Microbiome Publications from UVA

Microbiome Publications from UVA

(October 2019 - September 2020)

 

  1. Gut microbiome communication with bone marrow regulates susceptibility to amebiasis. Journal of Clinical Investigation. May 2020. Stacey L. Burgess, Jhansi L. Leslie, Md. Jashim Uddin, David Noah Oakland, Carol A. Gilchrist, G. Brett Moreau, Koji Watanabe, Mahmoud M. Saleh, Morgan Simpson, Brandon A. Thompson, David T. Auble, Stephen D. Turner, Natasa Giallourou, Jonathan Swann, Zhen Pu, Jennie Z. Ma, Rashidul Haque, and William A. Petri, Jr.

 

  1. Gram-negative Microbiota Blooms in Premature Twins Discordant for Parenteral Nutrition-associated Cholestasis. J Pediatr Gastroenterol Nutr. May 2020 Suchitra K. Hourigan, Thomas J. Moutinho Jr., Andrew Berenz, Jason Papin, Pallabi Guha, Lois Bangiolo, Sandra Oliphant, Marina Provenzano, Raj Baveja, Robin Baker, Thierry Vilboux, Shira Levy, Varsha Deopujari, James P. Nataro, John E. Niederhuber, Sean R. Moore

 

  1. Role of Microbiota-Derived Bile Acids in Enteric Infections. Cell. June 2020. Casey M Theriot and William A Petri Jr. 

 

  1. Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. PLoS Comput Biology. April 2020. Matthew L Jenior, Thomas J Moutinho Jr., Bonnie V Dougherty, Jason A Papin.

 

  1. Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract. Scientific Reports. September 2020. David M. Johanson II, Jennifer E. Goertz, Ioana A. Marin, John Costello, Christopher C. Overall, and Alban Gaultier

 

  1. MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. March 2020. Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E. Ebert, Janaka N. Edirisinghe, José P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Mark Poolman, Nathan D. Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J. Sánchez, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev & Cheng Zhang

 

  1. Evaluation of K18-hACE2 Mice as a Model of SARS-CoV-2 Infection. The American Society of Tropical Medicine and Hygiene. July 2020. Gregory Brett Moreau, Stacey L. Burgess, Jeffrey M. Sturek, Alexandra N. Donlan, William A. Petri Jr. and Barbara J. Mann

 

  1. Histone deacetylase inhibition by gut microbe-generated short chain fatty acids entrains intestinal epithelial circadian rhythms. Biorxiv. June 2020. Deborah H. Luzader, Jibraan A. Fawad, Thomas J. Moutinho Jr., Paul G. Mitchell, Kathleen Brown-Steinke, Jesse Y. Zhao, Andrew E. Rosselot, Craig A. McKinney, Christian I. Hong, C. James Chou, Jason A. Papin, & Sean R. Moore.

 

  1. Immune Profiling To Predict Outcome of Clostridioides difficile Infection. mBio. May 2020. Abhyankar MM, Ma JZ, Scully KW, Nafziger AJ, Frisbee AL, Saleh MM, Madden GR, Hays AR, Poulter M, Petri WA Jr.

 

  1. Role of Microbiota-Derived Bile Acids in Enteric Infections. Cell. June 2020. Theriot CM, Petri WA Jr.

 

  1. Gut microbial composition difference between pediatric ALL survivors and siblings. Pediatr Hematol Oncol. May 2020. Ronay Thomas, Wendy S W Wong, Reem Saadon, Thierry Vilboux, John Deeken, John Niederhuber, Suchitra K Hourigan, Elizabeth Yang.

 

  1. Assessment of the Urinary Microbiome in Children Younger Than 48 Months. Pediatric Infectious Disease. July 2020. Lauren Kinneman, Wei Zhu, Wendy S W Wong, Nicole Clemency, Marina Provenzano, Thierry Vilboux, Keary Jane't, Patricia Seo-Mayer, Rebecca Levorson, Maybelle Kou, David Ascher, John E Niederhuber, Suchitra K Hourigan.

