2022
Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT)
Dawud Abduweli Uyghurturk, Ying Lu, Janelle Urata, Christopher C. Dvorak, and Pamela Den Besten. Peerj, 2022
A novel in silico method employs chemical and protein similarity algorithms to accurately identify chemical transformations in the human gut microbiome
Annamarie Bustion, Ayushi Agrawal, Peter J. Turnbaugh, Katherine S. Pollard. bioRxiv, 2022
Human gut bacterial metabolism drives Th17 activation and colitis
Margaret Alexander, Qi Yan Ang, Renuka R. Nayak, Annamarie E. Bustion, Moriah Sandy, Bing Zhang, Vaibhav Upadhyay, Katherine S. Pollard, Susan V. Lynch, Peter J. Turnbaugh. Cell, 2022
FLG Deficiency in Mice Alters the Early-Life CD4+ T-Cell Response to Skin Commensal Bacteria
Jeanmarie R. Gonzalez, Anna Celli, Antonin Weckel, Miqdad O. Dhariwala, Geil R. Merana, Oluwasunmisola T. Ojewumi, Joy Okoro, Laura R. Dwyer, Victoria M. Tran, Jason M. Meyer, Theodora M. Mauro, Tiffany C. Scharschmidt. Journal of Investigative Dermatology, 2022
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Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome
Chih-Chiun J. Chang, Karina Somohano, Christine Zemsky, Anne-Catrin Uhlemann,
Jeffrey Liebmann, George A. Cioffi, Lama A. Al-Aswad, Susan V. Lynch, and
Bryan J. Winn. Investigative Ophthalmology & Visual Science, 2022
Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization
Xiaofan Jin, Feiqiao B. Yu, Jia Yan, Allison Weakley, and Katherine S. Pollard. bioRxiv, 2022
Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome
Chih-Chiun J. Chang; Karina Somohano; Christine Zemsky; Anne-Catrin Uhlemann; Jeffrey Liebmann; George A. Cioffi; Lama A. Al-Aswad; Susan V. Lynch and Bryan J. Winn. Investigative Ophthalmology & Visual Science, 2022
The best offense is a good beta-defensin
Miqdad O. Dhariwala, and Tiffany C . Scharschmidt. Immunity, 2022
Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy
Kathryn E. McCauley, Elze Rackaityte, Brandon LaMere, Douglas W. Fadrosh, Kei E. Fujimura, Ariane R. Panzer, Din L. Lin, Kole V. Lynch, Joanna Halkias, Ventura F. Mendoza, Trevor D. Burt, Casper Bendixsen, Kathrine Barnes, Haejin Kim, Kyra Jones, Dennis R. Ownby, Christine C. Johnson, Christine M. Seroogy, James E. Gern 8, Homer A. Boushey, and Susan V. Lynch. Cell Reports Medicine, 2022
Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism
Peter Spanogiannopoulos, Than S. Kyaw, Ben G. H. Guthrie, Patrick H. Bradley, Joyce V. Lee, Jonathan Melamed, Ysabella Noelle Amora Malig, Kathy N. Lam, Daryll Gempis, Moriah Sandy, Wesley Kidder, Erin L. Van Blarigan, Chloe E. Atreya, Alan Venook, Roy R. Gerona, Andrei Goga, Katherine S. Pollard & Peter J. Turnbaugh. Nature Microbiology, 2022
Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
Xiaoyuan Zhou, Ryan Baumann, Xiaohui Gao, Myra Mendoza, Sneha Singh, Ilana Katz Sand, Zongqi Xia, Laura M. Cox, Tanuja Chitnis, Hongsup Yoon, Laura Moles, Stacy J. Caillier, Adam Santaniello, Gail Ackermann, Adil Harroud, Robin Lincoln, Refujia Gomez, Antonio González Peña, Elise Digga, Daniel Joseph Hakim, Yoshiki Vazquez-Baeza, Karthik Soman, Shannon Warto, Greg Humphrey, Mauricio Farez, Lisa Ann Gerdes, Jorge R. Oksenberg, Scott S. Zamvil, Siddharthan Chandran, Peter Connick, David Otaegui, Tamara Castillo-Triviño, Stephen L. Hauser, Jeffrey M. Gelfand, Howard L. Weiner, Reinhard Hohlfeld, Hartmut Wekerle, Jennifer Graves, Amit Bar-Or, Bruce A.C. Cree, Jorge Correale, Rob Knight, Sergio E. Baranzini. Cell, 2022
Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
Eric Armstrong, Anke Hemmerling, Steve Miller, Kerianne E Burke, Sara J Newmann, Sheldon R Morris, Hilary Reno, Sanja Huibner, Maria Kulikova,
Nico Nagelkerke, Bryan Coburn, Craig R Cohen, Rupert Kaul. The Lancet Microbe, 2022
A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation
Mustafa O¨ zcam, Jee-Hwan Oh, Restituto Tocmo, Tim S. Bugni, Jens Walter, Jan-Peter van Pijkeren.
