flow cytometry
Research Article | Host-Microbe BiologyQuantifying Live Microbial Load in Human Saliva Samples over Time Reveals Stable Composition and Dynamic LoadHuman microbiomes are dynamic ecosystems often composed of hundreds of unique microbial taxa. To detect fluctuations over time in the human oral microbiome, we developed a novel workflow to quantify live microbial cells with flow cytometry in parallel with next-generation sequencing, and applied this method to over 150 unstimulated, timed saliva samples.
Research Article | Applied and Environmental ScienceAssessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow CytometryThe manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects.
Research Article | Ecological and Evolutionary ScienceComplementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest SoilMicrobial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of...
Research Article | Applied and Environmental ScienceRandomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow CytometryA major goal in microbial ecology is to understand how microbial community structure influences ecosystem functioning. Various methods to directly associate bacterial taxa to functional groups in the environment are being developed. In this study, we applied machine learning methods to relate taxonomic data obtained from marker gene surveys to functional groups identified by flow cytometry. This allowed us to identify the taxa that are...
Research Article | Ecological and Evolutionary Science16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated SoilAlthough the majority of microorganisms in natural ecosystems are dormant, relatively little is known about the dynamics of the active and dormant microbial pools through both space and time. The limited knowledge of microbial activity-dormancy dynamics is in part due to uncertainty in the methods currently used to quantify active taxa. Here, we directly compared two of the most common methods (16S ratios and active cell staining) for...