The Burkholderia Genome Database: facilitating flexible queries and comparative analyses

Summary: As the genome sequences of multiple strains of a given bacterial species are obtained, more generalized bacterial genome databases may be complemented by databases that are focused on providing more information geared for a distinct bacterial phylogenetic group and its associated research community. The Burkholderia Genome Database represents a model for such a database, providing a powerful, user-friendly search and comparative analysis interface that contains features not found in other genome databases. It contains continually updated, curated and tracked information about Burkholderia cepacia complex genome annotations, plus other Burkholderia species genomes for comparison, providing a high-quality resource for its targeted cystic fibrosis research community

The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses

The composition, abundance, and diversity of midgut bacteria in mosquitoes can influence pathogen transmission. We used 16S rRNA microbiome profiling to survey midgut microbial diversity in pooled samples of laboratory colonized dengue-refractory, Cali-MIB, and dengue-susceptible, Cali-S Aedes aegypti (Linnaeus). The 16S rRNA sequences from the sugar-fed midguts of adult females clustered to 63 amplicon sequence variants (ASVs), primarily from Proteobacteria, Firmicutes, Flavobacteria, and Actinobacteria. An average of five ASVs dominated the midguts, and most ASVs were present in both Cali-MIB and Cali-S midguts. No differences in abundance were noted at any phylogenetic level (Phylum, Class, Order, Family, Genus) by analysis of composition of microbiome (w = 0). No community diversity metrics were significantly different between refractory and susceptible mosquitoes. These data suggest that phenotypic differences in the susceptibility to dengue virus between Cali-MIB and Cali-S are not likely due to major differences in midgut bacterial communities

Efficacy of Bifidobacterium animalis subsp. lactis (BB-12), B. infantis and Lactobacillus acidophilus (La-5) probiotics to prevent gut dysbiosis in preterm infants of 28+0–32+6 weeks of gestation: a randomised, placebocontrolled, double-blind, multicentre trial: the PRIMAL Clinical Study Protocol

Introduction The healthy ‘eubiosis’ microbiome in infancy is regarded as the microbiome derived from term, vaginally delivered, antibiotic free, breastfed infants at 4–6 months. Dysbiosis is regarded as a deviation from a healthy state with reduced microbial diversity and deficient capacity to control drug-resistant organisms. Preterm infants are highly sensitive to early gut dysbiosis. Latter has been associated with sepsis and necrotising enterocolitis, but may also contribute to long-term health problems. Probiotics hold promise to reduce the risk for adverse short-term outcomes but the evidence from clinical trials remains inconclusive and none has directly assessed the effects of probiotics on the microbiome at high resolution. Methods and analysis A randomised, double blind, placebo-controlled study has been designed to assess the safety and efficacy of the probiotic mix of Bifidobacterium animalis subsp. lactis, B. infantis and Lactobacillus acidophilus in the prevention of gut dysbiosis in preterm infants between 28+0 and 32+6 weeks of gestation. The study is conducted in 18 German neonatal intensive care units. Between April 2018 and March 2020, 654 preterm infants of 28+0–32+6 weeks of gestation will be randomised in the first 48 hours of life to 28 days of once daily treatment with either probiotics or placebo. The efficacy endpoint is the prevention of gut dysbiosis at day 30 of life. A compound definition of gut dysbosis is used: (1) colonisation with multidrug-resistant organisms or gram-negative bacteria with high epidemic potential or (2) a significant deviation of the gut microbiota composition as compared with healthy term infants. Dysbiosis is determined by (1) conventional microbiological culture and (2) phylogenetic microbiome analysis by high-throughput 16S rRNA and metagenome sequencing. Persistence of dysbiosis will be assessed at 12-month follow-up visits. Side effects and adverse events related to the intervention will be recorded. Key secondary endpoint(s) are putative consequences of dysbiosis. A subgroup of infants will be thoroughly phenotyped for immune parameters using chipcytometry. Ethics and dissemination Ethics approval was obtained in all participating sites. Results of the trial will be published in peer-review journals, at scientific meetings, on the website (www.primal-study.de) and via social media of parent organisations. Trial registration number DRKS00013197; Pre-results

NFDI4Microbiota – national research data infrastructure for microbiota research

Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role in human and environmental health. Growing awareness of this fact has led to a huge increase in microbiological research and applications in a variety of fields. Driven by technological advances that allow high-throughput molecular characterization of microbial species and communities, microbiological research now offers unparalleled opportunities to address current and emerging needs. As well as helping to address global health threats such as antimicrobial resistance and viral pandemics, it also has a key role to play in areas such as agriculture, waste management, water treatment, ecosystems remediation, and the diagnosis, treatment and prevention of various diseases. Reflecting this broad potential, billions of euros have been invested in microbiota research programs worldwide. Though run independently, many of these projects are closely related. However, Germany currently has no infrastructure to connect such projects or even compare their results. Thus, the potential synergy of data and expertise is being squandered. The goal of the NFDI4Microbiota consortium is to serve and connect this broad and heterogeneous research community by elevating the availability and quality of research results through dedicated training, and by facilitating the generation, management, interpretation, sharing, and reuse of microbial data. In doing so, we will also foster interdisciplinary interactions between researchers. NFDI4Microbiota will achieve this by creating a German microbial research network through training and community-building activities, and by creating a cloud-based system that will make the storage, integration and analysis of microbial data, especially omics data, consistent, reproducible, and accessible across all areas of life sciences. In addition to increasing the quality of microbial research in Germany, our training program will support widespread and proper usage of these services. Through this dual emphasis on education and services, NFDI4Microbiota will ensure that microbial research in Germany is synergistic and efficient, and thus excellent. By creating a central resource for German microbial research, NDFDI4Microbiota will establish a connecting hub for all NFDI consortia that work with microbiological data, including GHGA, NFDI4Biodiversity, NFDI4Agri and several others. NFDI4Microbiota will provide non-microbial specialists from these consortia with direct and easy access to the necessary expertise and infrastructure in microbial research in order to facilitate their daily work and enhance their research. The links forged through NFDI4Microbiota will not only increase the synergy between NFDI consortia, but also elevate the overall quality and relevance of microbial research in Germany

