bioinformatics
Editor's Pick Observation | Host-Microbe BiologyAn Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung ViromesMeta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.
Research Article | Applied and Environmental ScienceFunctional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “Candidatus Liberibacter asiaticus”Huanglongbing (HLB) disease is threatening citrus production worldwide. The causative agent is “Candidatus Liberibacter asiaticus.” Prior work using mapping-based approaches identified prophage-like sequences in some “Ca. Liberibacter asiaticus” genomes but not all. Here, we utilized a de novo approach that expands the number of prophage-like elements found in “Ca. Liberibacter asiaticus” from 16 to...
Commentary | Host-Microbe BiologymSphere of Influence: Systematically Decoding Microbial Chemical CommunicationLaura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how “Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters” by P. Cimermancic et al. (Cell 158:412–421, 2014, https://doi.org/10.1016/j.cell.2014.06.034) and “A Systematic Analysis of Biosynthetic Gene Clusters in the Human...
Research Article | Host-Microbe BiologyIdentification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish PopulationKnowing the limitations of taxonomy-based research, there is an emerging need for the development of higher-resolution techniques. The significance of this research is demonstrated by the novel method used for the analysis of function-level metagenomes. BiomeScout—the presented technology—utilizes proprietary algorithms for the detection of differences between functionalities present in metagenomic samples.
Resource Report | Clinical Science and EpidemiologySCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence DataSCCmec in MRSA is acknowledged to be of importance not only because it contains the mecA or mecC gene but also for staphylococcal adaptation to different environments, e.g., in hospitals, the community, and livestock. Typing of SCCmec by PCR techniques has, because of its heterogeneity, been challenging, and whole-genome sequencing has only partially solved this since no good bioinformatic tools have...
Research Article | Host-Microbe BiologyDeep Sequencing of RNA from Blood and Oral Swab Samples Reveals the Presence of Nucleic Acid from a Number of Pathogens in Patients with Acute Ebola Virus Disease and Is Consistent with Bacterial Translocation across the GutOur results highlight the identification of an array of pathogens in the blood of patients with Ebola virus disease (EVD). This has not been done before, and the data have important implications for the treatment of patients with EVD, particularly considering antibiotic stewardship. We show that EVD patients who were also infected with Plasmodium, particularly at higher loads, had more adverse outcomes than patients with lower...
Research Article | Clinical Science and EpidemiologyWhole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniaeKlebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome...
Editor's Pick Research Article | Ecological and Evolutionary ScienceOptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic UnitsThe analysis of microbial communities from diverse environments using 16S rRNA gene sequencing has expanded our knowledge of the biogeography of microorganisms. An important step in this analysis is the assignment of sequences into taxonomic groups based on their similarity to sequences in a database or based on their similarity to each other, irrespective of a database. In this study, we present a new algorithm for the latter approach...