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microbiota

  • Open Access
    Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese
    Research Article | Applied and Environmental Science
    Microbiota Assessments for the Identification and Confirmation of Slit Defect-Causing Bacteria in Milk and Cheddar Cheese

    Food production involves numerous control points for microorganisms to ensure quality and safety. These control points (e.g., pasteurization) are difficult to develop for fermented foods wherein some microbial contaminants are also expected to provide positive contributions to the final product and spoilage microbes may constitute only a small proportion of all microorganisms present.

    Zhengyao Xue, Jason T. Brooks, Zachary Quart, Eric T. Stevens, Mary E. Kable, Jessie Heidenreich, Jeremy McLeod, Maria L. Marco
  • Open Access
    Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data
    Research Article | Applied and Environmental Science
    Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data

    To solve the problem of amplicon sequencing cannot discern the microbiota absolute abundance, we proposed a gradient internal standard absolute quantification method. We used Chinese liquor fermentation as a model system to demonstrate the reliability and accuracy of the method.

    Shilei Wang, Qun Wu, Ying Han, Rubing Du, Xiaoyong Wang, Yao Nie, Xiaowei Du, Yan Xu
  • Open Access
    Phages versus Antibiotics To Treat Infected Diabetic Wounds in a Mouse Model: a Microbiological and Microbiotic Evaluation
    Research Article | Therapeutics and Prevention
    Phages versus Antibiotics To Treat Infected Diabetic Wounds in a Mouse Model: a Microbiological and Microbiotic Evaluation

    The management of diabetic foot infections is frequently a dead end for surgeons and infectious disease specialists. When the pathogen to be treated is not resistant to conventional antibiotics, the latter tend to unbalance the intestinal microbiota, which is linked to multiple pathologies. A local treatment with bacteriophages, in addition to being as much or even more effective than antibiotics from a clinical and microbiological...

    Jean-François Huon, Emmanuel Montassier, Anne-Gaëlle Leroy, Matthieu Grégoire, Marie-Anne Vibet, Jocelyne Caillon, David Boutoille, Dominique Navas
  • Open Access
    Correlations between α-Linolenic Acid-Improved Multitissue Homeostasis and Gut Microbiota in Mice Fed a High-Fat Diet
    Research Article | Host-Microbe Biology
    Correlations between α-Linolenic Acid-Improved Multitissue Homeostasis and Gut Microbiota in Mice Fed a High-Fat Diet

    Insufficient intake of n-3 polyunsaturated fatty acids is an important issue in modern Western-style diets. A large amount of evidence now suggests that a balanced intestinal microecology is considered an important part of health. Our results show that α-linolenic acid administration significantly improved the host metabolic phenotype and gut microbiota of mice fed a high-fat diet, and there was a correlation between the...

    Xiaoyu Gao, Songlin Chang, Shuangfeng Liu, Lei Peng, Jing Xie, Wenming Dong, Yang Tian, Jun Sheng
  • Open Access
    Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship
    Research Article | Host-Microbe Biology
    Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship

    In a healthy colon, the microbiota produces a vast amount of metabolites that are essential to maintaining homeostasis in the colon microenvironment. In fact, these metabolites produced by the microbiota have been linked to diseases such as obesity, cardiovascular disease, and colorectal cancer. In this study, we used healthy nonhuman primate models to investigate the relationship between microbiota and tissue metabolites. We found that...

    Ce Yuan, Melanie Graham, Christopher Staley, Subbaya Subramanian
  • Open Access
    Recombinant HcGAPDH Protein Expressed on Probiotic <em>Bacillus subtilis</em> Spores Protects Sheep from <em>Haemonchus contortus</em> Infection by Inducing both Humoral and Cell-Mediated Responses
    Research Article | Host-Microbe Biology
    Recombinant HcGAPDH Protein Expressed on Probiotic Bacillus subtilis Spores Protects Sheep from Haemonchus contortus Infection by Inducing both Humoral and Cell-Mediated Responses

    Initial analyses of the abomasal microbiota of sheep using 16S rRNA sequencing suggested that probiotic bacteria played a protective role in against H. contortus infection. A recombinant Bacillus subtilis expressing a fusion protein CotB-HcGAPDH on its spore’s surface induced strong Th1 immune response in a murine model. The same probiotic recombinant, upon...

    Yi Yang, Guiheng Zhang, Jie Wu, Xueqiu Chen, Danni Tong, Yimin Yang, Hengzhi Shi, Chaoqun Yao, Lenan Zhuang, Jianbin Wang, Aifang Du
  • 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

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