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microbiota

  • Open Access
    Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder
    Research Article | Applied and Environmental Science
    Tracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder

    Microorganisms can enter and persist in dairy at several stages of the processing chain. Detection of microorganisms within dairy food processing is currently a time-consuming and often inaccurate process. This study provides evidence that high-throughput sequencing can be used as an effective tool to accurately identify microorganisms along the processing chain. In addition, it demonstrates that the populations of microbes change from...

    Aoife J. McHugh, Conor Feehily, Mark A. Fenelon, David Gleeson, Colin Hill, Paul D. Cotter
  • Open Access
    Depletion of <em>Blautia</em> Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening
    Research Article | Host-Microbe Biology
    Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening

    Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin...

    Alfonso Benítez-Páez, Eva M. Gómez del Pugar, Inmaculada López-Almela, Ángela Moya-Pérez, Pilar Codoñer-Franch, Yolanda Sanz
  • Open Access
    Correlations between the Composition of the Bovine Microbiota and Vitamin B<sub>12</sub> Abundance
    Research Article | Host-Microbe Biology
    Correlations between the Composition of the Bovine Microbiota and Vitamin B12 Abundance

    In this paper, we examined the microbiome of the bovine rumen, feces, and milk and attempted to understand how the bacterial communities at each site affected the production and movement of vitamin B12 around the animal’s body. It was determined that the composition of the bovine rumen microbiome correlates well with vitamin B12 concentration, indicating that the rumen microbiota may be a good target for...

    Julian Franco-Lopez, Melissa Duplessis, An Bui, Coralie Reymond, William Poisson, Lya Blais, Jasmine Chong, Rachel Gervais, Daniel E. Rico, Roger I. Cue, Christiane L. Girard, Jennifer Ronholm
  • Open Access
    Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines
    Research Article | Novel Systems Biology Techniques
    Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

    Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to...

    Q. R. Ducarmon, B. V. H. Hornung, A. R. Geelen, E. J. Kuijper, R. D. Zwittink
  • Open Access
    Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation
    Research Article | Applied and Environmental Science
    Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation

    Solid-state fermentation (SSF) plays pivotal roles not only in human food but also farm animal diets. Soybean meal (SBM) and corn account for approximately 70% of the global feed consumption. However, the nutritional value of conventional SBM and corn mixed substrates (MS) is limited by antinutritional factors, causing substantial economic loss in livestock production. Although emerging studies have reported that SSF can improve the...

    Cheng Wang, Changyou Shi, Weifa Su, Mingliang Jin, Bocheng Xu, Lihong Hao, Yu Zhang, Zeqing Lu, Fengqin Wang, Yizhen Wang, Huahua Du
  • Open Access
    Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer
    Research Article | Host-Microbe Biology
    Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer

    Bacteria and bacterial biofilms have been implicated in colorectal cancer (CRC), but it is still unclear what genes these microbial communities express and how they influence the host. MicroRNAs regulate host gene expression and have been explored as potential biomarkers for CRC. An emerging area of research is the ability of microRNAs to impact growth and gene expression of members of the intestinal microbiota. This study examined the...

    Sarah Tomkovich, Raad Z. Gharaibeh, Christine M. Dejea, Jillian L. Pope, Jinmai Jiang, Kathryn Winglee, Josee Gauthier, Rachel C. Newsome, Ye Yang, Anthony A. Fodor, Thomas D. Schmittgen, Cynthia L. Sears, Christian Jobin
  • Open Access
    Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice
    Research Article | Host-Microbe Biology
    Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice

    Several previous studies have pointed to environmental chemical exposure during windows of development as a contributing factor in neurodevelopmental disorders and correlated these disorders with microbiota dysbiosis; however, little is known about how the chemicals specifically alter the microbiota to interfere with development. The findings reported in this paper unambiguously establish that a pollutant linked with neurodevelopmental...

    Ming Lei, Rani Menon, Sara Manteiga, Nicholas Alden, Carrie Hunt, Robert C. Alaniz, Kyongbum Lee, Arul Jayaraman
  • Open Access
    Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia
    Research Article | Host-Microbe Biology
    Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia

    Bronchopulmonary dysplasia (BPD) is a serious inflammatory condition of the lung and is the most common complication associated with preterm birth. A large body of evidence now suggests that the gut microbiota can influence immunity and inflammation systemically; however, the role of the gut microbiota in BPD has not been evaluated to date. Here, we report that there are significant differences in the gut microbiota of infants born at...

    Feargal J. Ryan, Damian P. Drew, Chloe Douglas, Lex E. X. Leong, Max Moldovan, Miriam Lynn, Naomi Fink, Anastasia Sribnaia, Irmeli Penttila, Andrew J. McPhee, Carmel T. Collins, Maria Makrides, Robert A. Gibson, Geraint B. Rogers, David J. Lynn
  • Open Access
    <em>MetaMed</em>: Linking Microbiota Functions with Medicine Therapeutics
    Opinion/Hypothesis | Therapeutics and Prevention
    MetaMed: Linking Microbiota Functions with Medicine Therapeutics

    Understanding how the human microbiome affects human health has consequences for treating disease and minimizing unwanted side effects in clinical research.

    Han Zhao, Shaliu Fu, Yifei Yu, Zhanbing Zhang, Ping Li, Qin Ma, Wei Jia, Kang Ning, Shen Qu, Qi Liu
  • 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

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