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  • Articles
    • Latest Articles
    • COVID-19 Research and News from ASM Journals
    • mSphere of Influence: Commentaries from Early Career Microbiologists
    • Archive
  • Topics
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bioinformatics

  • Open Access
    Comprehensive Bioinformatic Assessments of the Variability of <span class="named-content genus-species" id="named-content-1">Neisseria gonorrhoeae</span> Vaccine Candidates
    Research Article | Therapeutics and Prevention
    Comprehensive Bioinformatic Assessments of the Variability of Neisseria gonorrhoeae Vaccine Candidates

    Neisseria gonorrhoeae, the Gram-negative bacterium responsible for the sexually transmitted infection gonorrhea, is categorized as a high-priority pathogen for research and development efforts. N. gonorrhoeae’s “superbug” status, its high morbidity, and the serious health impact associated with...

    Benjamin I. Baarda, Ryszard A. Zielke, Alaina K. Holm, Aleksandra E. Sikora
  • Open Access
    Genes Influencing Phage Host Range in <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> on a Species-Wide Scale
    Research Article | Ecological and Evolutionary Science
    Genes Influencing Phage Host Range in Staphylococcus aureus on a Species-Wide Scale

    Staphylococcus aureus is a widespread, hospital- and community-acquired pathogen, many strains of which are antibiotic resistant. It causes diverse diseases, ranging from local to systemic infection, and affects both the skin and many internal organs, including the heart, lungs, bones, and brain.

    Abraham G. Moller, Kyle Winston, Shiyu Ji, Junting Wang, Michelle N. Hargita Davis, Claudia R. Solís-Lemus, Timothy D. Read
  • Open Access
    An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes
    Editor's Pick Observation | Host-Microbe Biology
    An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes

    Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.

    Lamia Wahba, Nimit Jain, Andrew Z. Fire, Massa J. Shoura, Karen L. Artiles, Matthew J. McCoy, Dae-Eun Jeong
  • Open Access
    Functional and Comparative Genomic Analysis of Integrated Prophage-Like Sequences in “<em>Candidatus</em> Liberibacter asiaticus”
    Research Article | Applied and Environmental Science
    Functional 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...

    Marian Dominguez-Mirazo, Rong Jin, Joshua S. Weitz
  • Open Access
    mSphere of Influence: Systematically Decoding Microbial Chemical Communication
    Commentary | Host-Microbe Biology
    mSphere of Influence: Systematically Decoding Microbial Chemical Communication

    Laura 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...

    Laura A. Mike
  • Open Access
    Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population
    Research Article | Host-Microbe Biology
    Identification of Differentiating Metabolic Pathways between Infant Gut Microbiome Populations Reveals Depletion of Function-Level Adaptation to Human Milk in the Finnish Population

    Knowing 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.

    Jan Majta, Krzysztof Odrzywolek, Bozena Milanovic, Vladyslav Hubar, Sonia Wrobel, Emilia Strycharz-Angrecka, Szymon Wojciechowski, Kaja Milanowska
  • Open Access
    SCC<em>mec</em>Finder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome <em>mec</em> in <span class="named-content genus-species" id="named-content-1">Staphylococcus aureus</span> Using Whole-Genome Sequence Data
    Resource Report | Clinical Science and Epidemiology
    SCCmecFinder, a Web-Based Tool for Typing of Staphylococcal Cassette Chromosome mec in Staphylococcus aureus Using Whole-Genome Sequence Data

    SCCmec 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...

    Hülya Kaya, Henrik Hasman, Jesper Larsen, Marc Stegger, Thor Bech Johannesen, Rosa Lundbye Allesøe, Camilla Koldbæk Lemvigh, Frank Møller Aarestrup, Ole Lund, Anders Rhod Larsen
  • Open Access
    Deep 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 Gut
    Research Article | Host-Microbe Biology
    Deep 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 Gut

    Our 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...

    Miles W. Carroll, Sam Haldenby, Natasha Y. Rickett, Bernadett Pályi, Isabel Garcia-Dorival, Xuan Liu, Gary Barker, Joseph Akoi Bore, Fara Raymond Koundouno, E. Diane Williamson, Thomas R. Laws, Romy Kerber, Daouda Sissoko, Nóra Magyar, Antonino Di Caro, Mirella Biava, Tom E. Fletcher, Armand Sprecher, Lisa F. P. Ng, Laurent Rénia, N’faly Magassouba, Stephan Günther, Roman Wölfel, Kilian Stoecker, David A. Matthews, Julian A. Hiscox
  • Open Access
    Whole-Genome Sequencing of Human Clinical <span class="named-content genus-species" id="named-content-1">Klebsiella pneumoniae</span> Isolates Reveals Misidentification and Misunderstandings of <span class="named-content genus-species" id="named-content-2">Klebsiella pneumoniae</span>, <span class="named-content genus-species" id="named-content-3">Klebsiella variicola</span>, and <span class="named-content genus-species" id="named-content-4">Klebsiella quasipneumoniae</span>
    Research Article | Clinical Science and Epidemiology
    Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

    Klebsiella 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...

    S. Wesley Long, Sarah E. Linson, Matthew Ojeda Saavedra, Concepcion Cantu, James J. Davis, Thomas Brettin, Randall J. Olsen
  • Open Access
    OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units
    Editor's Pick Research Article | Ecological and Evolutionary Science
    OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

    The 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...

    Sarah L. Westcott, Patrick D. Schloss
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