Latest Articles
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.
Special Issue Perspective | Ecological and Evolutionary ScienceAdvancing Genome-Resolved Metagenomics beyond the ShotgunExploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required...
Special Issue Perspective | Synthetic BiologyNatural Products and Synthetic Biology: Where We Are and Where We Need To GoThe biosynthetic talent of microorganisms has been harnessed for drug discovery for almost a century. Microbial metabolites not only account for the majority of antibiotics available today, but have also led to anticancer, immunosuppressant, and cholesterol-lowering drugs.
Special Issue Perspective | Ecological and Evolutionary ScienceA Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”Microbes drive critical ecosystem functions and affect global nutrient cycling along with human health and disease. They do so under strong constraints exerted by viruses, which shape microbial communities’ structure and shift host cell metabolism during infection.
Special Issue Perspective | Ecological and Evolutionary ScienceUncovering the Metabolic Strategies of the Dormant Microbial Majority: towards Integrative ApproachesA grand challenge in microbiology is to understand how the dormant majority lives. In natural environments, most microorganisms are not growing and instead exist in a spectrum of dormant states.
Special Issue Perspective | Applied and Environmental ScienceMoving towards a Robust Definition for a “Healthy” Indoor MicrobiomeBuildings of the future should be designed to support human health, both by promoting the presence of beneficial microbes and by reducing exposure to harmful ones. However, we still do not have a robust definition of what constitutes a “healthy” indoor microbiome.
Research Article | Host-Microbe BiologyA Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut MicrobiomeThe composition of the gut microbiome associates with a wide range of human diseases, but the mechanisms underpinning these associations are not well understood. To shift toward a mechanistic understanding, we integrated distinct metagenomic data sets to identify functions encoded in the gut microbiome that associate with multiple diseases, which may be important to human health. Additionally, we identified functions that associate with...
Editor's Pick Research Article | Host-Microbe BiologySocial-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper CellsHow do stressful life events increase the risk for autoimmune disorders? Here we show that chronic social stress in mice promotes the expression of virulent genes in the gut microbiota and alters the microbial translocation into the mesenteric lymph nodes. Our results also suggest that the consequent immune response to the stress-affected microbiota may endanger the tolerance for self. The presence of specific translocated bacteria and...