Reconciliation between operational taxonomic units and species boundaries

The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches. Clustering those amplicon sequencing reads into operational taxonomic units (OTUs) using a fixed cut-off is a commonly used approach to estimate microbial diversity. A 97% threshold was chosen with the intended purpose that resulting OTUs could be interpreted as a proxy for bacterial species. Our results show that the robustness of such a generalised cut-off is questionable when applied to short amplicons only covering one or two variable regions of the 16S rRNA gene. It will lead to biases in diversity metrics and makes it hard to compare results obtained with amplicons derived with different primer sets. The method introduced within this work takes into account the differential evolutional rates of taxonomic lineages in order to define a dynamic and taxonomic-dependent OTU clustering cut-off score. For a taxonomic family consisting of species showing high evolutionary conservation in the amplified variable regions, the cut-off will be more stringent than 97%. By taking into consideration the amplified variable regions and the taxonomic family when defining this cut-off, such a threshold will lead to more robust results and closer correspondence between OTUs and species. This approach has been implemented in a publicly available software package called DynamiC

Chronic lameness caused by vascular compression of the iliac artery and vein by a malignant melanoma in the pelvis of a grey Spanish gelding

An 11‐year‐old grey Spanish gelding was presented with chronic lameness of the right hindlimb, with abduction of the limb during the swing phase. Based on a comprehensive lameness examination, the problem was localised to the pelvic region. Rectal and ultrasonographic examinations revealed a mass in the pelvic region in close association with the iliac artery and vein, and ultrasonographic indications of vascular compression. Considering the clinical presentation of a grey middle‐aged horse with multifocal melanoma‐like nodules at the level of the perineum, tail base, preputium and penis, a malignant melanoma with secondary vascular or neurological compression was suspected. Post‐mortem and histological examination confirmed the diagnosis of malignant melanoma with vascular compression of the iliac artery and vein and infiltrative growth in the iliac vein

The type and concentration of inoculum and substrate as well as the presence of oxygen impact the water kefir fermentation process

Eleven series of water kefir fermentation processes differing in the presence of oxygen and the type and concentration of inoculum and substrate, were followed as a function of time to quantify the impact of these parameters on the kinetics of this process via a modeling approach. Increasing concentrations of the water kefir grain inoculum increased the water kefir fermentation rate, so that the metabolic activity during water kefir fermentation was mainly associated with the grains. Water kefir liquor could also be used as an alternative means of inoculation, but the resulting fermentation process progressed slower than the one inoculated with water kefir grains, and the production of water kefir grain mass was absent. Substitution of sucrose with glucose and/or fructose reduced the water kefir grain growth, whereby glucose was fermented faster than fructose. Lacticaseibacillus paracasei (formerly known as Lactobacillus paracasei), Lentilactobacillus hilgardii (formerly known as Lactobacillus hilgardii), Liquorilactobacillus nagelii (formerly known as Lactobacillus nagelii), Saccharomyces cerevisiae, and Dekkera bruxellensis were the main microorganisms present. Acetic acid bacteria were present in low abundances under anaerobic conditions and only proliferated under aerobic conditions. Visualization of the water kefir grains through scanning electron microscopy revealed that the majority of the microorganisms was attached onto their surface. Lactic acid bacteria and yeasts were predominantly associated with the grains, whereas acetic acid bacteria were predominantly associated with the liquor

Improvement in hospital Quality of Care (QoC) after the introduction of rotavirus vaccination:An evaluation study in Belgium

During each winter period hospital emergency rooms and pediatric wards are often overwhelmed by high patient influx with infectious diseases leading to chaotic conditions with poor quality of care (QoC) delivery as a consequence. The conditions could be improved if we were able to better control the influx by introducing for instance better prevention strategies against some of the most frequent infectious diseases. New prevention strategies using vaccination against rotavirus infection were introduced in Belgium in November 2006. We developed a measure of hospital QoC suitable for assessing the impact of pediatric rotavirus vaccination. The study is retrospective collecting routine data on bed and staff management in one pediatric hospital in Belgium. The data were divided in pre- and post-vaccination periods during rotavirus-epidemic and non-epidemic periods. The scores were constructed using Explanatory Factor Analysis (EFA). All patients enrolled were admitted to the pediatric ward over the period from 1 January 2004 to 31 December 2009. The results of the epidemic period indicated that bed-day occupancy, bed-day turnover and unplanned readmissions for acute gastroenteritis were lower in the post-vaccination compared with the pre-vaccination periods. The QoC scores were therefore significantly lower (indicating improved QoC) after the introduction of rotavirus vaccination, compared with pre-vaccination. The data suggests that the reduction in the winter peak of rotavirus-related hospitalizations after the introduction of the vaccine reduces pressure on hospital resources and improves the quality of hospital care. The findings should be further tested in similar settings

清代内モンゴルにおける農地所有とその契約に関する研究―帰化城トゥメト旗を中心に―

博士（学術）神戸大

Characterisation of the Nematode Community of a Low-Activity Cold Seep in the Recently Ice-Shelf Free Larsen B Area, Eastern Antarctic Peninsula

Background: Recent climate-induced ice-shelf disintegration in the Larsen A (1995) and B (2002) areas along the Eastern Antarctic Peninsula formed a unique opportunity to assess sub-ice-shelf benthic community structure and led to the discovery of unexplored habitats, including a low-activity methane seep beneath the former Larsen B ice shelf. Since both limited particle sedimentation under previously permanent ice coverage and reduced cold-seep activity are likely toinfluence benthic meiofauna communities, we characterised the nematode assemblage of this low-activity cold seep and compared it with other, now seasonally ice-free, Larsen A and B stations and other Antarctic shelf areas (Weddell Sea and Drake Passage), as well as cold-seep ecosystems world-wide.Principal Findings: The nematode community at the Larsen B seep site differed significantly from other Antarctic sites in terms of dominant genera, diversity and abundance. Densities in the seep samples were high (.2000 individuals per 10 cm2) and showed below-surface maxima at a sediment depth of 2–3 cm in three out of four replicates. All samples were dominated by one species of the family Monhysteridae, which was identified as a Halomonhystera species that comprised between 80 and 86% of the total community. The combination of high densities, deeper density maxima and dominance of one species is shared by many cold-seep ecosystems world-wide and suggested a possible dependence upon a chemosynthetic food source. Yet stable 13C isotopic signals (ranging between 221.9760.86% and 224.8561.89%) were indicative of a phytoplankton-derived food source.Conclusion: The recent ice-shelf collapse and enhanced food input from surface phytoplankton blooms were responsible for the shift from oligotrophic pre-collapse conditions to a phytodetritus-based community with high densities and low diversity. The parthenogenetic reproduction of the highly dominant Halomonhystera species is rather unusual for marine nematodes and may be responsible for the successful colonisation by this single species