Immune status, and not HIV infection or exposure, drives the development of the oral microbiota.

Even with antiretroviral therapy, children born to HIV-infected (HI) mothers are at a higher risk of early-life infections and morbidities including dental disease. The increased risk of dental caries in HI children suggest immune-mediated changes in oral bacterial communities, however, the impact of perinatal HIV exposure on the oral microbiota remains unclear. We hypothesized that the oral microbiota of HI and perinatally HIV-exposed-but-uninfected (HEU) children will significantly differ from HIV-unexposed-and-uninfected (HUU) children. Saliva samples from 286 child-participants in Nigeria, aged ≤ 6 years, were analyzed using 16S rRNA gene sequencing. Perinatal HIV infection was significantly associated with community composition (HI vs. HUU-p = 0.04; HEU vs. HUU-p = 0.11) however, immune status had stronger impacts on bacterial profiles (p < 0.001). We observed age-stratified associations of perinatal HIV exposure on community composition, with HEU children differing from HUU children in early life but HEU children becoming more similar to HUU children with age. Our findings suggest that, regardless of age, HIV infection or exposure, low CD4 levels persistently alter the oral microbiota during this critical developmental period. Data also indicates that, while HIV infection clearly shapes the developing infant oral microbiome, the effect of perinatal exposure (without infection) appears transient.

Analyzing endodontic infections by deep coverage pyrosequencing.

Bacterial diversity in endodontic infections has not been sufficiently studied. The use of modern pyrosequencing technology should allow for more comprehensive analysis than traditional Sanger sequencing. This study investigated bacterial diversity in endodontic infections through taxonomic classification based on 16S rRNA gene sequences generated by 454 GS-FLX pyrosequencing and conventional Sanger capillary sequencing technologies. Sequencings were performed on 7 specimens from endodontic infections. On average, 47 vs. 28,590 sequences were obtained per sample for Sanger sequencing vs. pyrosequencing, representing a 600-fold difference in "depth-of-coverage". Based on Ribosomal Database Project (RDP II) Classifier analysis, pyrosequencing identified 179 bacterial genera in 13 phyla, which was significantly more than Sanger sequencing. The phylum Bacteroidetes was the most prevalent bacterial phylum. These results indicate that bacterial communities in endodontic infections are more diverse than previously demonstrated. In addition, deep-coverage pyrosequencing of the 16S rRNA gene revealed low-abundance micro-organisms with potential clinical implications.

The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea.

Saturated thalassic brines are among the most physically demanding habitats on Earth: few microbes survive in them. Salinibacter ruber is among these organisms and has been found repeatedly in significant numbers in climax saltern crystallizer communities. The phenotype of this bacterium is remarkably similar to that of the hyperhalophilic Archaea (Haloarchaea). The genome sequence suggests that this resemblance has arisen through convergence at the physiological level (different genes producing similar overall phenotype) and the molecular level (independent mutations yielding similar sequences or structures). Several genes and gene clusters also derive by lateral transfer from (or may have been laterally transferred to) haloarchaea. S. ruber encodes four rhodopsins. One resembles bacterial proteorhodopsins and three are of the haloarchaeal type, previously uncharacterized in a bacterial genome. The impact of these modular adaptive elements on the cell biology and ecology of S. ruber is substantial, affecting salt adaptation, bioenergetics, and photobiology.

Cell wall-associated protein A as a tool for immunolocalization of Staphylococcus aureus in infected human airway epithelium.

Staphylococcus aureus is a common human pathogen involved in non-bronchial diseases and in genetic and acquired bronchial diseases. In this study, we applied an immunolabeling approach for in vivo and in vitro detection of S. aureus, based on the affinity of staphylococcal protein A (SpA) for the Fc region of immunoglobulins, especially IgG. Most strains of S. aureus, including clinical strains, can be detected with this labeling technique. The approach can be used for detection and localization with transmission electron microscopy or light-fluorescence microscopy of S. aureus in infected tissues such as human bronchial tissue from cystic fibrosis (CF) patients. The methodology can also be applied to cell culture models with the aim of characterizing bacterial adherence to epithelial cells in backscattered electron imaging with scanning electron microscopy. Application to the study of S. aureus adherence to airway epithelium showed that the bacteria did not adhere in vivo to intact airway epithelium. In contrast, bacteria adhered to the basolateral plasma membrane of columnar cells, to basal cells, to the basement membrane and were identified beneath the lamina propria when the epithelium was injured and remodeled, or in vitro when the epithelial cells were dedifferentiated.

Differentiated and functional human airway epithelium regeneration in tracheal xenografts.

To investigate the regeneration process of a well-differentiated and functional human airway epithelium, we adapted an in vivo xenograft model in which adult human nasal epithelial cells adhere and progressively repopulate denuded rat tracheae grafted in nude mice. The proliferating activity, the degree of differentiation, and the barrier integrity of the repopulated epithelium were studied during the regeneration process at optical and ultrastructural levels with immunocytochemistry and a permeability tracer. Three days after implantation in nude mice, tracheal xenografts were partially repopulated with a flattened nonciliated and poorly differentiated leaky epithelium. By the end of the first week after the graft, cell proliferation produced on the entire surface of the rat trachea an epithelium that was stratified into multiple layers and tightly sealed. During successive weeks, cell proliferation dramatically decreased. Moreover, the epithelium became progressively columnar, secretory, ciliated, and transiently leaky. At 4-5 wk, a fully differentiated pseudostratified functional epithelial barrier impermeable to a low-molecular-weight tracer was reconstituted. The regeneration of a well-differentiated and functional human airway epithelium in rat tracheae grafted in nude mice includes several steps that mimic the regeneration dynamics of airway epithelium after injury.

HCO3(-)-dependent alkalinizing transporter in adult rat ventricular myocytes: characterization and modulation.

The present work was designed to identify the HCO3(-)-dependent alkalinizing carrier in ventricular myocytes of normal and diabetic adult rats and to determine to what extent this system contributes to acid-equivalent extrusion after an intracellular acidification. We also examined the possible influence of intracellular Ca2+ (Cai2-) and glycolytic inhibition on the carrier activation. Intracellular pH (pHi) was recorded using seminaphthorhodafluor-1. The NH4+ method was used to induce an intracellular acid load. Evidence is provided for the existence of a Cl(-)-independent Na(+)-HCO3- cotransport contributing to pHi recovery from an intracellular acid load in ventricular cells of adult rats. Na(+)-HCO3- cotransport accounts for 33% of the total acid-equivalent efflux (JHe) from normal adult myocytes after intracellular acidification at pHi 6.75 in CO2/HCO3(-)-buffered solution. In addition, the activity of this carrier, which is not affected either by decreasing Cai2+ or by inhibiting Ca2+/calmodulin protein kinase II, is down-regulated by inhibition of glycolysis. Under pathophysiological conditions such as diabetes, although total JHe was significantly decreased compared with normal myocytes, JHe carried by Na(+)-HCO3- cotransport remained unchanged. However, because of a decrease in Na+/H+ exchange, the contribution of this carrier to total JHe increased with decreasing pHi (i.e., under conditions that may be associated with an ischemic episode), reaching approximately 58% of total JHe at pHi 6.75 (vs. approximately 33% in normal myocytes.