Different responses of the oral, nasal and lung microbiomes to cigarette smoke.

To examine the role of smoking on the bacterial community composition of the upper and the lower respiratory tract, a monocentric, controlled prospective study was performed, including healthy smokers, ex-smokers and never-smokers. Smokers were further grouped according to their smoking history. Bacterial diversity was analysed using a molecular barcoding approach based on directly extracted DNA. Our study shows for the first time distinct bacterial response patterns in the upper and lower respiratory tract to cigarette smoking leading to a higher abundance of opportunistic pathogens. The clinical significance of these dysbioses for health needs to be further explored.

Nano-Sized Copper (Oxide) on Alumina Granules for Water Filtration: Effect of Copper Oxidation State on Virus Removal Performance.

Virus removal can be successfully achieved based on an electrostatic adsorption mechanism. The key requirement for this process is to develop filter materials that can be produced by low-cost technologies and are suitable in large-scale production for real applications. In this study, we report development of spray-dried alumina granules modified with copper (oxide) nanoparticles and critically assess the effect of copper oxidation state on virus removal capacity. Using plate-shaped alumina as a support material resulted in porous structure, which in turn ensured prolonged contact time of contaminated water with the material. Subsequently, copper (oxide) nanoparticles provided a large number of adsorption sites. Flow experiments revealed that copper(I) oxide and metallic copper were the active phases in virus removal and 99.9% of MS2 bacteriophages could be removed. However, almost no virus removal was observed in the presence of copper(II) oxide. Contrasting virus removal characteristics are associated with the different surface charge of copper species, as determined by zeta potential measurements.

Expanded and updated data and a query pipeline for iBeetle-Base.

The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/.

Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.

The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and ß-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.

Two consecutive large outbreaks of Salmonella Muenchen linked to pig farming in Germany, 2013 to 2014: Is something missing in our regulatory framework?

In 2013, raw pork was the suspected vehicle of a large outbreak (n = 203 cases) of Salmonella Muenchen in the German federal state of Saxony. In 2014, we investigated an outbreak (n = 247 cases) caused by the same serovar affecting Saxony and three further federal states in the eastern part of Germany. Evidence from epidemiological, microbiological and trace-back investigations strongly implicated different raw pork products as outbreak vehicles. Trace-back analysis of S. Muenchen-contaminated raw pork sausages narrowed the possible source down to 54 pig farms, and S. Muenchen was detected in three of them, which traded animals with each other. One of these farms had already been the suspected source of the 2013 outbreak. S. Muenchen isolates from stool of patients in 2013 and 2014 as well as from food and environmental surface swabs of the three pig farms shared indistinguishable pulsed-field gel electrophoresis patterns. Our results indicate a common source of both outbreaks in the primary production of pigs. Current European regulations do not make provisions for Salmonella control measures on pig farms that have been involved in human disease outbreaks. In order to prevent future outbreaks, legislators should consider tightening regulations for Salmonella control in causative primary production settings.

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.

Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

Potato-associated arbuscular mycorrhizal fungal communities in the Peruvian Andes.

The world's fourth largest food crop, potato, originates in the Andes. Here, the community composition of arbuscular mycorrhizal fungi (AMF) associated with potato in Andean ecosystems is described for the first time. AMF were studied in potato roots and rhizosphere soil at four different altitudes from 2,658 to 4,075 m above mean sea level (mamsl) and in three plant growth stages (emergence, flowering, and senescence). AMF species were distinguished by sequencing an approx. 1,500 bp nuclear rDNA region. Twenty species of AMF were identified, of which 12 came from potato roots and 15 from rhizosphere soil. Seven species were found in both roots and soil. Interestingly, altitude affected species composition with the highest altitude exhibiting the greatest species diversity. The three most common colonizers of potato roots detected were Funneliformis mosseae, an unknown Claroideoglomus sp., and Rhizophagus irregularis. Notably, the potato-associated AMF diversity observed in this Andean region is much higher than that reported for potato in other ecosystems. Potato plants were colonized by diverse species from 8 of the 11 Glomeromycota families. Identification of the AMF species is important for their potential use in sustainable management practices to improve potato production in the Andean region.

Spirosoma endophyticum sp. nov., isolated from Zn- and Cd-accumulating Salix caprea.

