Commensal or pathogen - a challenge to fulfil Koch's Postulates

1. Infectious diseases have a large impact on poultry health and economics. Elucidating the pathogenesis of a certain disease is crucial to implement control strategies.

2. Multiplication of a pathogen and its characterisation in vitro are basic requirements to perform experimental studies. However, passaging of the pathogen in vitro can influence the pathogenicity, a process targeted for live vaccine development, but limits the reproduction of clinical signs.

3. Numerous factors can influence the outcome of experimental infections with some importance on the pathogen, application route and host as exemplarily outlined for Histomonas meleagridis, Gallibacterium anatis and fowl aviadenoviruses (FAdVs).

4. In future, more comprehensive and detailed settings are needed to obtain as much information as possible from animal experiments. Processing of samples with modern diagnostic tools provides the option to closely monitor the host–pathogen interaction.

Histomonosis in poultry: previous and current strategies for prevention and therapy

Histomonosis is a parasitic disease of poultry with worldwide prevalence. The disease can cause morbidity and mortality in chicken and turkey flocks entailing severe economic losses. In the first half of the last century, there was a high demand to control histomonosis as the turkey industry was severely affected by the disease. Consequently, numerous chemical compounds were tested for their efficacy against Histomonas meleagridis with varying outcomes, that are summarized and specified in this review. At the same time, preliminary attempts to protect birds with cultured histomonads indicated the possibility of vaccination. Several years ago antihistomonal drugs were banned in countries with tight regulations on pharmaceuticals in order to comply with the demand of consumer protection. As a consequence, outbreaks of histomonosis in poultry flocks increased and the disease became endemic again. New approaches to prevent and treat histomonosis are, therefore, needed and recently performed studies focused on various areas to combat the disease, from alternative chemotherapeutic substances to plant-derived compounds until vaccination, altogether reviewed here. Considering existing regulations and the overall outcome of experimental studies, it can be concluded that vaccination is very promising, despite the fact that various challenges need to be addressed until the first ever developed vaccine based upon live flagellates in human or bird medicine can be marketed.

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities

Mangroves are complex and dynamic ecosystems highly dependent on diverse microbial activities. In the last decades, these ecosystems have been exposed to and affected by diverse human activities, such as waste disposal and accidental oil spills. Complex microbial communities inhabiting the soil and sediment of mangroves comprise microorganisms that have developed mechanisms to adapt to organic and inorganic contaminants. The resistance of these microbes to contaminants is an attractive property and also the reason why soil and sediment living microorganisms and their enzymes have been considered promising for environmental detoxification. The aim of the present study was to identify active microbial genes in heavy metals, i.e., Cu, Zn, Cd, Pb and Hg, and antibiotic resistomes of polluted and pristine mangrove sediments through the comparative analysis of metatranscriptome data. The concentration of the heavy metals Zn, Cr, Pb, Cu, Ni, Cd, and Hg and abundance of genes and transcripts involved in resistance to toxic compounds (the cobalt-zinc-cadmium resistance protein complex; the cobalt-zinc-cadmium resistance protein CzcA and the cation efflux system protein CusA) have been closely associated with sites impacted with petroleum, sludge and other urban waste. The taxonomic profiling of metatranscriptome sequences suggests that members of Gammaproteobacteria and Deltaproteobacteria classes contribute to the detoxification of the polluted soil. Desulfobacterium autotrophicum was the most abundant microorganism in the oil-impacted site and displayed specific functions related to heavy metal resistance, potentially playing a key role in the successful persistence of the microbial community of this site.

Observation of B→D(*) π^(+)π^(-)ℓ^(-)ν Decays in e^(+)e^(-) Collisions at the Υ(4S) Resonance

We report on measurements of the decays of B¯ mesons into the semileptonic final states B¯→D^(*)π^(+)π^(-)ℓ^(-)ν¯, where D^(*) represents a D or D^(*) meson and ℓ^(-) is an electron or a muon. These measurements are based on 471×10^(6) BB ¯ pairs recorded with the BABAR detector at the SLAC asymmetric B factory PEP-II. We determine the branching fraction ratios R_{π^{+}π^{-}}^{(*)}=B(B[over ¯]→D^{(*)}π^{+}π^{-}ℓ^{-}ν[over ¯])/B(B[over ¯]→D^{(*)}ℓ^{-}ν[over ¯]) using events in which the second B meson is fully reconstructed. We find R_{π^{+}π^{-}}=0.067±0.010±0.008 and R_{π^{+}π^{-}}^{*}=0.019±0.005±0.004, where the first uncertainty is statistical and the second is systematic. Based on these results and assuming isospin invariance, we estimate that B[over ¯]→D^{(*)}ππℓ^{-}ν[over ¯] decays, where π denotes either a π^{±} and π^{0} meson, account for up to half the difference between the measured inclusive semileptonic branching fraction to charm hadrons and the corresponding sum of previously measured exclusive branching fractions.

