Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome

Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation

Changes in Human Fecal Microbiota Due to Chemotherapy Analyzed by TaqMan-PCR, 454 Sequencing and PCR-DGGE Fingerprinting

BACKGROUND: We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. METHODOLOGY/PRINCIPAL FINDINGS: Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037) following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. CONCLUSIONS/SIGNIFICANCE: Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C. difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics

The use of organic acids to combat Salmonella in poultry: a mechanistic explanation of the efficacy

International audienceSalmonella is a human pathogen that is commonly found in poultry products. It is possible to decrease chicken carcass and egg contaminations by adding organic acids to the feed or drinking water at appropriate times. Medium chain fatty acids are be more antibacterial against Salmonella than short-chain fatty acids. The antibacterial effect of these acids is species specific. Bacteria that are unable to decrease intracellular pH accumulate organic acid anions in accordance with the pH gradient across their cell membranes. The short-chain fatty acid butyrate specifically down-regulates expression of invasion genes in Salmonella at low doses. Also medium-chain fatty acids and propionate decrease the ability of Salmonella to invade epithelial cells, in contrast to acetic acid. Because not all bacteria are affected in a similar fashion by organic acids, it may be possible to use probiotic and prebiotic bacteria to achieve beneficial effects. If diets can be designed to stimulate organic acid production in the caecum, it may be possible to control Salmonella via even easier and more cost effective measures, compared with addition of acids to feed or drinking water

Use of ultrasound by registered nurses—a systematic literature review

© 2017 European Dialysis and Transplant Nurses Association/European Renal Care Association Background: In Western Australia (WA), most stable patients undergoing haemodialysis receive treatment in a satellite setting where no doctors are on-site during treatment hours, so nurses must make critical decisions about fluid removal. Some patients regularly experience adverse events during dialysis (intradialytic), often due to excessive ultrafiltration goals, with intradialytic hypotension being particularly challenging. Ultrasound of the inferior vena cava has been previously demonstrated being a rapid and non-invasive method for volume assessment on haemodialysis patients, thus could hold valuable information for the treating nurse. Aim: This paper examines the existing literature in regards to the use of ultrasound measurements of the inferior vena cava in patients on haemodialysis for objective assessment of their intravascular volume status by renal nurses. Method: A systematic literature review was performed within medical and nursing databases including CINAHL Plus with Full Text, SCOPUS, Web of Science and MEDLINE. Results: Renal nurses are conscious of the significance of intradialytic hypotension and have only limited options for its prevention. Ultrasound of the inferior vena cava could add another objective dimension for intravascular volume assessment and prevention of intradialytic hypotension, but to date renal nurses have not been using this technique. Conclusions: Ultrasound of the inferior vena cava has the potential to assist in defining the ultrafiltration goal for that particular dialysis session, thus reducing the risk of intradialytic hypotension. Additionally, it has potential to change current renal nursing practice when added to clinical nursing assessment methods. Further studies are required to validate this assessment tool carried out by a renal nurse compared with a skilled ultrasonographer