comparative genomics
Research Article | Host-Microbe BiologyDolosigranulum pigrum Cooperation and Competition in Human Nasal MicrobiotaStaphylococcus 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...
Research Article | Clinical Science and EpidemiologyAcinetobacter baumannii NCIMB8209: a Rare Environmental Strain Displaying Extensive Insertion Sequence-Mediated Genome Remodeling Resulting in the Loss of Exposed Cell Structures and Defensive MechanismsAcinetobacter baumannii is an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae,...
Research Article | Ecological and Evolutionary SciencePhylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with CitrusXanthomonas 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...
Research Article | Host-Microbe BiologyInsights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. UniversitiesU.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...
Research Article | Applied and Environmental ScienceMethylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater EnvironmentsMost 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...
Research Article | Ecological and Evolutionary ScienceIn Silico Identification of Three Types of Integrative and Conjugative Elements in Elizabethkingia anophelis Strains Isolated from around the WorldElizabethkingia 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...
Editor's Pick Research Article | Host-Microbe BiologyGenotypic and Phenotypic Diversity of Herpes Simplex Virus 2 within the Infected Neonatal PopulationHerpes 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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceCharacterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatusAspergillus 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...
Research Article | Ecological and Evolutionary SciencePotential Mechanism of Detoxification of Cyanide Compounds by Gut Microbiomes of Bamboo-Eating PandasThe 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...
Editor's Pick Research Article | Ecological and Evolutionary ScienceGenomic, Network, and Phylogenetic Analysis of the Oomycete Effector ArsenalThe oomycetes are a class of microscopic, filamentous eukaryotes and include ecologically significant animal and plant pathogens. Oomycetes secrete large arsenals of effector proteins that degrade host cell components, manipulate host immune responses, and induce necrosis, enabling parasitic colonization. In this study, we catalogued the number and evolution of effectors in 37 oomycete species whose genomes have been completely...