeptide showed 78 to 100% amino acid sequence identity with the partial sequence of CfpA from T. denticola, T. vincentii, and T. pallidum subsp. pertenue. Wild-type T. phagedenis and a PFF-deficient isolate were analyzed by electron microscopy to assess the structural relationship of the cytoplasmic filaments and the PFF. The number of cytoplasmic filaments per cell of T. phagedenis (mean, 5.7) was compared with the number of PFF at each end of the cell (mean, 4.7); the results suggest that there is no direct one-to-one correlation at the cell end. Moreover, a structural link between these structures could not be demonstrated. The cytoplasmic filaments were also analyzed by electron microscopy at different stages of cell growth; this analysis revealed that they are cleaved before or during septum formation and before the nascent formation of PFF. A PFF-deficient mutant of T. phagedenis possessed cytoplasmic filaments similar to those of the wild type, suggesting that intact PFF are not required for their assembly and regulation. The extensive conservation of CfpA among pathogenic spirochetes suggests an important function, and structural analysis suggests that it is unlikely that the cytoplasmic filaments and the flagellar apparatus are physically linked

Native cellular architecture of Treponema denticola revealed by cryo-electron tomography

Using cryo-electron tomography, we are developing a refined description of native cellular structures in the pathogenic spirochete Treponema denticola. Tightly organized bundles of periplasmic flagella were readily observed in intact plunge-frozen cells. The periplasmic space was measured in both wild-type and aflagellate strains, and found to widen by less than the diameter of flagella when the latter are present. This suggests that a structural change occurs in the peptidoglycan layer to accommodate the presence of the flagella. In dividing cells, the flagellar filaments were found to bridge the cytoplasmic cylinder constriction site. Cytoplasmic filaments, adjacent to the inner membrane, run parallel to the tightly organized flagellar filaments. The cytoplasmic filaments may be anchored by a narrow plate-like structure. The tapering of the cell ends was conserved between cells, with a patella-shaped structure observed in the periplasm at the tip of each cytoplasmic cylinder. Several incompletely characterized structures have been observed in the periplasm between dividing cells, including a cable-like structure linking two cytoplasmic cylinders and complex foil-shaped structures

“Fecal microbiome in epidemiologic studies” - Letter

We congratulate Sinha et al. on their recent report (1) comparing fecal sample collection methods for epidemiologic studies of the gut microbiome. These data contribute to the increasing body of literature describing robust methodological frameworks for specimen collection and processing (2, 3). However, their claim that fixation of stool using RNAlater® results in “considerable changes to the microbiome diversity” contrasts with previous findings (2, 3), including those from their earlier reports (4, 5). We have previously demonstrated that self-collected stool stabilized with RNAlater® or other fixatives yields high fidelity and reproducibility in compositional profiling of DNA and RNA from shotgun sequence data, compared to immediately-frozen specimens (3). Additionally, fixation offers several distinct advantages crucial for large-scale population-based studies: a straightforward self-collection procedure; sample stabilization without deep-freezing during shipping, receiving, and processing; and versatility for multiple molecular analyses. The authors’ finding that specimens preserved in RNAlater® had poor correlation with immediately frozen specimens (1) could be explained, for example, by improper fixation resulting from an excess of specimen relative to preservative volume (1–2 g:2.5 ml, compared to the manufacturer-recommended ratio of 1 g:5–10 ml; Thermo Fisher Scientific Inc., Waltham, MA)

Tomographic reconstruction of treponemal cytoplasmic filaments reveals novel bridging and anchoring components

An understanding of the involvement of bacterial cytoplasmic filaments in cell division requires the elucidation of the structural organization of those filamentous structures. Treponemal cytoplasmic filaments are composed of one protein, CfpA, and have been demonstrated to be involved in cell division. In this study, we used electron tomography to show that the filaments are part of a complex with a novel molecular organization that includes at least two distinct features decorating the filaments. One set of components appears to anchor the filaments to the cytoplasmic membrane. The other set of components appears to bridge the cytoplasmic filaments on the cytoplasmic side, and to be involved in the interfilament spacing within the cell. The filaments occupy between 3 and 18% of the inner surface of the cytoplasmic membrane. These results reveal a novel filamentous molecular organization of independent filaments linked by bridges and continuously anchored to the membrane

The effect of relationship status on communicating emotions through touch

Research into emotional communication to date has largely focused on facial and vocal expressions. In contrast, recent studies by Hertenstein, Keltner, App, Bulleit, and Jaskolka (2006) and Hertenstein, Holmes, McCullough, and Keltner (2009) exploring nonverbal communication of emotion discovered that people could identify anger, disgust, fear, gratitude, happiness, love, sadness and sympathy from the experience of being touched on either the arm or body by a stranger, without seeing the touch. The study showed that strangers were unable to communicate the self-focused emotions embarrassment, envy and pride, or the universal emotion surprise. Literature relating to touch indicates that the interpretation of a tactile experience is significantly influenced by the relationship between the touchers (Coan, Schaefer, & Davidson, 2006). The present study compared the ability of romantic couples and strangers to communicate emotions solely via touch. Results showed that both strangers and romantic couples were able to communicate universal and prosocial emotions, whereas only romantic couples were able to communicate the self-focused emotions envy and pride