Towards the biogeography of prokaryotic genes

Funding was provided by the European Union’s Horizon 2020 Research and Innovation Programme (grant 686070: DD-DeCaF to P.B.) and Marie Skłodowska-Curie Actions (grant 713673 to A.R.d.R.), the European Research Council (ERC) MicrobioS (ERC-AdG-669830 to P.B.), JTC project jumpAR (01KI1706 to P.B.), a BMBF Grant (grant 031L0181A: LAMarCK to P.B.), the European Molecular Biology Laboratory (P.B.), the ETH and Helmut Horten Foundation (S.S.), the National Key R&D Program of China (grant 2020YFA0712403 to X.-M.Z.), (grant 61932008 to X.-M.Z.; grant 61772368 to X.-M.Z.; grant 31950410544 to L.P.C.), the Shanghai Municipal Science and Technology Major Project (grant 2018SHZDZX01 to X.-M.Z. and L.P.C.) and Zhangjiang Lab (X.-M.Z. and L.P.C.), the International Development Research Centre (grant 109304, EMBARK under the JPI AMR framework; to L.P.C.), la Caixa Foundation (grant 100010434, fellowship code LCF/BQ/DI18/11660009 to A.R.d.R.), the Severo Ochoa Program for Centres of Excellence in R&D from the Agencia Estatal de Investigación of Spain (grant SEV-2016-0672 (2017–2021) to C.P.C.), the Ministerio de Ciencia, Innovación y Universidades (grant PGC2018-098073-A-I00 MCIU/AEI/FEDER to J.H.-C. and J.G.-L.), the Innovation Fund Denmark (grant 4203-00005B, PNM), the Biotechnology and Biological Sciences research Council (BBSrC) Gut MicroInstitute Strategic Programmebes and Health BB/r012490/1 and its constituent project BBS/e/F/000Pr10355 (F.H.). R.A. is a member of the Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences.Peer reviewe

Metagenomic analysis of river microbial communities

As concern over the availability of freshwater increases, so does the interest in river microorganisms due to their importance in drinking water safety and signalling environmental contamination. However, foundational understanding of their variability in rivers is lacking, especially for viruses. Here, I present work to improve the understanding of planktonic microbial communities in rivers over time in the context of varying environmental conditions and contrasting land use. DNA-sequencing based metagenomic and phylogenetic marker gene (16S, 18S, g23) approaches were used to profile microbial communities, coupled with measures of environmental and chemical conditions. I analysed microbial community profiles from monthly samples collected over one year from three watersheds with agricultural, urban, or minimal land use. Viral, bacterial, and microeukaryotic planktonic communities were synchronous overall, but had contrasting geographic patterns and the strength of their synchrony, as well as their relationships with environmental conditions, were heterogenous across sampling sites. These differences illustrated that bacteria are important yet insufficient representatives of microbial community dynamics despite their prevalence in microbiome research. However, this emphasis on bacteria has produced richer reference databases, which enabled a gene-specific analysis. Using a reference-based approach, I found that communities with lower water quality due to agricultural activity had higher abundances of nutrient metabolism and bacteriophage gene families. Based on these water quality associated findings and on complementary analyses, I identified potential biomarkers to demonstrate that bacterial river metagenome data could feasibly support the development of new assays for water quality monitoring. To complement these studies of anthropogenic contamination, I studied bacteria in river biofilms across a natural gradient of metal concentrations at a potential mining site. Clear relationships among metal concentrations, pH, and microbiomes were evident and this study provided fundamental knowledge of microbial communities at a potential mine site before disruption from development. Throughout these studies, the scarcity of reference information for microbial communities in lotic freshwater provided an opportunity to identify weaknesses in popular microbiome analysis methods and present approaches better suited to poorly characterised environments. Overall, my work aims to improve the understanding of planktonic river microbial community variability, both for the advancement of basic science and to support future development of more effective water quality monitoring approaches

Bewust kiezen voor een vervolgopleiding: opleiden van VMBO-zorg naar MBO-zorg (niveau 2)

Recentelijk bezocht minister Van Bijsterveldt een praktijkschool voor VMBO in Parkstad Heerlen. Zij benoemde het belang voor een leerling om op kleinschalig niveau vorm te geven aan het doorgaan van de ene opleiding in de andere. Dicht bij de leerling staan en dicht bij de leerling zijn ontwikkeling volgen. Dit is onder andere mogelijk door een bijpassende vorm te vinden van leren en werken in de beroepspraktijk. Het project ‘Onderwijs in de praktijk’ is hier een voorbeeld van

L'Écho : grand quotidien d'information du Centre Ouest

29 août 19201920/08/29 (A49).Appartient à l’ensemble documentaire : PoitouCh