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comparative genomics

  • Open Access
    Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus <em>Cryphonectria</em>
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Comparative Genomics Analyses of Lifestyle Transitions at the Origin of an Invasive Fungal Pathogen in the Genus Cryphonectria

    Forest and agroecosystems, as well as animal and human health, are threatened by emerging pathogens. Following decimation of chestnuts in the United States, the fungal pathogen Cryphonectria parasitica colonized Europe. After establishment, the pathogen population gave rise to a highly successful lineage that spread rapidly across the continent. Core to our understanding of what makes a successful pathogen is the genetic...

    Lea Stauber, Simone Prospero, Daniel Croll
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Dolosigranulum pigrum</span> Cooperation and Competition in Human Nasal Microbiota
    Research Article | Host-Microbe Biology
    Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota

    Staphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum...

    Silvio D. Brugger, Sara M. Eslami, Melinda M. Pettigrew, Isabel F. Escapa, Matthew T. Henke, Yong Kong, Katherine P. Lemon
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Acinetobacter baumannii</span> NCIMB8209: a Rare Environmental Strain Displaying Extensive Insertion Sequence-Mediated Genome Remodeling Resulting in the Loss of Exposed Cell Structures and Defensive Mechanisms
    Research Article | Clinical Science and Epidemiology
    Acinetobacter baumannii NCIMB8209: a Rare Environmental Strain Displaying Extensive Insertion Sequence-Mediated Genome Remodeling Resulting in the Loss of Exposed Cell Structures and Defensive Mechanisms

    Acinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae,...

    Guillermo D. Repizo, Martín Espariz, Joana L. Seravalle, Juan Ignacio Díaz Miloslavich, Bruno A. Steimbrüch, Howard A. Shuman, Alejandro M. Viale
  • Open Access
    Phylogenomic Insights into Diversity and Evolution of Nonpathogenic <em>Xanthomonas</em> Strains Associated with Citrus
    Research Article | Ecological and Evolutionary Science
    Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus

    Xanthomonas citri is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, Xanthomonas is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a Xanthomonas community associated with citrus and other plants. Our...

    Kanika Bansal, Sanjeet Kumar, Prabhu B. Patil
  • Open Access
    Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities
    Research Article | Host-Microbe Biology
    Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities

    U.S. university students are at a higher risk of invasive meningococcal disease than the general population. The responsible pathogen, Neisseria meningitidis, can be carried asymptomatically in the oropharynx; the dynamics of meningococcal carriage and the genetic features that distinguish carriage versus disease states are not completely understood. Through our...

    Sandeep J. Joseph, Nadav Topaz, How-Yi Chang, Melissa J. Whaley, Jeni T. Vuong, Alexander Chen, Fang Hu, Susanna E. Schmink, Laurel T. Jenkins, Lorraine D. Rodriguez-Rivera, Jennifer D. Thomas, Anna M. Acosta, Lucy McNamara, Heidi M. Soeters, Sarah Mbaeyi, Xin Wang
  • Open Access
    <em>Methylotetracoccus oryzae</em> Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments
    Research Article | Applied and Environmental Science
    Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments

    Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study...

    Mohammad Ghashghavi, Svetlana E. Belova, Paul L. E. Bodelier, Svetlana N. Dedysh, Martine A. R. Kox, Daan R. Speth, Peter Frenzel, Mike S. M. Jetten, Sebastian Lücker, Claudia Lüke
  • Open Access
    <em>In Silico</em> Identification of Three Types of Integrative and Conjugative Elements in <span class="named-content genus-species" id="named-content-1">Elizabethkingia anophelis</span> Strains Isolated from around the World
    Research Article | Ecological and Evolutionary Science
    In Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the World

    Elizabethkingia anophelis is an opportunistic human pathogen, and the genetic diversity between strains from around the world becomes apparent as more genomes are sequenced. Genome comparison identified three types of putative ICEs in 31 of 36 strains. The diversity of ICEs suggests that they had different origins. One of the ICEs was discovered previously from a...

    Jiannong Xu, Dong Pei, Ainsley Nicholson, Yuhao Lan, Qing Xia
  • Open Access
    Genotypic and Phenotypic Diversity of Herpes Simplex Virus 2 within the Infected Neonatal Population
    Editor's Pick Research Article | Host-Microbe Biology
    Genotypic and Phenotypic Diversity of Herpes Simplex Virus 2 within the Infected Neonatal Population

    Herpes simplex virus (HSV) causes invasive disease in half of infected neonates, resulting in significant mortality and permanent cognitive morbidity. The factors that contribute to invasive disease are not understood. This study revealed diversity among HSV isolates from infected neonates and detected the first associations between viral genetic variations and clinical disease manifestations. We found that viruses isolated from...

    Lisa N. Akhtar, Christopher D. Bowen, Daniel W. Renner, Utsav Pandey, Ashley N. Della Fera, David W. Kimberlin, Mark N. Prichard, Richard J. Whitley, Matthew D. Weitzman, Moriah L. Szpara
  • Open Access
    Characterizing the Pathogenic, Genomic, and Chemical Traits of <em>Aspergillus fischeri</em>, a Close Relative of the Major Human Fungal Pathogen <em>Aspergillus fumigatus</em>
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus

    Aspergillus fumigatus is the primary cause of aspergillosis, a devastating ensemble of diseases associated with severe morbidity and mortality worldwide. A. fischeri is a close relative of A. fumigatus but is not generally...

    Matthew E. Mead, Sonja L. Knowles, Huzefa A. Raja, Sarah R. Beattie, Caitlin H. Kowalski, Jacob L. Steenwyk, Lilian P. Silva, Jessica Chiaratto, Laure N. A. Ries, Gustavo H. Goldman, Robert A. Cramer, Nicholas H. Oberlies, Antonis Rokas
  • Open Access
    Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas
    Research Article | Ecological and Evolutionary Science
    Potential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating Pandas

    The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), two obligate bamboo feeders, have distinct phylogenetic positions in the order Carnivora. Bamboo is extraordinarily rich in plant secondary metabolites, such as allied phenolic and polyphenolic compounds and even toxic cyanide...

    Lifeng Zhu, Zhisong Yang, Ran Yao, Liangliang Xu, Hua Chen, Xiaodong Gu, Tonggui Wu, Xuyu Yang

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