NextMed, Augmented and Virtual Reality platform for 3D medical imaging visualization

The visualization of the radiological results with more advanced techniques than the current ones, such as Augmented Reality and Virtual Reality technologies, represent a great advance for medical professionals, by eliminating their imagination capacity as an indispensable requirement for the understanding of medical images. The problem is that for its application it is necessary to segment the anatomical areas of interest, and this currently involves the intervention of the human being. The Nextmed project is presented as a complete solution that includes DICOM images import, automatic segmentation of certain anatomical structures, 3D mesh generation of the segmented area, visualization engine with Augmented Reality and Virtual Reality, all thanks to different software platforms that have been implemented and detailed, including results obtained from real patients. We will focus on the visualization platform using both Augmented and Virtual Reality technologies to allow medical professionals to work with 3d model representation of medical images in a different way taking advantage of new technologies

Geología y mineralogía del yacimiento polimetálico de Au-As (Ag-Pb-Zn-Cu-Sb) de Valiña-Azúmara (Lugo, NO de España)

Valiña-Azúmara is a polymetallic Au-As (Ag-Pb-Zn-Cu-Sb) deposit, located in the province of Lugo (NW Spain), that was mined for arsenic at the beginning of the 20th century. The mineralization is hosted in a Variscan thrust fault with a dip direction of N247-261ºE, and N-S and NE-SW Late-Variscan faults. These structures are hosted in black slates, Cambrian in age. To a lesser extent, the mineralization also occurs disseminated within narrow, weakly silicified and sericited selvages. Mineralization is divided into two hypogene stages. The first consists of quartz, calcite, rutile, sericite, arsenopyrite and pyrite. Two types of pyrite (Py-I and Py-II) are defined according to their chemical and textural characteristics. Py-II occurs as overgrowth of previous Py-I crystals. Py-II is As-rich (≤1.7 wt.%) and often contains traces of Te, Zn, Cu, Bi, Sb and Au. The mineralized drill core sections show a significant correlation between Au and As. This is due to Au occurring as invisible Au within the Py-II grains, with contents of up to 176 ppm. The Au/As ratios of Py-II indicate that Au was deposited as Au1+, as solid solution within the pyrite structure. The second stage of mineralization is enriched in Ag-Pb-Zn-Cu-Sb, replacing the first stage, and consists of quartz, calcite, chlorite, sphalerite, jamesonite, Ag-rich tetrahedrite, freibergite, chalcopyrite, pyrrhotite and galena. Although jamesonite shows traces of Ag, the Cu-Ag sulfosalts are the main carriers of the Ag mineralization in the deposit, with contents that vary from 13.7 to 23.9 wt.% of Ag. In the most superficial levels of the area, secondary Fe oxide and hydroxide, scorodite and anglesite developed due to the oxidation of the ore.Valiña-Azúmara es un yacimiento filoniano de Au-As (Ag-Pb-Zn-Cu-Sb) situado en la provincia de Lugo (NO España), que fue explotado por arsénico a principios del siglo XX. La mineralización se encuentra encajada en un cabalgamiento Varisco de dirección de buzamiento N247-261°E y en fracturas tardivariscas de dirección N-S y NE-SO que cortan a filitas negras de edad Cámbrica. En menor medida la mineralización también se encuentra diseminada en el encajante, en finas salbandas levemente sericitizadas y silicificadas. La mineralización se divide en dos etapas hipogénicas. La primera está constituida por cuarzo, calcita, rutilo, sericita, arsenopirita y pirita. En base a su composición y textura, se diferencian dos tipos de pirita, Py-I y Py II. La Py-II suele encontrarse recrecida sobre la Py I, formando bandas poligonales. Esta pirita está enriquecida en As (≤1,7% en peso) y contiene trazas de otros metales como Te, Zn, Cu, Bi, Sb y Au. Los tramos mineralizados de sondeo del yacimiento presentan correlación geoquímica entre los elementos Au y As, debido a que el Au se halla en forma de oro refractario dentro de los cristales de pirita arsenical (Py-II), los cuales llegan a presentar concentraciones en Au de hasta 176 ppm. La relación Au/As de la Py-II sugiere que el oro se encuentra en forma de Au+1, en solución sólida dentro de la estructura cristalina del mineral. La segunda etapa de mineralización está enriquecida en Ag-Pb-Zn-Cu-Sb y consiste en cuarzo, calcita, clorita, esfalerita, jamesonita, cobres grises (tetraedrita argentífera y freibergita), calcopirita, pirrotina y galena. Esta etapa se encuentra rellenando fracturas y cavidades intersticiales en los minerales de la etapa anterior, reemplazándolos en parte. Los principales minerales portadores de Ag son los cobres grises, con contenidos que varían entre 13,7 y 23,9% en peso. En la parte más superficial del yacimiento, la alteración supergénica de la mena primaria dio como resultado la formación de óxidos e hidróxidos de hierro, escorodita y anglesita