First Observation of CP Violation in B[over ¯]^{0}→D_{CP}^{(*)}h^{0} Decays by a Combined Time-Dependent Analysis of BABAR and Belle Data

We report a measurement of the time-dependent CP asymmetry of B[over ¯]^{0}→D_{CP}^{(*)}h^{0} decays, where the light neutral hadron h^{0} is a π^{0}, η, or ω meson, and the neutral D meson is reconstructed in the CP eigenstates K^{+}K^{-}, K_{S}^{0}π^{0}, or K_{S}^{0}ω. The measurement is performed combining the final data samples collected at the ϒ(4S) resonance by the BABAR and Belle experiments at the asymmetric-energy B factories PEP-II at SLAC and KEKB at KEK, respectively. The data samples contain (471±3)×10^{6} BB[over ¯] pairs recorded by the BABAR detector and (772±11)×10^{6} BB[over ¯] pairs recorded by the Belle detector. We measure the CP asymmetry parameters -η_{f}S=+0.66±0.10(stat)±0.06(syst) and C=-0.02±0.07(stat)±0.03(syst). These results correspond to the first observation of CP violation in B[over ¯]^{0}→D_{CP}^{(*)}h^{0} decays. The hypothesis of no mixing-induced CP violation is excluded in these decays at the level of 5.4 standard deviations.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes

Grapes harbor complex microbial communities. It is well known that yeasts, typically Saccharomyces cerevisiae, and bacteria, commonly the lactic acid fermenting Oenococcus oeni, work sequentially during primary and secondary wine fermentation. In addition to these main players, several microbes, often with undesirable effects on wine quality, have been found in grapes and during wine fermentation. However, still little is known about the dynamics of the microbial community during the fermentation process. In previous studies culture dependent methods were applied to detect and identify microbial organisms associated with grapes and grape products, which resulted in a picture that neglected the non-culturable fraction of the microbes. To obtain a more complete picture of how microbial communities change during grape fermentation and how different fermentation techniques might affect the microbial community composition, we employed next-generation sequencing (NGS)—a culture-independent method. A better understanding of the microbial dynamics and their effect on the final product is of great importance to help winemakers produce wine styles of consistent and high quality. In this study, we focused on the bacterial community dynamics during wine vinification by amplifying and sequencing the hypervariable V1–V3 region of the 16S rRNA gene—a phylogenetic marker gene that is ubiquitous within prokaryotes. Bacterial communities and their temporal succession was observed for communities associated with organically and conventionally produced wines. In addition, we analyzed the chemical characteristics of the grape musts during the organic and conventional fermentation process. These analyses revealed distinct bacterial population with specific temporal changes as well as different chemical profiles for the organically and conventionally produced wines. In summary these results suggest a possible correlation between the temporal succession of the bacterial population and the chemical wine profiles.

[Glottis injection to improve voice function : Review of more than 500 operations]

BACKGROUND

Hoarseness due to insufficient glottal closure can be treated by injection laryngoplasty (augmentation). Vocal fold injections can be performed as an in-office procedure or under general anesthesia. As injection materials have recently improved and different injection approaches are available, injection laryngoplasties are performed much more frequently.

OBJECTIVES

Advantages and disadvantages of injection materials, laryngeal approaches, and differential indications are described.

MATERIALS AND METHODS

Literature research and experience of more than 500 laryngeal injection procedures are provided.

RESULTS AND CONCLUSIONS

Sophisticated use of available injection materials can provide a satisfying improvement of voice function with minimal patient discomfort. Adequate indication is mandatory for a favorable outcome. Further improvement regarding biocompatibility and the duration of injection materials is desirable.

