Exceptional points in optical systems: A resonant-state expansion study

Exceptional points (EPs) in open optical systems are rigorously studied using the resonant-state expansion (RSE). A spherical resonator, specifically a homogeneous dielectric sphere in a vacuum, perturbed by two point-like defects which break the spherical symmetry and bring the optical modes to EPs, is used as a worked example. The RSE is a non-perturbative approach encoding the information about an open optical system in matrix form in a rigorous way, and thus offering a suitable tool for studying its EPs. These are simultaneous degeneracies of the eigenvalues and corresponding eigenfunctions of the system, which are rigorously described by the RSE and illustrated for perturbed whispering-gallery modes (WGMs). An exceptional arc, which is a line of adjacent EPs, is obtained analytically for perturbed dipolar WGMs. Perturbation of high-quality WGMs with large angular momentum and their EPs are found by reducing the RSE equation to a two-state problem by means of an orthogonal transformation of a large RSE matrix. WGM pairs of opposite chirality away from EPs are shown to have the same chirality at EPs. This chirality can be observed in circular dichroism measurements, as it manifested itself in a squared-Lorentzian part of the optical spectra, which we demonstrate here analytically and numerically in the Purcell enhancement factor for the perturbed dipolar WGMs.Comment: 24 pages. 13 figures (3 in Appendix). To be submitted in Physical Review A. Authors: K S Netherwood (primary author), H Riley (initial concept work), E A Muljarov (theme leader

Evolutionary, ecological and biotechnological perspectives on plasmids resident in the human gut mobile metagenome

Numerous mobile genetic elements (MGE) are associated with the human gut microbiota and collectively referred to as the gut mobile metagenome. The role of this flexible gene pool in development and functioning of the gut microbial community remains largely unexplored, yet recent evidence suggests that at least some MGE comprising this fraction of the gut microbiome reflect the co-evolution of host and microbe in the gastro-intestinal tract. In conjunction, the high level of novel gene content typical of MGE coupled with their predicted high diversity, suggests that the mobile metagenome constitutes an immense and largely unexplored gene-space likely to encode many novel activities with potential biotechnological or pharmaceutical value, as well as being important to the development and functioning of the gut microbiota. Of the various types of MGE that comprise the gut mobile metagenome, plasmids are of particular importance since these elements are often capable of autonomous transfer between disparate bacterial species, and are known to encode accessory functions that increase bacterial fitness in a given environment facilitating bacterial adaptation. In this article current knowledge regarding plasmids resident in the human gut mobile metagenome is reviewed, and available strategies to access and characterize this portion of the gut microbiome are described. The relative merits of these methods and their present as well as prospective impact on our understanding of the human gut microbiota is discussed

Impact of digestive and oropharyngeal decontamination on the intestinal microbiota in ICU patients

Selective digestive microbial decontamination (SDD) is hypothesized to benefit patients in intensive care (ICU) by suppressing Gram-negative potential pathogens from the colon without affecting the anaerobic intestinal microbiota. The purpose of this study was to provide more insight to the effects of digestive tract and oropharyngeal decontamination on the intestinal microbiota by means of a prospective clinical trial in which faecal samples were collected from ICU patients for intestinal microbiota analysis. The faecal samples were collected from ICU patients enrolled in a multicentre trial to study the outcome of SDD and selective oral decontamination (SOD) in comparison with standard care (SC). Fluorescent in situ hybridization (FISH) was used to analyze the faecal microbiota. The numbers of bacteria from different bacterial groups were compared between the three regimens. The total counts of bacteria per gram faeces did not differ between regimens. The F. prausnitzii group of bacteria, representing an important group among intestinal microbiota, was significantly reduced in the SDD regimen compared to the SC and SOD. The Enterobacteriaceae were significantly suppressed during SDD compared to both SOD and SC; enterococci increased in SDD compared to both other regimens. The composition of the intestinal microbiota is importantly affected by SDD. The F. prausnitzii group was significantly suppressed during SDD. This group of microbiota is a predominant producer of butyrate, the main energy source for colonocytes. Reduction of this microbiota is an important trade-off while reducing gram-negative bacteria by SDD

An investigation of horizontal transfer of feed introduced DNA to the aerobic microbiota of the gastrointestinal tract of rats

Background: Horizontal gene transfer through natural transformation of members of the microbiota of the lower gastrointestinal tract (GIT) of mammals has not yet been described. Insufficient DNA sequence similarity for homologous recombination to occur has been identified as the major barrier to interspecies transfer of chromosomal DNA in bacteria. In this study we determined if regions of high DNA similarity between the genomes of the indigenous bacteria in the GIT of rats and feed introduced DNA could lead to homologous recombination and acquisition of antibiotic resistance genes. Results: Plasmid DNA with two resistance genes (nptII and aadA) and regions of high DNA similarity to 16S rRNA and 23S rRNA genes present in a broad range of bacterial species present in the GIT, where constructed and added to standard rat feed. Six rats, with a normal microbiota, were fed DNA containing pellets daily over four days before sampling of the microbiota from the different GI compartments (stomach, small intestine, cecum and colon). In addition, two rats were included as negative controls. Antibiotic resistant colonies growing on selective media were screened for recombination with feed introduced DNA by PCR targeting unique sites in the putatively recombined regions. Conclusions: The analyses showed that extensive ingestion of DNA (100 \ub5g plasmid) per day did not lead to increased proportions of kanamycin resistant bacteria, nor did it produce detectable transformants among the aerobic microbiota examined for 6 rats (detection limit <1 transformant per 1.1 x 108 cultured bacteria). The key methodological challenges to HGT detection in animal feedings trials are identified and discussed

Bacterial Intestinal Flora Associated with Enterotoxaemia in Belgian Blue Calves

The enterotoxaemia syndrome in Belgian Blue calves is characterised by a high case fatality rate, sudden death, lesions of haemorrhagic enteritis of the small intestine and, quite often an absence of other clinical signs but its cause has not been yet identified. As a first step in this identification, the aerobic and anaerobic intestinal flora of a population of 78 calves, originating from farms located in southern Belgium and that died in circumstances defined as "calf enterotoxaemia" (study population) and of 64 calves that died in other circumstances (control population) were studied qualitatively and quantitatively. The colonies were identified after subcultures with appropriate API sugar sets. Anaerobically Clostridium perfringens was isolated in higher numbers (mean values of 10(7)-10(7.5) colony forming units (CFU) versus 10(4)-10(5) CFU per ml of intestinal content) and from more animals (79 versus 19%) in the study population than in the control population, although individual results from both populations could overlap. Other clostridial species, i.e. mainly urease-negative C. sordellii and C. bifermentans, were isolated in high numbers (>10(6) CFU per ml of intestinal content) from a few animals in the study population only. All but one of the 705 C. perfringens isolates from both populations belonged to the A toxin type and none of the urease-negative C. sordellii was toxigenic. Gram-negative anaerobes were not isolated in high numbers from any of the samples. Aerobically beta-haemolytic E. coli were significantly more frequent among the study population, but were isolated from only 25% of the animals. Salmonella Typhimurium was isolated from only two animals in the study population. Less than 1% of the E. coli isolated were verotoxigenic and one-third were necrotoxigenic. At this stage only non-enterotoxigenic type A C. perfringens are thus statistically associated with the enterotoxaemia syndrome in Belgian Blue calves and fulfil the first of the Koch's postulates