 

  1. Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome. MicroOrganisms. Jan 2020. Wendy S W Wong, Priya Sabu, Varsha Deopujari, Shira Levy, Ankit A Shah, Nicole Clemency, Marina Provenzano, Reem Saadoon, Akhil Munagala, Robin Baker, Rajiv Baveja, Noel T Mueller, Maria Gloria Dominguez-Bello, Kathi Huddleston, John E Niederhuber., Suchitra K Hourigan.

 

  1. Studying the urine microbiome in superficial bladder cancer: samples obtained by midstream voiding versus cystoscopy. BMC Urology. Jan 2020. Suchitra K Hourigan, Wei Zhu, Wendy S W Wong, Nicole C Clemency, Marina Provenzano, Thierry Vilboux, John E Niederhuber, John Deeken, Simon Chung, Kim McDaniel-Wiley, Donald Trump. 

 

  1. Bacterial Baptism: Scientific, Medical, and Regulatory Issues Raised by Vaginal Seeding of C-Section-Born Babies. J. Law Medical Ethics. Jan 2020. Noel T Mueller, Suchitra K Hourigan, Diane E Hoffmann, Lauren Levy, Erik C von Rosenvinge, Betty Chou, Maria-Gloria Dominguez-Bello.

 

  1. 'Vaginal seeding' after a caesarean section provides benefits to newborn children: FOR: Does exposing caesarean-delivered newborns to the vaginal microbiome affect their chronic disease risk? The critical need for trials of 'vaginal seeding' during caesarean section. BJOG. Jan 2020. Noel T Mueller, Maria Gloria Dominguez-Bello, Lawrence J Appel, Suchitra K Hourigan.

 

  1. tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. RNA Biology. Jan 2020. Zhangli Su, Elizabeth L. Frost, Catherine R. Lammert, Roza K. Przanowska, John R. Lukens, and Anindya Dutta 

 

  1. Metabolic maturation in the first 2 years of life in resource-constrained settings and its association with postnatal growth. Science Advances. April 2020. N. Giallourou, F. Fardus-Reid, G. Panic, K. Veselkov, B. J. J. McCormick, M. P. Olortegui, T. Ahmed, E. Mduma, P. P. Yori, M. Mahfuz, E. Svensen, M. M. M. Ahmed, J. M. Colston, M. N. Kosek, and J. R. Swann.

 

  1. Immune Profiling To Predict Outcome of Clostridioides difficile Infection. mBio. May 2020. Mayuresh M. Abhyankar, Jennie Z. Ma, Kenneth W. Scully, Andrew J. Nafziger, Alyse L. Frisbee, Mahmoud M. Saleh, Gregory R. Madden, Ann R. Hays, Mendy Poulter, William A. Petri Jr.

 

  1. Considering the Immune System during Fecal Microbiota Transplantation for Clostridioides difficile Infection. Trends Mol Med. May 2020. Alyse L Frisbee, and William A Petri Jr. 

 

  1. Rapid in Vitro Assessment of Clostridioides difficile Inhibition by Probiotics Using Dielectrophoresis to Quantify Cell Structure Alterations. ACS Infect Dis. May 2020. John H Moore, Carlos Honrado, Victoria Stagnaro, Glynis Kolling, Cirle A Warren, and  Nathan S Swami

 

  1. Quantifying bacterial spore germination by single-cell impedance cytometry for assessment of host microbiota susceptibility to Clostridioides difficile infection. Biosens Bioelectron. October 2020. John H Moore, Armita Salahi, Carlos Honrado, Christopher Warburton, Cirle A Warren, and Nathan S Swami

 

  1. Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. ISME J. July 2020. Zhang Wang, Yuqiong Yang, Zhengzheng Yan, Haiyue Liu, Boxuan Chen, Zhenyu Liang, Fengyan Wang, Bruce E Miller, Ruth Tal-Singer, Xinzhu Yi, Jintian Li 4, Martin R Stampfli, Hongwei Zhou, Christopher E Brightling, James R Brown, Martin Wu, Rongchang Chen, and Wensheng Shu

