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    Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera.

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    Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type,

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  • Microbial Strategies for Survival in the Glass Sponge ...

    Few studies have explored the microbiomes of Limestone sponges (Hexactinellida). The present study seeks to elucidate the composition of the microbiota associated with the Limestone sponge Vazella pourtalesii and the functional strategies of the main symbionts. We combined microscopic approaches with metagenome-guided microbial genome reconstruction and amplicon community profiling toward this

  • A New Pneumococcal Capsule Type, 10D, is the

    Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes. Herein, we report a new and the 100th capsule type,

  • Bactopia: a Flexible Pipeline for Complete Analysis of ...

    Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera.

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    Traore SI, Seck EH, et al. (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1: 16203. OpenUrl CrossRef PubMed ↵ Lam KN, Martens EC, and ; Charles TC (2018) Developing a Bacteroides system for function-based screening of DNA from the human gut microbiome. mSystems 3: e00195-17. OpenUrl Abstract / FREE Full Text ↵ Larson B, Banks P ...

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    A typical PCR (25 µL) contained 1× Q5 reaction buffer, 200 µM dNTPs, 0.5 µM of each primer (SI Appendix, Table S14, no. 1 to 30 for the gananamide cluster and no. 31 to 44 for the peloruside cluster), 20 to 50 ng template DNA, and 0.5 U Q5 High-Fidelity DNA Polymerase. The reaction was heated to 98 °C for 30 s followed by 30 cycles of 98 °C for 10 s, 62 °C for 20 s, and 72 °C for 30 s ...

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    Zhou et al. use metatranscriptomic sequencing to profile immune signatures in the bronchoalveolar lavage fluid of COVID-19 patients. COVID-19 patients exhibit robust innate immune responses with notable hypercytokinemia and increased expression of IFN-stimulated genes. This analysis provides timely information for understanding SARS-CoV-2-host interactions and COVID-19 pathogenesis.

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  • Determination of host proteins composing the ...

    Coronaviruses can infect the nose and throat and are a main cause of the common cold. Infections are usually mild and short-lived, but sometimes they can turn nasty. In 2002 and 2012, two dangerous new coronaviruses emerged and caused diseases known as SARS and MERS. These viruses caused much more serious symptoms and in some cases proved deadly.

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