A Gram-reaction-negative, yellow-pigmented strain, designated EX36(T), was characterized using a polyphasic approach comprising phylogenetic, morphological and genotypic analyses. The endophytic strain was isolated from Zn/Cd-accumulating Salix caprea in Arnoldstein, Austria. Analysis of the 16S rRNA gene demonstrated that the novel strain is most closely related to members of the genus Spirosoma (95 % sequence similarity with Spirosoma linguale). The genomic DNA G+C content was 47.2 mol%. The predominant quinone was and the major cellular fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C16 : 1ω5c, iso-C17 : 0 3-OH and iso-C15 : 0. On the basis of its phenotypic and genotypic properties, strain EX36(T) should be classified as a novel species of the genus Spirosoma, for which the name Spirosoma endophyticum sp. nov. is proposed. The type strain is EX36(T) ( = DSM 26130(T) = LMG 27272(T)).

The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats.

BACKGROUND: The fruit fly Drosophila melanogaster lives in natural habitats and has also long been used as a model organism in biological research. In this study, we used a molecular barcoding approach to analyse the airways microbiome of larvae of D. melanogaster, which were obtained from eggs of flies of the laboratory strain w1118 and from immune deficient flies (NF-kB-K), and from wild-caught flies. To assess intergenerational transmission of microbes, all eggs were incubated under the same semi-sterile conditions. RESULTS: The airway microbiome of larvae from both lab-strains was dominated by the two families Acetobacteraceae and Lactobacillaceae, while larvae from wild-caught flies were dominated by Lactobacillaceae, Anaplasmataceae and Leuconostocaceae. Barcodes linked to Anaplasmataceae could be further assigned to Wolbachia sp., which is a widespread intracellular pathogen in arthropods. For Leuconostoceae, the most abundant reads were assigned to Weissella sp. Both Wolbachia and Weissella affect the development of the insects. Finally, a relative high abundance of Serratia sp. was found in larvae from immune deficient relish-/- compared to w1118 and wild-caught fly airways. CONCLUSIONS: Our results show for the first time that larvae from D. melanogaster harbor an airway microbiome, which is of low complexity and strongly influenced by the environmental conditions and to a lesser extent by the immune status. Furthermore, our data indicate an intergenerational transmission of the microbiome as shaped by the environment.

Oral application of vancomycin alters murine lung microbiome and pulmonary immune responses.

Early life exposures to antibiotics negatively impact respiratory health and are associated with an increased risk of childhood asthma. It is explained that the lung is inclined to develop chronic inflammatory phenotypes due to early antibiotic alteration in the gut microbiome. We investigated whether a gut-targeted antibiotic has an impact on the lung microbiome and on pulmonary immunity. Fourteen-day old C57BL/6 mice were administered with vancomycin via oral gavage for 3 days (1 time/day). Control groups were treated with clarithromycin and phosphate-buffered saline (PBS), respectively. Five days after treatment, the cecum and lung microbiome, and pulmonary immune response were analyzed. Vancomycin treatment decreased the relative abundance of the genera Clostridium XIVa and Alistipes and the family Lachnospiraceae in the cecum. Furthermore, the relative abundance of the family Parabacteroidetes and the genus Lactobacillus were increased, whereas the abundance of the phylum Firmicutes was decreased. In the lung, vancomycin treatment reduced bacteria belonging to Clostridium XIVa and the family Lachnospiraceae as compared to those in the clarithromycin treated group. Lung cells from the vancomycin-treated mice released higher levels of interleukin (IL)-4 and IL-13 compared to those from the PBS group, and increased levels of IL-6, IFN-γ, and TNFα compared to lung cells from the clarithromycin and PBS treated mice. Our pilot study suggests that alteration in the gut microbiome could affect bacterial composition and immunity of the lung hence proposes a gut-lung microbiome axis in early life.

Millisecond photonic sintering of iron oxide doped alumina ceramic coatings.

The sintering of alumina (Al2O3) traditionally occurs at high temperatures (up to ca. 1700 °C) and in significantly long times (up to several hours), which are required for the consolidation of the material by diffusion processes. Here we investigate the photonic sintering of alumina particles using millisecond flash lamp irradiation with extreme heating rates up to 108 K/min. The limitation of the low visible light absorption of alumina is resolved by adding colored α-Fe2O3 nanoparticles, which initiated the grain growth during sintering. After the millisecond-long light pulses from a xenon flash lamp, a bimodal mixture of α-Al2O3 precursor particles was sintered and iron segregation at the grain boundaries was observed. The proposed photonic sintering approach based on doping with colored centers may be extended to other refractory ceramics with low absorption in the visible light range once appropriate high-absorbing dopants are identified.

Using enriched semantic event chains to model human action prediction based on (minimal) spatial information.

