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metabolome

  • Open Access
    Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets
    Research Article | Host-Microbe Biology
    Human Milk-Fed Piglets Have a Distinct Small Intestine and Circulatory Metabolome Profile Relative to That of Milk Formula-Fed Piglets

    Exclusive HM feeding for newborns is recommended at least for the first 6 months of life. However, when breastfeeding is not possible, MF is recommended as a substitute.

    Fernanda Rosa, Katelin S. Matazel, Ahmed A. Elolimy, Sean H. Adams, Anne Bowlin, Keith D. Williams, Lars Bode, Laxmi Yeruva
  • Open Access
    The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in <span class="named-content genus-species" id="named-content-1">Azospirillum brasilense</span>
    Research Article | Molecular Biology and Physiology
    The Protein-Protein Interaction Network Reveals a Novel Role of the Signal Transduction Protein PII in the Control of c-di-GMP Homeostasis in Azospirillum brasilense

    The PII proteins sense and integrate important metabolic signals which reflect the cellular nutrition and energy status. Such extraordinary ability was capitalized by nature in such a way that the various PII proteins regulate different facets of metabolism by controlling the activity of a range of target proteins by protein-protein interactions. Here, we determined the PII protein interaction network in the plant growth-promoting...

    Edileusa C. M. Gerhardt, Erick Parize, Fernanda Gravina, Flávia L. D. Pontes, Adrian R. S. Santos, Gillize A. T. Araújo, Ana C. Goedert, Alysson H. Urbanski, Maria B. R. Steffens, Leda S. Chubatsu, Fabio O. Pedrosa, Emanuel M. Souza, Karl Forchhammer, Elena Ganusova, Gladys Alexandre, Gustavo A. de Souza, Luciano F. Huergo
  • Open Access
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic
    Observation | Novel Systems Biology Techniques
    Evaluating Organism-Wide Changes in the Metabolome and Microbiome following a Single Dose of Antibiotic

    We are just beginning to understand the unintended effects of antibiotics on our microbiomes and health. In this study, we aimed to define an approach by which one could obtain a comprehensive picture of (i) how antibiotics spatiotemporally impact commensal microbes throughout the gut and (ii) how these changes influence host chemistry throughout the body. We found that just a single dose of antibiotic altered host chemistry in a...

    Alison Vrbanac, Kathryn A. Patras, Alan K. Jarmusch, Robert H. Mills, Samuel R. Shing, Robert A. Quinn, Fernando Vargas, David J. Gonzalez, Pieter C. Dorrestein, Rob Knight, Victor Nizet
  • Open Access
    Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease
    Research Article | Host-Microbe Biology
    Gut Microbiota and Metabolome Alterations Associated with Parkinson’s Disease

    To our knowledge, this is one of the few studies thus far that correlates the composition of the gut microbiota with the direct analysis of fecal metabolites in patients with Parkinson’s disease. Overall, our data highlight microbiota modifications correlated with numerous fecal metabolites. This suggests that Parkinson’s disease is associated with gut dysregulation that involves a synergistic relationship between gut microbes and...

    Sarah Vascellari, Vanessa Palmas, Marta Melis, Silvia Pisanu, Roberto Cusano, Paolo Uva, Daniela Perra, Veronica Madau, Marianna Sarchioto, Valentina Oppo, Nicola Simola, Micaela Morelli, Maria Laura Santoru, Luigi Atzori, Maurizio Melis, Giovanni Cossu, Aldo Manzin
  • Open Access
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy
    Research Article | Clinical Science and Epidemiology
    High-Resolution Longitudinal Dynamics of the Cystic Fibrosis Sputum Microbiome and Metabolome through Antibiotic Therapy

    Subjects with cystic fibrosis battle polymicrobial lung infections throughout their lifetime. Although antibiotic therapy is a principal treatment for CF lung disease, we have little understanding of how antibiotics affect the CF lung microbiome and metabolome and how much the community changes on daily timescales. By analyzing 594 longitudinal CF sputum samples from six adult subjects, we show that the sputum microbiome and metabolome...

    Ruma Raghuvanshi, Karla Vasco, Yoshiki Vázquez-Baeza, Lingjing Jiang, James T. Morton, Danxun Li, Antonio Gonzalez, Lindsay DeRight Goldasich, Gregory Humphrey, Gail Ackermann, Austin D. Swafford, Douglas Conrad, Rob Knight, Pieter C. Dorrestein, Robert A. Quinn
  • 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
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs
    Research Article | Host-Microbe Biology
    Metabolome-Informed Microbiome Analysis Refines Metadata Classifications and Reveals Unexpected Medication Transfer in Captive Cheetahs

    Metabolome-informed analyses can enhance omics studies by enabling the correct partitioning of samples by identifying hidden confounders inadvertently misrepresented or omitted from carefully curated metadata. We demonstrate here the utility of metabolomics in a study characterizing the microbiome associated with liver disease in cheetahs. Metabolome-informed reinterpretation of metagenome and metabolome profiles factored in an...

    Julia M. Gauglitz, James T. Morton, Anupriya Tripathi, Shalisa Hansen, Michele Gaffney, Carolina Carpenter, Kelly C. Weldon, Riya Shah, Amy Parampil, Andrea L. Fidgett, Austin D. Swafford, Rob Knight, Pieter C. Dorrestein
  • Open Access
    Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice
    Research Article | Host-Microbe Biology
    Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice

    Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota....

    Kai Shan, Hongyan Qu, Keru Zhou, Liangfang Wang, Congmin Zhu, Haiqin Chen, Zhennan Gu, Jing Cui, Guoling Fu, Jiaqi Li, Heyan Chen, Rong Wang, Yumin Qi, Wei Chen, Yong Q. Chen
  • Open Access
    <span class="named-content genus-species" id="named-content-1">Pseudomonas aeruginosa</span> Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients
    Research Article | Novel Systems Biology Techniques
    Pseudomonas aeruginosa Alters Its Transcriptome Related to Carbon Metabolism and Virulence as a Possible Survival Strategy in Blood from Trauma Patients

    While a considerable body of knowledge regarding sepsis in trauma patients is available, the potential influence of trauma-induced changes in the blood of these patients on the pathogenesis of Pseudomonas aeruginosa is basically an unexplored area. Rather than using standard laboratory media, we grew P....

    Moamen M. Elmassry, Nithya S. Mudaliar, Kameswara Rao Kottapalli, Sharmila Dissanaike, John A. Griswold, Michael J. San Francisco, Jane A. Colmer-Hamood, Abdul N. Hamood
  • Open Access
    Alterations in Gut Glutamate Metabolism Associated with Changes in Gut Microbiota Composition in Children with Autism Spectrum Disorder
    Research Article | Host-Microbe Biology
    Alterations in Gut Glutamate Metabolism Associated with Changes in Gut Microbiota Composition in Children with Autism Spectrum Disorder

    Multiple lines of evidence suggest that the gut microbiota may play an important role in the pathogenesis of ASD, but the specific mechanism is still unclear. Through a comprehensive gut metagenomic and metabolome study of children with ASD, alterations in gut metabolite composition were found in children with ASD, and these alterations were linked to changes in gut microbiota composition. This may give us a deeper understanding of the...

    Mingbang Wang, Jing Wan, Han Rong, Fusheng He, Hui Wang, Jiaxiu Zhou, Chunquan Cai, Yan Wang, Ruihuan Xu, Zhaoqing Yin, Wenhao Zhou

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