 

  1. Rationale, design and baseline characteristics of the Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes Obes Metab. July 2020. Elizabeth T Jensen, Alain G Bertoni, Osa L Crago, Kristi L Hoffman, Alexis C Wood, Zorayr Arzumanyan, Lok-Sze Kelvin Lam, Kathryn Roll, Kevin Sandow, Martin Wu, Stephen S Rich, Jerome I Rotter, Yii-Der I Chen, Joseph F Petrosino, and Mark O Goodarzi

 

  1. Dietary serine-microbiota interaction enhances chemotherapeutic toxicity without altering drug conversion. Nature Communications. May 2020. Wenfan Ke, James A Saba, Cong-Hui Yao, Michael A Hilzendeger, Anna Drangowska-Way, Chintan Joshi, Vinod K Mony, Shawna B Benjamin, Sisi Zhang, Jason Locasale, Gary J Patti, Nathan Lewis, and Eyleen J O'Rourke

 

  1. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol. September 2020. Martin Kapun, Maite G Barrón, Fabian Staubach, Darren J Obbard, R Axel W Wiberg, Jorge Vieira, Clément Goubert, Omar Rota-Stabelli, Maaria Kankare, María Bogaerts-Márquez, Annabelle Haudry, Lena Waidele, Iryna Kozeretska, Elena G Pasyukova, Volker Loeschcke, Marta Pascual, Cristina P Vieira, Svitlana Serga, Catherine Montchamp-Moreau, Jessica Abbott, Patricia Gibert, Damiano Porcelli, Nico Posnien, Alejandro Sánchez-Gracia, Sonja Grath, Élio Sucena, Alan O Bergland, Maria Pilar Garcia Guerreiro, Banu Sebnem Onder, Eliza Argyridou, Lain Guio, Mads Fristrup Schou, Bart Deplancke, Cristina Vieira, Michael G Ritchie, Bas J Zwaan, Eran Tauber, Dorcas J Orengo, Eva Puerma, Montserrat Aguadé, Paul Schmidt, John Parsch, Andrea J Betancourt, Thomas Flatt, and Josefa González

 

  1. Amixicile depletes the ex vivo periodontal microbiome of anaerobic bacteria. J Oral Biosci. June 2020. Qin Gui, Kane W Ramsey, Paul S Hoffman, and Janina P Lewis.

 

  1. Neuroimmunomodulation of tissue injury and disease: an expanding view of the inflammatory reflex pathway. Bioelectron Med. September 2019. Shinji Tanaka, Benjamin Hammond, Diane L Rosin, and Mark D Okusa. 

 

  1. Nutrients influence the dynamics of Klebsiella pneumoniae carbapenemase producing enterobacterales in transplanted hospital sinks. Water Res. June 2020. Shireen Meher Kotay, Hardik I Parikh, Katie Barry, Hyun Soon Gweon, William Guilford, Joanne Carroll, Amy J Mathers

 

  1. Design and rationale of a multi-center, pragmatic, open-label randomized trial of antimicrobial therapy - the study of clinical efficacy of antimicrobial therapy strategy using pragmatic design in Idiopathic Pulmonary Fibrosis (CleanUP-IPF) clinical trial. Respir Res. Mar 2020. Kevin J Anstrom, Imre Noth, Kevin R Flaherty, Rex H Edwards, Joan Albright, Amanda Baucom, Maria Brooks, Allan B Clark, Emily S Clausen, Michael T Durheim, Dong-Yun Kim, Jerry Kirchner, Justin M Oldham, Laurie D Snyder, Andrew M Wilson, Stephen R Wisniewski, Eric Yow, Fernando J Martinez, and CleanUP-IPF Study Team

 

