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microbial ecology

  • Open Access
    BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities
    Methods and Protocols
    BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

    The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on “in-house” reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time expensive, error- and bias-prone process lacks standardization, cripples the potential for...

    Brendan A. Daisley, Gregor Reid
  • Open Access
    EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
    Research Article
    EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

    Phylogenetic trees are integral data structures for the analysis of microbial communities. Recent work has also shown the utility of trees constructed from certain metabolomic data sets, further highlighting their importance in microbiome research.

    Kalen Cantrell, Marcus W. Fedarko, Gibraan Rahman, Daniel McDonald, Yimeng Yang, Thant Zaw, Antonio Gonzalez, Stefan Janssen, Mehrbod Estaki, Niina Haiminen, Kristen L. Beck, Qiyun Zhu, Erfan Sayyari, James T. Morton, George Armstrong, Anupriya Tripathi, Julia M. Gauglitz, Clarisse Marotz, Nathaniel L. Matteson, Cameron Martino, Jon G. Sanders, Anna Paola Carrieri, Se Jin Song, Austin D. Swafford, Pieter C. Dorrestein, Kristian G. Andersen, Laxmi Parida, Ho-Cheol Kim, Yoshiki Vázquez-Baeza, Rob Knight
  • Open Access
    Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale
    Research Article
    Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

    This is the first systematic study about spatial and temporal variation of virioplankton communities in estuaries by using deep metagenomics sequencing. It is among the highest-quality viromic data sets to date, showing remarkably consistent sequencing depth and quality across samples.

    Mengqi Sun, Yuanchao Zhan, David Marsan, David Páez-Espino, Lanlan Cai, Feng Chen
  • Open Access
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification
    Research Article | Molecular Biology and Physiology
    Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

    Nitrate-reducing bacteria (NRB) and sulfate-reducing bacteria (SRB) colonize diverse anoxic environments, including soil subsurface, groundwater, and wastewater. NRB and SRB compete for resources, and their interplay has major implications on the global cycling of nitrogen and sulfur species, with undesirable outcomes in some contexts.

    Anne E. Otwell, Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, Serdar Turkarslan, Sean M. Gibbons, Dwayne A. Elias, David A. Stahl, Gary Siuzdak, Nitin S. Baliga
  • Open Access
    A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation
    Research Article | Ecological and Evolutionary Science
    A Novel Group of Promiscuous Podophages Infecting Diverse Gammaproteobacteria from River Communities Exhibits Dynamic Intergenus Host Adaptation

    In natural environments, phages coexist and interact with a broad variety of bacteria, posing a conundrum for narrow-host-range phage maintenance in diverse communities. This context is rarely considered in the study of host-phage interactions, typically focused on narrow-host-range viruses and their infectivity in target bacteria isolated from sources distinct to where the phages were retrieved from.

    Daniel Cazares, Adrian Cazares, Wendy Figueroa, Gabriel Guarneros, Robert A. Edwards, Pablo Vinuesa
  • Open Access
    Computational Analysis of Microbial Flow Cytometry Data
    Minireview | Applied and Environmental Science
    Computational Analysis of Microbial Flow Cytometry Data

    Flow cytometry is an important technology for the study of microbial communities. It grants the ability to rapidly generate phenotypic single-cell data that are both quantitative, multivariate and of high temporal resolution.

    Peter Rubbens, Ruben Props
  • Open Access
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways
    Minireview | Host-Microbe Biology
    Ecological Succession of Polymicrobial Communities in the Cystic Fibrosis Airways

    Antimicrobial therapies against cystic fibrosis (CF) lung infections are largely aimed at the traditional, well-studied CF pathogens such as Pseudomonas aeruginosa and Burkholderia cepacia complex, despite the fact that the CF lung harbors a complex and dynamic polymicrobial community. A clinical...

    Rutvij A. Khanolkar, Shawn T. Clark, Pauline W. Wang, David M. Hwang, Yvonne C. W. Yau, Valerie J. Waters, David S. Guttman
  • Open Access
    Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States
    Editor's Pick Research Article | Host-Microbe Biology
    Infant Skin Bacterial Communities Vary by Skin Site and Infant Age across Populations in Mexico and the United States

    This study contributes to the sparse literature on the infant skin microbiome in general, and the virtually nonexistent literature on the infant skin microbiome in a field setting. While microbiome research often addresses patterns at a national scale, this study addresses the influence of population-level factors, such as maternal socioeconomic status and contact with caregivers, on infant skin bacterial communities. This approach...

    Melissa B. Manus, Sahana Kuthyar, Ana Gabriela Perroni-Marañón, Alejandra Núñez-de la Mora, Katherine R. Amato
  • Open Access
    Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design
    Research Article | Applied and Environmental Science
    Measurement Error and Resolution in Quantitative Stable Isotope Probing: Implications for Experimental Design

    One of the biggest challenges in microbial ecology is correlating the identity of microorganisms with the roles they fulfill in natural environmental systems. Studies of microbes in pure culture reveal much about their genomic content and potential functions but may not reflect an organism’s activity within its natural community. Culture-independent studies supply a community-wide view of composition and function in the context of...

    Ella T. Sieradzki, Benjamin J. Koch, Alex Greenlon, Rohan Sachdeva, Rex R. Malmstrom, Rebecca L. Mau, Steven J. Blazewicz, Mary K. Firestone, Kirsten S. Hofmockel, Egbert Schwartz, Bruce A. Hungate, Jennifer Pett-Ridge
  • Open Access
    Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms
    Research Article | Applied and Environmental Science
    Continental-Scale Microbiome Study Reveals Different Environmental Characteristics Determining Microbial Richness, Composition, and Quantity in Hotel Rooms

    This is the first microbiome study to characterize the microbiome data and associated environmental characteristics in hotel environments. In this study, we found concordant variation between fungal compositional variation and absolute quantity and discordant variation between community variation/quantity and richness. Our study can be used to promote hotel hygiene standards and provide resource information for future microbiome and...

    Xi Fu, Yanling Li, Qianqian Yuan, Gui-hong Cai, Yiqun Deng, Xin Zhang, Dan Norbäck, Yu Sun

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