Predicting other people's upcoming action is key to successful social interactions. Previous studies have started to disentangle the various sources of information that action observers exploit, including objects, movements, contextual cues and features regarding the acting person's identity. We here focus on the role of static and dynamic inter-object spatial relations that change during an action. We designed a virtual reality setup and tested recognition speed for ten different manipulation actions. Importantly, all objects had been abstracted by emulating them with cubes such that participants could not infer an action using object information. Instead, participants had to rely only on the limited information that comes from the changes in the spatial relations between the cubes. In spite of these constraints, participants were able to predict actions in, on average, less than 64% of the action's duration. Furthermore, we employed a computational model, the so-called enriched Semantic Event Chain (eSEC), which incorporates the information of different types of spatial relations: (a) objects' touching/untouching, (b) static spatial relations between objects and (c) dynamic spatial relations between objects during an action. Assuming the eSEC as an underlying model, we show, using information theoretical analysis, that humans mostly rely on a mixed-cue strategy when predicting actions. Machine-based action prediction is able to produce faster decisions based on individual cues. We argue that human strategy, though slower, may be particularly beneficial for prediction of natural and more complex actions with more variable or partial sources of information. Our findings contribute to the understanding of how individuals afford inferring observed actions' goals even before full goal accomplishment, and may open new avenues for building robots for conflict-free human-robot cooperation.

Cholesterol metabolism promotes B-cell positioning during immune pathogenesis of chronic obstructive pulmonary disease.

The development of chronic obstructive pulmonary disease (COPD) pathogenesis remains unclear, but emerging evidence supports a crucial role for inducible bronchus-associated lymphoid tissue (iBALT) in disease progression. Mechanisms underlying iBALT generation, particularly during chronic CS exposure, remain to be defined. Oxysterol metabolism of cholesterol is crucial to immune cell localization in secondary lymphoid tissue. Here, we demonstrate that oxysterols also critically regulate iBALT generation and the immune pathogenesis of COPD In both COPD patients and cigarette smoke (CS)-exposed mice, we identified significantly upregulated CH25H and CYP7B1 expression in airway epithelial cells, regulating CS-induced B-cell migration and iBALT formation. Mice deficient in CH25H or the oxysterol receptor EBI2 exhibited decreased iBALT and subsequent CS-induced emphysema. Further, inhibition of the oxysterol pathway using clotrimazole resolved iBALT formation and attenuated CS-induced emphysema in vivo therapeutically. Collectively, our studies are the first to mechanistically interrogate oxysterol-dependent iBALT formation in the pathogenesis of COPD, and identify a novel therapeutic target for the treatment of COPD and potentially other diseases driven by the generation of tertiary lymphoid organs.

Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage.

Potato (Solanum tuberosum) is an important staple crop worldwide, it has been cultivated in the Andean Altiplano under low-input farming practices at high altitudes and under harsh environment for centuries. We analyzed secondary metabolite (SM) gene diversity encoded in the potato rhizosphere microbiome during plant growth at three distinct sites located in the Andes at high altitudes by 454-pyrosequencing of non-ribosomal peptide and polyketide biosynthetic genes. Phylogenetic analysis indicated that the majority of rhizosphere SM-encoding sequences differed from previously known sequences and may have distinct ancestors. In particular, actinobacterial methyl-malonyl-CoA transferase and acyl carrier protein from Firmicutes, both involved in the synthesis of SMs, showed widespread distribution of clades which were clearly distinct from sequences deposited in public databases, and only 11% of these sequences could be linked to the production of specific classes of SMs. Although the same cultivar was analyzed, SM gene composition radically differed among plant growth stages and across sites, suggesting a distinct repertoire of SM genes that likely encode diverse SM structures. Also, great diversity of non-ribosomal peptide and polyketide biosynthetic pathways in potato-associated microbiomes in the Andean highlands may represent a rich source of novel natural products.

Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development.

The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The 'stable' component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the 'dynamic' component comprised OTUs that were enriched at specific vegetation stages.

A new plastination technique for head slices containing brain.

The results of plastination of head slices are unsatisfactory when muscles, connective tissue and the brain are impregnated with one and the same resin. The epoxy- or polyester-plastination technique renders transparent either the head without the brain (e.g. E 12) or the brain without the adjacent tissues (e.g. P 40). A new technique is described which allows a homogenous transparency of both the head and the brain.

Concentrations of clindamycin in the mandibular bone of companion animals.

Concentrations of clindamycin in the mandible were determined in 17 dogs and 13 cats with severe plaque, gingivitis/periodontitis, and calculus that were treated orally with clindamycin (11 mg/kg) once daily for 5 days prior to professional teeth cleaning and extractions. The animals were patients at the Dental Department of the Clinic for Surgery and Ophthalmology of the University of Veterinary Medicine in Vienna, Austria. Clindamycin levels were determined during postextractional alveoloplasty. Approximately 1 to 3 mm3 of mandible was removed from the intraradicular septum in multirooted teeth and from the protruding labial/buccal alveolar rim with a small rongeur. The mean concentration of clindamycin was 8.18 microg/g in dogs (range=3.16 to 24.08 microg/g) and 17.43 microg/g in cats (range=2.45 to 51.60 microg/g). The concentration of clindamycin in the mandibles of dogs and cats may be useful to combat infections after periodontal procedures, tooth extractions, or injuries to the mandible.

