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Applied and Environmental Science

  • Open Access
    Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir
    Research Article | Applied and Environmental Science
    Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir

    Traditional 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...

    Aaron M. Walsh, Fiona Crispie, Kieran Kilcawley, Orla O’Sullivan, Maurice G. O’Sullivan, Marcus J. Claesson, Paul D. Cotter
  • Open Access
    Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome
    Research Article | Applied and Environmental Science
    Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome

    The 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...

    J. A. Frank, M. Ø. Arntzen, L. Sun, L. H. Hagen, A. C. McHardy, S. J. Horn, V. G. H. Eijsink, A. Schnürer, P. B. Pope
  • Open Access
    What Have We Learned about the Microbiomes of Indoor Environments?
    Editor's Pick Minireview | Applied and Environmental Science
    What 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...

    Brent Stephens
  • Open Access
    Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents
    Research Article | Applied and Environmental Science
    Multiplexed Metagenomic Deep Sequencing To Analyze the Composition of High-Priority Pathogen Reagents

    Both 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.

    Michael R. Wilson, Greg Fedewa, Mark D. Stenglein, Judith Olejnik, Linda J. Rennick, Sham Nambulli, Friederike Feldmann, W. Paul Duprex, John H. Connor, Elke Mühlberger, Joseph L. DeRisi
  • Open Access
    Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization
    Editor's Pick Research Article | Applied and Environmental Science
    Zonal Soil Type Determines Soil Microbial Responses to Maize Cropping and Fertilization

    Microbial 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...

    Mengxin Zhao, Bo Sun, Linwei Wu, Qun Gao, Feng Wang, Chongqing Wen, Mengmeng Wang, Yuting Liang, Lauren Hale, Jizhong Zhou, Yunfeng Yang
  • Open Access
    Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
    Editor's Pick Research Article | Applied and Environmental Science
    Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

    Mass 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...

    Tiffany Hsu, Regina Joice, Jose Vallarino, Galeb Abu-Ali, Erica M. Hartmann, Afrah Shafquat, Casey DuLong, Catherine Baranowski, Dirk Gevers, Jessica L. Green, Xochitl C. Morgan, John D. Spengler, Curtis Huttenhower
  • Open Access
    Avoiding Pandemic Fears in the Subway and Conquering the Platypus
    Commentary | Applied and Environmental Science
    Avoiding Pandemic Fears in the Subway and Conquering the Platypus

    Metagenomics 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...

    A. Gonzalez, Y. Vázquez-Baeza, J. B. Pettengill, A. Ottesen, D. McDonald, R. Knight
  • Open Access
    <em>Thermus</em> and the Pink Discoloration Defect in Cheese
    Research Article | Applied and Environmental Science
    Thermus and the Pink Discoloration Defect in Cheese

    Pink 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...

    Lisa Quigley, Daniel J. O’Sullivan, David Daly, Orla O’Sullivan, Zuzana Burdikova, Rostislav Vana, Tom P. Beresford, R. Paul Ross, Gerald F. Fitzgerald, Paul L. H. McSweeney, Linda Giblin, Jeremiah J. Sheehan, Paul D. Cotter
  • Open Access
    MetaPalette: a <em>k</em>-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
    Research Article | Applied and Environmental Science
    MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation

    Taxonomic 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-...

    David Koslicki, Daniel Falush
  • Open Access
    Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton
    Research Article | Applied and Environmental Science
    Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton

    There 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...

    Cristina M. Herren, Kyle C. Webert, Katherine D. McMahon

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