Latest Articles
Special Issue Perspective | Host-Microbe BiologyMissing Links: the Role of Primates in Understanding the Human MicrobiomeThe gut microbiome can influence host energy balances and metabolic programming. While this information is valuable in a disease context, it also has important implications for understanding host energetics from an ecological and evolutionary perspective.
Special Issue Perspective | Ecological and Evolutionary ScienceExploring the Evolution of Virulence Factors through Bioinformatic Data MiningThe molecular evolution of virulence factors is a central theme in our understanding of bacterial pathogenesis and host-microbe interactions. Using bioinformatics and genome data mining, recent studies have shed light on the evolution of important virulence factor families and the mechanisms by which they have adapted and diversified in function.
Special Issue Perspective | Applied and Environmental ScienceCulturing the Uncultured: Risk versus RewardIsolation of new microorganisms is challenging, but cultures are invaluable resources for experimental validation of phenotype, ecology, and evolutionary processes. Although the number of new isolates continues to grow, the majority of cultivars still come from a limited number of phylogenetic groups and environments, necessitating investment in new cultivation efforts.
Special Issue Perspective | Host-Microbe BiologyThe Significance of Microbial Symbionts in Ecosystem ProcessesIt is increasingly accepted that the microbial symbionts of eukaryotes can have profound effects on host ecology and evolution. However, the relative contribution that they make directly to ecosystem processes, like energy and nutrient flows, is less explicitly acknowledged and, in many cases, only poorly constrained.
Special Issue Perspective | Novel Systems Biology TechniquesStrengthening Insights in Microbial Ecological Networks from Theory to ApplicationsNetworks encode the interactions between the components in complex systems and play an essential role in understanding complex systems. Microbial ecological networks provide a system-level insight for comprehensively understanding complex microbial interactions, which play important roles in microbial community assembly.
Special Issue Perspective | Host-Microbe BiologyMetaproteomics: Much More than Measuring Gene Expression in Microbial CommunitiesMetaproteomics is the large-scale identification and quantification of proteins from microbial communities and thus provides direct insight into the phenotypes of microorganisms on the molecular level. Initially, metaproteomics was mainly used to assess the “expressed” metabolism and physiology of microbial community members.
Research Article | Ecological and Evolutionary ScienceElemental Composition, Phosphorous Uptake, and Characteristics of Growth of a SAR11 Strain in Batch and Continuous CultureWhile SAR11 bacteria contribute a significant fraction to the total picoplankton biomass in the ocean and likely are major players in organic C and nutrient cycling, the cellular characteristics and metabolic features of most lineages have either only been hypothesized from genomes or otherwise not measured in controlled laboratory experimentation. The dearth of data on even the most basic characteristics for what is arguably the most...
Research Article | Novel Systems Biology TechniquesNetwork Integrative Genomic and Transcriptomic Analysis of Carbapenem-Resistant Klebsiella pneumoniae Strains Identifies Genes for Antibiotic Resistance and VirulenceKlebsiella pneumoniae is a major bacterial pathogen that causes pneumonia and urinary tract infections in human. K. pneumoniae infections are treated with carbapenem, but carbapenem-resistant K. pneumoniae has been spreading...
Editor's Pick Research Article | Clinical Science and EpidemiologyMicrofluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway MetagenomicsThe airway microbial community, which takes important pathogenic roles for respiratory diseases, is far from clear in terms of taxonomy and gene functions. One of the critical reasons is the heavy contamination of host cell/DNA in airway samples, which hinders the subsequent sequencing of the whole genomic contents of the microbial community—the metagenome. Here, we describe a protocol for airway sample preparation which couples a...
Special Issue Perspective | Host-Microbe BiologyDefining Microbiome Health through a Host LensWe are walking ecosystems, inoculated at birth with a unique set of microbes that are integral to the functioning of our bodies. The physiology of our commensal microbiota is intertwined with our metabolism, immune function, and mental state.