Distribution and diversity of bacterial secretion systems across metagenomic datasets.

Bacteria can manipulate their surrounding environment through the secretion of proteins into other living organisms and into the extracellular milieu. In Gram stain negative bacteria this process is mediated by different types of secretion systems from type I through type VI secretion system (T1SS-T6SS). In this study the prevalence of these secretion systems in 312 publicly available microbiomes derived from a wide range of ecosystems was investigated by a gene-centric approach.

Characterization of the SPI-1 and Rsp type three secretion systems in Pseudomonas fluorescens F113.

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar beet rhizosphere. The recent annotation of the F113 genome sequence has revealed that this strain encodes a wide array of secretion systems, including two complete type three secretion systems (T3SSs) belonging to the Hrp1 and SPI-1 families. While Hrp1 T3SSs are frequently encoded in other P.

Subtilomycin: a new lantibiotic from Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans.

Bacteriocins are attracting increased attention as an alternative to classic antibiotics in the fight against infectious disease and multidrug resistant pathogens. Bacillus subtilis strain MMA7 isolated from the marine sponge Haliclona simulans displays a broad spectrum antimicrobial activity, which includes Gram-positive and Gram-negative pathogens, as well as several pathogenic Candida species. This activity is in part associated with a newly identified lantibiotic, herein named as subtilomycin.

Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.

Background: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application.

Molecular evolution of LysR-type transcriptional regulation in Pseudomonas aeruginosa.

Signal perception and transduction through tightly coordinated circuits is integral to the survival and persistence of microbes in diverse ecological niches. The capacity to adapt to changes in the environment is central to their ability to thrive under adverse circumstances. Signal dependent transcriptional regulators are a key mechanism through which microbes assimilate environmental cues and mediate the appropriate adaptive response.

Physico-chemical characteristics and methanogen communities in swine and dairy manure storage tanks: spatio-temporal variations and impact on methanogenic activity.

Greenhouse gas emissions represent a major environmental problem associated with the management of manure from the livestock industry. Methane is the primary GHG emitted during manure outdoor storage. In this paper, the variability of two swine and two dairy manure storage tanks was surveyed, in terms of physico-chemical and microbiological parameters.

[Anal intraepithelial neoplasia].

Anal intraepithelial lesions are caused by chronic infection with oncogenic types of human papillomavirus. Their incidence and prevalence are increasing, especially among patients with HIV infection. Their natural history is not well known, but high-grade intraepithelial lesions seem to have an important risk to progress to squamous cell carcinoma.

Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples.

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step.

Diagnostic yield of capsule endoscopy in refractory celiac disease.

Objectives: Capsule endoscopy (CE) allows for the assessment of the small bowel in numerous intestinal diseases, including celiac disease (CD). The main advantage of CE is the complete visualization of the intestinal mucosal surface. The objective of this study was to investigate whether CE can predict the severity of CD and detect complications.

N-acetylcysteine for the prevention of stricture after circumferential endoscopic submucosal dissection of the esophagus: a randomized trial in a porcine model.

Background: Circumferential endoscopic submucosal dissection (CESD) of the esophagus would allow for both the eradication of Barrett's esophagus and its related complications, such as advanced neoplasia. However, such procedures generally induce inflammatory repair resulting in a fibrotic stricture. N-acetylcysteine (NAC) is an antioxidant that has shown some efficacy against pulmonary and hepatic fibrosis.

Genome sequence of the biocontrol strain Pseudomonas fluorescens F113.

Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) that has biocontrol activity against fungal plant pathogens and is a model for rhizosphere colonization. Here, we present its complete genome sequence, which shows that besides a core genome very similar to those of other strains sequenced within this species, F113 possesses a wide array of genes encoding specialized functions for thriving in the rhizosphere and interacting with eukaryotic organisms.

Nutritional status affects treatment tolerability and survival in metastatic colorectal cancer patients: results of an AGEO prospective multicenter study.

Background: The possible impact of malnutrition on the tolerability and efficacy of modern chemotherapy regimens for metastatic colorectal cancer (mCRC) is unclear.

Methods: In this prospective, cross-sectional, multicenter study, we collected demographic, oncological and nutritional data for all consecutive mCRC patients during a 14-day period in eight hospitals. Nutritional status was assessed with the nutritional risk index (NRI), and patients were classified as severely malnourished when NRI was <83.

Methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks.

Greenhouse gas emissions represent a major problem associated with manure management in the livestock industry. A prerequisite to mitigate methane emissions occurring during manure storage is a clearer understanding of how the microbial consortia involved in methanogenesis function. Here, we have examined manure stored in outdoor tanks from two different farms, at different locations and depths.

Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists.

Bacteria and fungi can form a range of physical associations that depend on various modes of molecular communication for their development and functioning. These bacterial-fungal interactions often result in changes to the pathogenicity or the nutritional influence of one or both partners toward plants or animals (including humans). They can also result in unique contributions to biogeochemical cycles and biotechnological processes.

A novel fingerprint method to assess the diversity of methanogens in microbial systems.

Understanding the ecology of methanogens in natural and engineered environments is a prerequisite to predicting or managing methane emissions. In this study, a novel high-throughput fingerprint method was developed for determining methanogen diversity and relative abundance within environmental samples. The method described here, designated amplicon length heterogeneity PCR of the mcrA gene (LH-mcrA), is based on the natural length variation in the mcrA gene.

Duodenal gangliocytic paraganglioma with lymph node metastasis and an 8-year follow-up: a case report.

Gangliocytic paraganglioma (GP) is a rare tumor, usually located in the second part of the duodenum. On pathological examination, GP is characterized by the association of the histological features of paragangliomas, ganglioneuromas, and carcinoid tumors. Classical clinical presentations are upper gastrointestinal bleeding and abdominal pain.

Sensitive determination of glyoxal, methylglyoxal and hydroxyacetaldehyde in environmental water samples by using dansylacetamidooxyamine derivatization and liquid chromatography/fluorescence.

In this study we improved the dansylacetamidooxyamine (DNSAOA)-LC-fluorescence method for the determination of aqueous-phase glyoxal (GL), methylglyoxal (MG) and hydroxyacetaldehyde (HA). As derivatization of dicarbonyls can potentially lead to complex mixtures, a thorough study of the reaction patterns of GL and MG with DNSAOA was carried out. Derivatization of GL and MG was shown to follow the kinetics of successive reactions, yielding predominantly doubly derivatized compounds.

Kinetics and reversibility of micropollutant sorption in sludge.

The fate of micropollutants throughout wastewater treatment systems is highly dependent on their sorption interactions with sludge matter. In this study, both the sorption and desorption kinetics of polycyclic aromatic hydrocarbons (PAHs) in activated sludge were shown to be very rapid in comparison to biodegradation kinetics. It was concluded that PAH transfer does not limit their biodegradation and that their fate is governed by the sorption/desorption equilibrium state.

Genomic analysis of the type VI secretion systems in Pseudomonas spp.: novel clusters and putative effectors uncovered.

Bacteria encode multiple protein secretion systems that are crucial for interaction with the environment and with hosts. In recent years, attention has focused on type VI secretion systems (T6SSs), which are specialized transporters widely encoded in Proteobacteria. The myriad of processes associated with these secretion systems could be explained by subclasses of T6SS, each involved in specialized functions.