Impact of long-term statin pretreatment on myocardial damage in ST elevation myocardial infarction (from the AIDA STEMI CMR Substudy).

Nonrandomized studies suggested lower mortality rates with statin pretreatment in patients with acute ST elevation myocardial infarction (STEMI). However, clinical data are still inconclusive and the mechanisms of these presumed beneficial effects require further exploration. Cardiac magnetic resonance (CMR) imaging offers the possibility of studying a variety of markers of myocardial damage and reperfusion injury after myocardial infarction. The aim of this study was to assess a possible link of statin pretreatment with myocardial damage in acute STEMI. The multicenter Abciximab i.v. versus i.c. in ST-elevation Myocardial Infarction CMR substudy enrolled 795 consecutive patients with acute STEMI who underwent primary angioplasty within 12 hours of symptom onset. CMR studies assessing left ventricular ejection fraction, infarct size, microvascular obstruction, area at risk, and myocardial salvage index were performed in a median of 3 days after the clinical event. We performed a retrospective analysis to evaluate the impact of statin pretreatment on myocardial damage. Information on statin pretreatment was available in 791 of 795 patients (99%). Of these, 122 (15%) had long-term statin pretreatment. CMR results showed no significant differences in the area at risk, left ventricular ejection fraction, infarct size, microvascular obstruction, and myocardial salvage index between patients with and without statin pretreatment. Furthermore, no differences in short- and long-term outcomes could be observed. In conclusion, in this CMR study, statin pretreatment in patients with STEMI was not associated with lesser myocardial damage.

The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.

Different regions of the bacterial 16S rRNA gene evolve at different evolutionary rates. The scientific outcome of short read sequencing studies therefore alters with the gene region sequenced. We wanted to gain insight in the impact of primer choice on the outcome of short read sequencing efforts. All the unknowns associated with sequencing data, i.e. primer coverage rate, phylogeny, OTU-richness and taxonomic assignment, were therefore implemented in one study for ten well established universal primers (338f/r, 518f/r, 799f/r, 926f/r and 1062f/r) targeting dispersed regions of the bacterial 16S rRNA gene. All analyses were performed on nearly full length and in silico generated short read sequence libraries containing 1175 sequences that were carefully chosen as to present a representative substitute of the SILVA SSU database. The 518f and 799r primers, targeting the V4 region of the 16S rRNA gene, were found to be particularly suited for short read sequencing studies, while the primer 1062r, targeting V6, seemed to be least reliable. Our results will assist scientists in considering whether the best option for their study is to select the most informative primer, or the primer that excludes interferences by host-organelle DNA. The methodology followed can be extrapolated to other primers, allowing their evaluation prior to the experiment.

Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae).

Adelgids (Insecta: Hemiptera: Adelgidae) are known as severe pests of various conifers in North America, Canada, Europe and Asia. Here, we present the first molecular identification of bacteriocyte-associated symbionts in these plant sap-sucking insects. Three geographically distant populations of members of the Adelges nordmannianae/piceae complex, identified based on coI and ef1alpha gene sequences, were investigated. Electron and light microscopy revealed two morphologically different endosymbionts, coccoid or polymorphic, which are located in distinct bacteriocytes. Phylogenetic analyses of their 16S and 23S rRNA gene sequences assigned both symbionts to novel lineages within the Gammaproteobacteria sharing <92% 16S rRNA sequence similarity with each other and showing no close relationship with known symbionts of insects. Their identity and intracellular location were confirmed by fluorescence in situ hybridization, and the names 'Candidatus Steffania adelgidicola' and 'Candidatus Ecksteinia adelgidicola' are proposed for tentative classification. Both symbionts were present in all individuals of all investigated populations and in different adelgid life stages including eggs, suggesting vertical transmission from mother to offspring. An 85 kb genome fragment of 'Candidatus S. adelgidicola' was reconstructed based on a metagenomic library created from purified symbionts. Genomic features including the frequency of pseudogenes, the average length of intergenic regions and the presence of several genes which are absent in other long-term obligate symbionts, suggested that 'Candidatus S. adelgidicola' is an evolutionarily young bacteriocyte-associated symbiont, which has been acquired after diversification of adelgids from their aphid sister group.