Search for Long-Lived Particles in e+ e- Collisions

We present a search for a neutral, long-lived particle L that is produced in e+ e- collisions and decays at a significant distance from the e+ e- interaction point into various flavor combinations of two oppositely charged tracks. The analysis uses an e+ e- data sample with a luminosity of 489.1  fb(-1) collected by the BABAR detector at the ϒ(4S), ϒ(3S), and ϒ(2S) resonances and just below the ϒ(4S). Fitting the two-track mass distribution in search of a signal peak, we do not observe a significant signal, and set 90% confidence level upper limits on the product of the L production cross section, branching fraction, and reconstruction efficiency for six possible two-body L decay modes as a function of the L mass. The efficiency is given for each final state as a function of the mass, lifetime, and transverse momentum of the candidate, allowing application of the upper limits to any production model. In addition, upper limits are provided on the branching fraction B(B→XsL), where Xs is a strange hadronic system.

Elviz - exploration of metagenome assemblies with an interactive visualization tool

Background

Metagenomics, the sequencing of DNA collected from an entire microbial community, enables the study of natural microbial consortia in their native habitats. Metagenomics studies produce huge volumes of data, including both the sequences themselves and metadata describing their abundance, assembly, predicted functional characteristics and environmental parameters. The ability to explore these data visually is critically important to meaningful biological interpretation. Current genomics applications cannot effectively integrate sequence data, assembly metadata, and annotation to support both genome and community-level inquiry.

Results

Elviz (Environmental Laboratory Visualization) is an interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing.

Conclusions

Compared to the current alternative of generating a succession of static figures, Elviz can greatly accelerate the speed of metagenome analysis. Elviz can be used to explore both user-submitted datasets and numerous metagenome studies publicly available at the Joint Genome Institute (JGI). Elviz is freely available at http://genome.jgi.doe.gov/viz and runs on most current web-browsers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0566-4) contains supplementary material, which is available to authorized users.

A single strain of Tetratrichomonas gallinarum causes fatal typhlohepatitis in red-legged partridges (Alectoris rufa) to be distinguished from histomonosis

Typhlohepatitis was observed in a flock of 2500 red-legged partridges in Great Britain, characterized by the sudden deaths of 15 birds within 2 days. Necropsy of five dead birds revealed severe lesions in the caeca with thickened caecal walls, a reddened lining and bloody contents. The livers contained multiple miliary lesions and similar pathological changes were found in the spleens of some birds. Microscopic examination of intestinal contents showed the occurrence of coccidial oocysts in two partridges. Different methods for the detection of bacteria from liver and intestine samples were conducted without positive results. Histopathological examination revealed the presence of protozoan parasites in the caecum, liver and spleen of the affected birds. In situ hybridization (ISH) for the detection of trichomonads resulted in positive findings and polymerase chain reaction (PCR) confirmed the presence of Tetratrichomonas gallinarum in the lesions. Additionally, archived tissues of red-legged partridges from different flocks suffering from severe typhlohepatitis in Great Britain in 2008 and 2009 were re-investigated by ISH and PCR. Beside the sporadic occurrence of histomonosis, in most of the cases trichomonads were detected by ISH in the caecum and liver of affected birds. Furthermore, dissemination of the flagellate into the lung and bursa of Fabricius could be demonstrated. Analyses of T. gallinarum DNA obtained from the different cases resulted in homologous nucleotide sequences. Altogether, the results demonstrate the circulation of a virulent strain of T. gallinarum in reared red-legged partridges.

Clinical signs and progression of lesions in the gizzard are not influenced by inclusion of ground oats or whole wheat in the diet following experimental infection with pathogenic fowl adenovirus serotype 1

In the present study the effects of dietary gizzard stimulation on the development and severity of adenoviral gizzard erosion were investigated. For this purpose, specific pathogen-free broilers were divided into six groups, investigating the influence of an oat-containing diet with higher fibre content, a whole wheat-containing diet and a control diet of nearly identical composition, but containing ground wheat. For each feed administered, one group of birds was experimentally infected on the 10th day of age by the oral route with virulent fowl adenovirus serotype 1 (FAdV-1), recently proven to induce gizzard erosions, while the respective negative control groups remained uninfected. Experimental feed was administered from 2 days post-infection onwards. No significant differences on gizzard health or in weight gain could be detected between uninfected control groups or between FAdV-1 infected groups that received different experimental feed. However, independent of the supplied diet, a significantly reduced weight gain was noted from 7 days post-infection onwards in FAdV-1 infected broilers compared to uninfected birds that received the same diet. Macroscopically, discolouration and erosion of the koilin layer and inflammation of the gizzard mucosa were observed in all FAdV-1 infected groups. Histologically, necrosis, degeneration of gizzard epithelial cells and multiple basophilic intranuclear inclusion bodies were observed. In summary, after experimental infection with FAdV-1 development of gizzard erosion in chickens was not influenced by the feeding regimes investigated. Therefore, it is unlikely that dietary gizzard stimulation influences the outcome of adenoviral gizzard erosion in vertically infected broilers.