  1. Evidence-Based Updates on the First Week of Exclusive Breastfeeding Among Infants ≥35 Weeks. Pediatrics. April 2020. Lori Feldman-Winter, Ann Kellams, Sigal Peter-Wohl, Julie Scott Taylor, Kimberly G. Lee, Mary J. Terrell, Lawrence Noble, Angela R. Maynor, Joan Younger Meek and Alison M. Stuebe

 

  1. ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis. PLoS Comp Bio. Mar 2020. Arshag D Mooradian, Sjoerd van der Post, Kristen M Naegle, and Jason M Held

 

  1. A survey of bacteria associated with various life stages of primary colonizers: Lucilia sericata and Phormia regina. Sci Justice. March 2020. Denise Wohlfahrt, M Shane Woolf, and Baneshwar Singh

 

  1. Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate. Environ Microbiol Rep. April 2020. Yun Wang, Martin Kapun , Lena Waidele, Sven Kuenzel, Alan O Bergland, and Fabian Staubach

 

  1. Evolving concepts in how viruses impact asthma: A Work Group Report of the Microbes in Allergy Committee of the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol. May 2020. Matthew C Altman, Avraham Beigelman, Christina Ciaccio, James E Gern, Peter W Heymann, Daniel J Jackson, Joshua L Kennedy, Kirsten Kloepfer, Robert F Lemanske Jr, Laurie M McWilliams, Lyndsey Muehling, Christy Nance, and R Stokes Peebles Jr 

 

  1. Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer. Plos One. May 2020. Ruizhong Miao, Taylor C. Badger, Kathleen Groesch, Paula L. Diaz-Sylvester, Teresa Wilson, Allen Ghareeb, Jongjin Anne Martin, Melissa Cregger, Michael Welge, Colleen Bushell, Loretta Auvil, Ruoqing Zhu, Laurent Brard, and Andrea Braundmeier-Fleming

 

  1. Diarrhea as a Potential Cause and Consequence of Reduced Gut Microbial Diversity Among Undernourished Children in Peru. Clin Infect Dis. August 2020. Saba Rouhani, Nicholas W Griffin, Pablo Peñataro Yori, Jeanette L Gehrig, Maribel Paredes Olortegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H Moulton, Eric R Houpt, Michael J Barratt, Margaret N Kosek, and Jeffrey I Gordon

 

  1. Gut Microbiota Features Associated With Campylobacter Burden and Postnatal Linear Growth Deficits in a Peruvian Birth Cohort. Clin Infect Dis. August 2020. Saba Rouhani, Nicholas W Griffin, Pablo Peñataro Yori, Maribel Paredes Olortegui, Mery Siguas Salas, Dixner Rengifo Trigoso, Lawrence H Moulton, Eric R Houpt, Michael J Barratt, Margaret N Kosek, and Jeffrey I Gordon

 

  1. Amixicile targets anaerobic bacteria within the oral microbiome. J Oral BioSci. Dec 2019. Qin Gui, Paul S Hoffman, and Janina P Lewis.

 

  1. The placental microbiome: yea, nay or maybe? BJOG. January 2020. D J Dudley.

 

  1. Influence of Maternal Prepregnancy Obesity and Excessive Gestational Weight Gain on Maternal and Child Gastrointestinal Microbiome Composition: A Systematic Review. Biol Res Nurs. January 2020. Caitlin Dreisbach, Stephanie Prescott, and Jeanne Alhusen

 

  1. Vendor-specific microbiome controls both acute and chronic murine lung allograft rejection by altering CD4 + Foxp3 + regulatory T cell levels. Am J Transplant. October 2019. Yizhan Guo, Qing Wang, Dongge Li, Oscar Okwudiri Onyema, Zhongcheng Mei, Amir Manafi, Anirban Banerjee, Bayan Mahgoub, Mark H Stoler, Thomas H Barker, David S Wilkes, Andrew E Gelman, Daniel Kreisel, and Alexander Sasha Krupnick