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The effect of feeding live Lactobacillus reuteri cells containing active bile salt hydrolase (BSH) on plasma cholesterol levels was studied in pigs. During an experiment lasting 13 weeks, twenty pigs were fed on a high-fat, high-cholesterol, low-fibre diet for the first 10 weeks, and a regular pig diet for the last 3 weeks. One group of animals received, twice daily, 11.25 (SD 0.16) loglo colony forming units of the potential probiotic bacteria for 4 weeks (from week 3 until week 7). From week 8 onwards, the treated group was again fed on the same diet as the control group without additions. The total faecal Lactobacillus counts were only significantly higher in the treated pigs during the fist 2 weeks of L. reuteri feeding. Based on limited data, it was suggested that the administered LactobacilZus species had caused a temporary shift within the indigenous Lactobacillus population rather than permanently colonizing the intestinal tract. The probiotic feeding brought about significant lowering (P 5 0.05) of total and LDL-cholesterol concentrations in the treated pigs compared with the control pigs, while no change in HDLcholesterol concentration was observed. The data for faecal output of neutral sterols and bile salts were highly variable between the animals of each group, yet they indicated an increased output in the treated pigs. Although the blood cholesterol levels went up in both groups during the 3 weeks following the Lactobacillus administration period, significantly lower serum total and LDL-cholesterol levels were observed in the treated pigs. During the final 3 weeks of normalization to the regular diet, cholesterol concentrations significantly decreased in both animal groups and the differences in total and LDL-cholesterol concentrations between the groups largely disappeared.

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The biofilm phenotype of Pseudomonas aeruginosa enables this opportunistic pathogen to develop resistance to the immune system and antimicrobial agents. Pseudomonas aeruginosa biofilms are generated under varying levels of shear stress, depending on the infection site. In the lung mucus of cystic fibrosis (CF) patients, P. aeruginosa forms matrix-enclosed microcolonies which cause chronic infections representing the major cause of mortality in CF patients. The lung mucus of CF patients is probably characterized by low fluid shear as the main shear-causing factor, i.e. mucociliary clearance, is absent. In this study, the influence of fluid shear on the growth behaviour of P. aeruginosa PA01 was investigated using a low-shear suspension culture device, the rotating wall vessel (RWV). Cultivation in low shear induced a self-aggregating phenotype of P. aeruginosa PA01, resulting in the formation of biofilms in suspension similar to what has been described in CF mucus. The addition of a ceramic bead to the culture medium in the RWV created a higher-shear condition which led to the formation of surface-attached rather than suspension biofilms. In low-shear culture conditions, a significant increase of the rhl N-butanoyl-l-homoserine lactone (C(4)-HSL) directed quorum sensing (QS) system, and the psl polysaccharide synthetic locus was demonstrated using gene expression analysis. Accordingly, the low-shear condition induced a higher production of rhamnolipids, which is controlled by the C(4)-HSL QS-system and is known to play a role in CF lung pathology. These results indicate that fluid shear has an impact on the growth phenotype of P. aeruginosa which might play a role in CF lung infections caused by this bacterium.

The purpose of this research was to address the anoxic oxidation of metallic iron and stainless steel powder by nitrate, nitrite, and anaerobic mixed cultures. In sterile batch reactors, both nitrate and nitrite (10 mg N/L) could chemically oxidize metallic iron, with a concomitant reduction to ammonium. Nitrate or nitrite reduction coupled to metal corrosion was not observed in the case of stainless steel powder. Combination of an anaerobic mixed culture and metallic iron led to (cathodically produced) H2 consumption and a complete nitrate or nitrite reduction (mainly to NH4 +). This caused a slightly enhanced metal oxidation. In the case of stainless steel, corrosion caused by denitrifying microorganisms was evidenced by data on nitrate/nitrite ions and solubilized iron. Experiments with increasing nitrite concentrations indicated that nitrite in the range of 50 mg of NO2 - -N/L inhibited the corrosion processes. Moreover, at concentrations above 140 mg NO2 - -N/L, a significant production of nitric oxide (NO) was detected. Differences between iron and stainless steel powder at low concentrations of nitrate or nitrite are most probably due to differences in kinetics:  metallic iron exhibited faster chemical than biological reactions as opposed to stainless steel. It is postulated that the inhibitory effect of higher nitrite concentrations could partly be due to the chemical formation of NO and its toxic effect on the microorganisms acting at the steel surface.

No abstract

BackgroundThe Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels.ResultsHere we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website (https://www.bioconductor.org/packages/release/bioc/html/ENmix.html).ConclusionsRELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3426-3) contains supplementary material, which is available to authorized users.

The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field of respiratory allergy.