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16S rRNA

  • Open Access
    Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics
    Research Article
    Air versus Water Chilling of Chicken: a Pilot Study of Quality, Shelf-Life, Microbial Ecology, and Economics

    As the poultry industry works to become more sustainable and to reduce the volume of food waste, it is critical to consider points in the processing system that can be altered to make the process more efficient. In this study, we demonstrate that the method used during chilling (air versus water chilling) influences the final product microbial community, quality, and physiochemistry.

    Aeriel D. Belk, Toni Duarte, Casey Quinn, David A. Coil, Keith E. Belk, Jonathan A. Eisen, Jason C. Quinn, Jennifer N. Martin, Xiang Yang, Jessica L. Metcalf
  • Open Access
    Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice
    Research Article | Clinical Science and Epidemiology
    Data Analysis Strategies for Microbiome Studies in Human Populations—a Systematic Review of Current Practice

    The human microbiome has emerged as an important factor in the development of health and disease. Growing interest in this topic has led to an increasing number of studies investigating the human microbiome using high-throughput sequencing methods.

    Sven Kleine Bardenhorst, Tom Berger, Frank Klawonn, Marius Vital, André Karch, Nicole Rübsamen
  • Open Access
    A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community
    Research Article | Host-Microbe Biology
    A 16S rRNA Gene and Draft Genome Database for the Murine Oral Bacterial Community

    Mouse model studies are frequently used in oral microbiome research, particularly to investigate diseases such as periodontitis and caries, as well as other related systemic diseases. We have reported here the details of the development of a curated reference database to characterize the oral microbial community in laboratory and some wild mice.

    Susan Joseph, Joseph Aduse-Opoku, Ahmed Hashim, Eveliina Hanski, Ricarda Streich, Sarah C. L. Knowles, Amy B. Pedersen, William G. Wade, Michael A. Curtis
  • Open Access
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes
    Research Article | Ecological and Evolutionary Science
    Chemical Profiling Provides Insights into the Metabolic Machinery of Hydrocarbon-Degrading Deep-Sea Microbes

    High-throughput technologies and emerging informatics tools have significantly advanced knowledge of hydrocarbon metabolism by marine microbes. However, research into microbes inhabiting deep-sea sediments (>1,000 m) is limited compared to those found in shallow waters. In this study, a nontargeted and nonclassical approach was used to examine the diversity of bacterial taxa and the metabolic profiles of hydrocarbon-degrading deep-...

    Aldo Moreno-Ulloa, Victoria Sicairos Diaz, Javier A. Tejeda-Mora, Marla I. Macias Contreras, Fernando Díaz Castillo, Abraham Guerrero, Ricardo Gonzalez Sanchez, Omar Mendoza-Porras, Rafael Vazquez Duhalt, Alexei Licea-Navarro
  • Open Access
    Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics
    Research Article | Host-Microbe Biology
    Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics

    The proximal colon and cecum are two intestinal regions in which the microbiome localizes to two spatially distinct compartments, the lumen and crypts. The differences in composition and function of luminal and crypt microbiome in the cecum and the effect of physiological stress on their compartmentalization remain poorly characterized. Here, we characterized the composition and function of the lumen-, mucus-, and crypt-associated...

    Alexander Zaborin, Beatriz Penalver Bernabe, Robert Keskey, Naseer Sangwan, Sanjiv Hyoju, Neil Gottel, Jack A. Gilbert, Olga Zaborina, John C. Alverdy
  • Open Access
    Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue
    Research Article | Host-Microbe Biology
    Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue

    Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between...

    Zongchao Mo, Peide Huang, Chao Yang, Sihao Xiao, Guojia Zhang, Fei Ling, Lin Li
  • Open Access
    Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry
    Research Article | Applied and Environmental Science
    Randomized Lasso Links Microbial Taxa with Aquatic Functional Groups Inferred from Flow Cytometry

    A 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...

    Peter Rubbens, Marian L. Schmidt, Ruben Props, Bopaiah A. Biddanda, Nico Boon, Willem Waegeman, Vincent J. Denef
  • Open Access
    Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing
    Research Article | Clinical Science and Epidemiology
    Identification of Initial Colonizing Bacteria in Dental Plaques from Young Adults Using Full-Length 16S rRNA Gene Sequencing

    Selective attachment of salivary bacteria to the tooth surface is an initial and repetitive phase in dental plaque development. We employed full-length 16S rRNA gene sequence analysis with a high taxonomic resolution using a third-generation sequencer, PacBio Sequel, to determine the bacterial composition during early plaque formation in 74 young adults accurately and in detail. The results revealed 21 bacterial taxa primarily involved...

    Yukari Ihara, Toru Takeshita, Shinya Kageyama, Rie Matsumi, Mikari Asakawa, Yukie Shibata, Yuki Sugiura, Kunio Ishikawa, Ichiro Takahashi, Yoshihisa Yamashita
  • Open Access
    16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
    Research Article | Ecological and Evolutionary Science
    16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

    Although 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...

    Alan W. Bowsher, Patrick J. Kearns, Ashley Shade
  • Open Access
    Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils
    Editor's Pick Research Article | Host-Microbe Biology
    Qualitative and Quantitative DNA- and RNA-Based Analysis of the Bacterial Stomach Microbiota in Humans, Mice, and Gerbils

    Clinical stomach interventions, such as acid inhibition or bypass surgery, have been linked to fecal microbiota alterations. We demonstrate that the stomach microbiota largely overlaps those of adjacent gastrointestinal locations and identify gradual decreases and increases in the relative abundances of specific bacteria within the stomach, suggesting selective enrichment and depletion. Moreover, similarities between stomach and...

    Philipp Wurm, Elisabeth Dörner, Christina Kremer, Julia Spranger, Cynthia Maddox, Bettina Halwachs, Ute Harrison, Thomas Blanchard, Rainer Haas, Christoph Högenauer, Gregor Gorkiewicz, W. Florian Fricke

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