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16S rRNA gene

  • 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
    The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics
    Research Article | Host-Microbe Biology
    The Gut Microbial Diversity of Newly Diagnosed Diabetics but Not of Prediabetics Is Significantly Different from That of Healthy Nondiabetics

    Gut microbiota is considered to play a role in disease progression, and previous studies have reported an association of microbiome dysbiosis with T2D. In this study, we have attempted to investigate gut microbiota of ND, PreDMs, NewDMs, and KnownDMs. We found that the genera Akkermansia and Blautia decreased significantly (P < 0.05) in treatment-naive diabetics and were restored in KnownDMs on antidiabetic...

    Akshay H. Gaike, Dhiraj Paul, Shrikant Bhute, Dhiraj P. Dhotre, Pranav Pande, Smitha Upadhyaya, Yugandhar Reddy, Ramya Sampath, Debjani Ghosh, D. Chandraprabha, Jhankar Acharya, Gautam Banerjee, Vilas P. Sinkar, Saroj S. Ghaskadbi, Yogesh S. Shouche
  • Open Access
    FORENSIC: an Online Platform for Fecal Source Identification
    Research Article | Applied and Environmental Science
    FORENSIC: an Online Platform for Fecal Source Identification

    FORENSIC is an online platform to identify sources of fecal pollution without the need to create reference libraries. FORENSIC is based on the ability of random forest classification to extract cohesive source microbial signatures to create classifiers despite individual variability and to detect the signatures in environmental samples. We primarily focused on defining sewage signals, which are associated with a high human health risk...

    Adélaïde Roguet, Özcan C. Esen, A. Murat Eren, Ryan J. Newton, Sandra L. McLellan
  • Open Access
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research
    Research Article | Novel Systems Biology Techniques
    Quantifying and Understanding Well-to-Well Contamination in Microbiome Research

    Microbiome research has uncovered magnificent biological and chemical stories across nearly all areas of life science, at times creating controversy when findings reveal fantastic descriptions of microbes living and even thriving in what were once thought to be sterile environments. Scientists have refuted many of these claims because of contamination, which has led to robust requirements, including the use of controls, for validating...

    Jeremiah J. Minich, Jon G. Sanders, Amnon Amir, Greg Humphrey, Jack A. Gilbert, Rob Knight
  • Open Access
    Selected Immunological Mediators and Cervical Microbial Signatures in Women with <span class="named-content genus-species" id="named-content-1">Chlamydia trachomatis</span> Infection
    Research Article | Host-Microbe Biology
    Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection

    To our knowledge, this is the first study that investigated the association of C. trachomatis with the cervical levels of lactoferrin and selected inflammatory mediators and their correlation with the different community state types characterizing the female genital ecosystem. C. trachomatis, known...

    Simone Filardo, Marisa Di Pietro, Giulia Tranquilli, Maria Agnese Latino, Nadia Recine, Maria Grazia Porpora, Rosa Sessa
  • Open Access
    Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling
    Methods and Protocols | Novel Systems Biology Techniques
    Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling

    Large-scale human microbiota studies require specimens collected from multiple sites and/or time points to maximize detection of the small effects in microbe-host interactions. However, batch biases caused by experimental protocols, such as sample collection, massively parallel sequencing, and bioinformatics analyses, remain critical and should be minimized. This work evaluated the effects of preservation solutions and bacterial 16S...

    Zigui Chen, Pak Chun Hui, Mamie Hui, Yun Kit Yeoh, Po Yee Wong, Martin C. W. Chan, Martin C. S. Wong, Siew C. Ng, Francis K. L. Chan, Paul K. S. Chan
  • Open Access
    Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota
    Research Article | Novel Systems Biology Techniques
    Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota

    The human gut microbiome is the subject of intense study due to its importance in health and disease. The majority of these studies have been based on the analysis of feces. However, little is known about how the microbial composition in fecal samples relates to the spatial distribution of microbial taxa along the gastrointestinal tract. By characterizing the microbial content both in intestinal tissue samples and in fecal samples...

    Eric J. de Muinck, Knut E. A. Lundin, Pål Trosvik
  • Open Access
    Meta-analysis To Define a Core Microbiota in the Swine Gut
    Research Article | Host-Microbe Biology
    Meta-analysis To Define a Core Microbiota in the Swine Gut

    The results of this meta-analysis demonstrate that “study” and GI sample location are the most significant factors in shaping the swine gut microbiota. However, in comparisons of results from different studies, some biological factors may be obscured by technical variation among studies. Nonetheless, there are some bacterial taxa that appear to form a core microbiota within the swine GI tract regardless of country of origin, diet, age,...

    Devin B. Holman, Brian W. Brunelle, Julian Trachsel, Heather K. Allen
  • Open Access
    Microbial Communities Are Well Adapted to Disturbances in Energy Input
    Editor's Pick Research Article | Ecological and Evolutionary Science
    Microbial Communities Are Well Adapted to Disturbances in Energy Input

    Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic “...

    Nuria Fernandez-Gonzalez, Julie A. Huber, Joseph J. Vallino
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