Applied and Environmental Science
Research Article | Applied and Environmental ScienceMicrobial Succession and Flavor Production in the Fermented Dairy Beverage KefirTraditional fermented foods represent relatively low-complexity microbial environments that can be used as model microbial communities to understand how microbes interact in natural environments. Our results illustrate the dynamic nature of kefir fermentations and microbial succession patterns therein. In the process, the link between individual species, and associated pathways, with flavor compounds is revealed and several genes that...
Research Article | Applied and Environmental ScienceNovel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic MicrobiomeThe microbial production of methane or “biogas” is an attractive renewable energy technology that can recycle organic waste into biofuel. Biogas reactors operating with protein-rich substrates such as household municipal or agricultural wastes have significant industrial and societal value; however, they are highly unstable and frequently collapse due to the accumulation of ammonia. We report the discovery of a novel uncultured...
Editor's Pick Minireview | Applied and Environmental ScienceWhat Have We Learned about the Microbiomes of Indoor Environments?The advent and application of high-throughput molecular techniques for analyzing microbial communities in the indoor environment have led to illuminating findings and are beginning to change the way we think about human health in relation to the built environment. Here I review recent studies on the microbiology of the built environment, organize their findings into 12 major thematic categories, and comment on how these studies have or...
Research Article | Applied and Environmental ScienceMultiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen ReagentsBoth the integrity and reproducibility of experiments using select agents depend in large part on unbiased validation to ensure the correct identity and purity of the species in question. Metagenomic deep sequencing (MDS) provides the required level of validation by allowing for an unbiased and comprehensive assessment of all the microbes in a laboratory stock.
Editor's Pick Research Article | Applied and Environmental ScienceZonal Soil Type Determines Soil Microbial Responses to Maize Cropping and FertilizationMicrobial communities are essential drivers of soil functional processes such as nitrification and heterotrophic respiration. Although there is initial evidence revealing the importance of soil type in shaping microbial communities, there has been no in-depth, comprehensive survey to robustly establish it as a major determinant of microbial community composition, functional gene structure, or ecosystem functioning. We examined bacterial...
Editor's Pick Research Article | Applied and Environmental ScienceUrban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the EnvironmentMass transit environments, specifically, urban subways, are distinct microbial environments with high occupant densities, diversities, and turnovers, and they are thus especially relevant to public health. Despite this, only three culture-independent subway studies have been performed, all since 2013 and all with widely differing designs and conclusions. In this study, we profiled the Boston subway system, which provides 238 million...
Commentary | Applied and Environmental ScienceAvoiding Pandemic Fears in the Subway and Conquering the PlatypusMetagenomics is increasingly used not just to show patterns of microbial diversity but also as a culture-independent method to detect individual organisms of intense clinical, epidemiological, conservation, forensic, or regulatory interest. A widely reported metagenomic study of the New York subway suggested that the pathogens Yersinia pestis and...
Research Article | Applied and Environmental ScienceThermus and the Pink Discoloration Defect in CheesePink discoloration in cheese is a defect affecting many cheeses throughout the world, leading to significant financial loss for the dairy industry. Despite decades of research, the cause of this defect has remained elusive. The advent of high-throughput, next-generation sequencing has revolutionized the field of food microbiology and, with respect to this study, provided a means of testing a possible microbial basis for this defect. In...
Research Article | Applied and Environmental ScienceMetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain VariationTaxonomic profiling is a challenging first step when analyzing a metagenomic sample. This work presents a method that facilitates fine-scale characterization of the presence, abundance, and evolutionary relatedness of organisms present in a given sample but absent from the training database. We calculate a “k-mer palette” which summarizes the information from all reads, not just those in conserved genes or containing taxon-...
Research Article | Applied and Environmental ScienceEnvironmental Disturbances Decrease the Variability of Microbial Populations within PeriphytonThere are many reasons why microbial community composition is difficult to model. For example, the high diversity and high rate of change of these communities make it challenging to identify causes of community turnover. Furthermore, the processes that shape community composition can be either deterministic, which cause communities to converge upon similar compositions, or stochastic, which increase variability in community composition...