microbial communities
Research Article | Applied and Environmental SciencePhenoGMM: Gaussian Mixture Modeling of Cytometry Data Quantifies Changes in Microbial Community StructureMicroorganisms are vital components in various ecosystems on Earth. In order to investigate the microbial diversity, researchers have largely relied on the analysis of 16S rRNA gene sequences from DNA.
Research Article | Applied and Environmental ScienceBacterial and Eukaryotic Small-Subunit Amplicon Data Do Not Provide a Quantitative Picture of Microbial Communities, but They Are Reliable in the Context of Ecological InterpretationsHigh-throughput sequencing (HTS) of amplified fragments of rRNA genes provides unprecedented insight into the diversity of prokaryotic and eukaryotic microorganisms. Unfortunately, HTS data are prone to quantitative biases, which may lead to an erroneous picture of microbial community composition and thwart efforts to advance its understanding. These concerns motivated us to investigate how accurately HTS data characterize the...
Commentary | Host-Microbe BiologymSphere of Influence: a Community To Study CommunitiesDominique Limoli studies polymicrobial interactions during cystic fibrosis respiratory disease. In this mSphere of Influence article, she reflects on how two papers (D. A. Hogan, S. D. Willger, E. L. Dolben, T. H. Hampton, et al., PLoS One 11:e0149998, 2016, https://doi.org/10.1371/journal.pone.0149998, and P. Jorth, B.
Commentary | Host-Microbe BiologymSphere of Influence: Systematically Decoding Microbial Chemical CommunicationLaura 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...
Editor's Pick Research Article | Clinical Science and EpidemiologyProfiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNAHere we demonstrate the use of an RNA-based analysis of specific taxa of interest, including bacteria and fungi, within microbial communities. This multiplex method may be useful as a means to identify samples with specific combinations of taxa and to gain information on how specific populations vary over time and space or in response to perturbation. A rapid means to measure bacterial and fungal populations may aid in the study of host...
Research Article | Applied and Environmental ScienceTaxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial CommunityUrban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge...
Research Article | Ecological and Evolutionary ScienceEcological Stability Properties of Microbial Communities Assessed by Flow CytometryMicrobial communities drive many processes which affect human well-being directly, as in the human microbiome, or indirectly, as in natural environments or in biotechnological applications. Due to their complexity, their dynamics over time is difficult to monitor, and current sequence-based approaches are limited with respect to the temporal resolution. However, in order to eventually control microbial community dynamics, monitoring...
Research Article | Applied and Environmental ScienceVirioplankton Assemblage Structure in the Lower River and Ocean Continuum of the AmazonThe Amazon River forms a vast plume in the Atlantic Ocean that can extend for more than 1,000 km. Microbial communities promote a globally relevant carbon sink system in the plume. Despite the importance of viruses for the global carbon cycle, the diversity and the possible roles of viruses in the Amazonia are poorly understood. The present work assesses, for the first time, the abundance and diversity of viruses simultaneously in the...
Research Article | Ecological and Evolutionary ScienceBacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog LakesLakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would...
Research Article | Ecological and Evolutionary SciencepH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment CulturesThe human gut is a dynamic environment in which microorganisms consistently interact with the host via their metabolic products. Some of the most important microbial metabolic products are fermentation products such as short-chain fatty acids. Production of these fermentation products and the prevalence of fermenting microbiota depend on pH, alkalinity, and available dietary sugars, but details about their metabolic interactions are...