Study of CP asymmetry in B^{0}-B[over ¯]^{0} mixing with inclusive dilepton events

We present a measurement of the asymmetry A_{CP} between same-sign inclusive dilepton samples ℓ^{+}ℓ^{+} and ℓ^{-}ℓ^{-} (ℓ=e, μ) from semileptonic B decays in ϒ(4S)→BB[over ¯] events, using the complete data set recorded by the BABAR experiment near the ϒ(4S) resonance, corresponding to 471×10^{6} BB[over ¯] pairs. The asymmetry A_{CP} allows comparison between the mixing probabilities P(B[over ¯]^{0}→B^{0}) and P(B^{0}→B[over ¯]^{0}), and therefore probes CP and T violation. The result, A_{CP}=[-3.9±3.5(stat)±1.9(syst)]×10^{-3}, is consistent with the standard model expectation.

Observation of two new Ξ(b)(-) baryon resonances

Two structures are observed close to the kinematic threshold in the Ξ(b)(0)π(-) mass spectrum in a sample of proton-proton collision data, corresponding to an integrated luminosity of 3.0  fb(-1), recorded by the LHCb experiment. In the quark model, two baryonic resonances with quark content bds are expected in this mass region: the spin-parity J(P)=(1/2)(+) and J(P)=(3/2)(+) states, denoted Ξ(b)('-) and Ξ(b)(*-). Interpreting the structures as these resonances, we measure the mass differences and the width of the heavier state to be m(Ξ(b)('-))-m(Ξ(b)(0))-m(π(-))=3.653±0.018±0.006  MeV/c(2), m(Ξ(b)(*-))-m(Ξ(b)(0))-m(π(-))=23.96±0.12±0.06  MeV/c(2), Γ(Ξ(b)(*-))=1.65±0.31±0.10  MeV, where the first and second uncertainties are statistical and systematic, respectively. The width of the lighter state is consistent with zero, and we place an upper limit of Γ(Ξ(b)('-))<0.08  MeV at 95% confidence level. Relative production rates of these states are also reported.

Composition of diet modifies colonization dynamics of Campylobacter jejuni in broiler chickens

AIMS

To evaluate the impact of diet composition on colonization dynamics of Camp. jejuni and on related physiological parameters in the chicken intestine.

METHODS AND RESULTS

A total of 54 1-day-old Ross 308 broiler chicks were randomly divided into three isocaloric and isonitrogenous dietary groups: maize-based (MB), wheat-based (WB) diet and wheat-based diet with NSP-degrading enzyme supplementation (WBES). Chickens were orally infected with 10(8)  CFU Camp. jejuni on day 14, and samples (n = 6) were collected on 7, 14 and 21 days postinfection (DPI), respectively. Colony forming units of Camp. jejuni of caecum and jejunum, short-chain fatty acid (SCFA) concentrations, pH values of the caecum, jejunal histomorphology and viscosity of jejunal chymus were measured. In case of WBES diet, lower Camp. jejuni colonization 14 DPI, higher jejunal viscosity, higher total SCFA concentrations in the caecum and enhanced jejunal histomorphology were observed compared to those measured in chickens fed MB diet.

CONCLUSIONS

The WBES diet altered Camp. jejuni colonization dynamics in the chicken intestine which resulted by higher SCFA concentrations in the caecum and by the change of gut morphology.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study proves that diet composition can modify Camp. jejuni colonization depending on sampling time point postinfection.

Search for a dark photon in e(+)e(-) collisions at BABAR

Dark sectors charged under a new Abelian interaction have recently received much attention in the context of dark matter models. These models introduce a light new mediator, the so-called dark photon (A^{'}), connecting the dark sector to the standard model. We present a search for a dark photon in the reaction e^{+}e^{-}→γA^{'}, A^{'}→e^{+}e^{-}, μ^{+}μ^{-} using 514  fb^{-1} of data collected with the BABAR detector. We observe no statistically significant deviations from the standard model predictions, and we set 90% confidence level upper limits on the mixing strength between the photon and dark photon at the level of 10^{-4}-10^{-3} for dark photon masses in the range 0.02-10.2  GeV. We further constrain the range of the parameter space favored by interpretations of the discrepancy between the calculated and measured anomalous magnetic moment of the muon.