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Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis
Byron J. Smith, Yvette Piceno, Martin Zydek, Bing Zhang Lara Aboud Syriani, Jonathan P. Terdiman, Zain Kassam, Averil Ma, Susan V. Lynch, Katherine S. Pollard, and Najwa El‑Nache. Scientific Reports 2022
Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
Eric Armstrong, Anke Hemmerling, Steve Miller, Kerianne E Burke, Sara J Newmann, Sheldon R Morris, Hilary Reno, Sanja Huibner, Maria Kulikova, Nico Nagelkerke, Bryan Coburn, Craig R Cohen, and Rupert Kaul. Lancet Microbe, 2022
Microbial stsueijignals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage
Iulia Rusu, Elvira Mennillo, Jared L. Bain, Zhongmei Li, Xiaofei Sun, Kimberly M. Ly, Yenny Y. Rosli, Mohammad Naser, Zunqiu Wang, Rommel Advincula, Philip Achacoso, Ling Shao, Bahram Razani, Ophir D. Klein, Alexander Marson, Jessie A. Turnbaugh, Peter J. Turnbaugh, Barbara A. Malynn, Averil Ma, and Michael G. Kattah. J Clin Invest. 2022
MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome‐metabolome data
Cecilia Noecker, Alexander Eng, Efrat Muller, Elhanan Borenstein. Bioinformatics, 2022.
DART takes aim at community editing
Connie W. Y. Ha & Suzanne Devkota, Nature Microbiology, 2022
2021
Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis
Kathryn E. McCauley, Gregory DeMuri, Kole Lynch, Douglas W. Fadrosh, Clark Santee, Nabeetha N. Nagalingam, Ellen R, Wald, Susan V. Lynch. PLOS One, 2021.
The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
Joshua Ladau, Katrina Abuabara, Angelica M. Walker, Marcin P. Joachimiak, Ishan Bansal, Yulun Wu, Elijah B. Hoffman, Chaincy Kuo, Nicola Falco, Jared Streich, Mark J. van der Laan, Haruko M. Wainwright, Eoin L. Brodie, Matthias Hess, Daniel Jacobson, and James B. Brown. MedRXiv (preprint), 2021.
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro
Zhou Jason Shi, Boris Dimitrov, Chunyu Zhao, Stephen Nayfach & Katherine S. Pollard. Nature Biotechnology, 2021.
Periodontal Disease: The Good, The Bad, and The Unknown
Lea M. Sedghi, Margot Bacino and Yvonne Lorraine Kapila.. Front. Cell. Infect. Microbiol., 2021.
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic, Yvonne L.Kapila. Computational and Structural Biotechnology Journal, 2021
Baby’s skin bacteria: first impressions are long-lasting
Miqdad O.Dhariwala, Tiffany C.Scharschmidt, Trends in Immunology, 2021
Human gut bacterial metabolism drives Th17 activation and colitis
Margaret Alexander, Qi Yan Ang, Renuka R.Nayak, Annamarie E.Bustion, Moriah Sandy, Bing Zhang, Vaibhav Upadhyay, Katherine S.Pollard, Susan V. Lynch, Peter J.Turnbaugh. Cell Host & Microbe, 2021.
Black In Immuno: harnessing social media and digital platforms to connect the dots
Joel Babdor, Amy C. Fan, Madina Wane, Berenice Mbiribindi, Alexis S. Mobley, Justine C. Noel & Elaine Kouame. Nature Reviews Immunology, 2021
Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome
Kathy N. Lam, Peter Spanogiannopoulos, Paola Soto-Perez, Allison M. Weakley, Feiqiao B. Yu, Peter J. Turnbaugh. Cell Reports, 2021
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Lea Sedghi, Vincent DiMassa, Anthony Harrington, Susan V. Lynch, Yvonne L. Kapila. Periodontology 2000, 2021
Maternal gut microbiome regulates immunity to RSV infection in offspring
Wendy Fonseca, Carrie-Anne Malinczak, Kei Fujimura, Danny Li, Kathryn McCauley, Jia L , Shannon K.K. Best, Diana Zhu, Andrew J. Rasky, Christine C. Johnson, Jennifer Bermick, Edward M. Zoratti, Dennis Ownby, Susan V. Lynch, Nicholas W. Lukacs, Catherine Ptaschinski. J Exp Med, 2021
Lung immune tone via gut-lung axis: gut-derived LPS and short-chain fatty acids’ immunometabolic regulation of lung IL-1β, FFAR2, and FFAR3 expression
Qing Liu, Xiaoli Tian, Daisuke Maruyama, Mehrdad Arjomandi, and Arun Prakash. Am J Physiol Lung Cell Mol Physiol, 2021
Caloric restriction disrupts the microbiota and colonization resistance
Reiner Jumpertz von Schwartzenberg, Jordan E. Bisanz, Svetlana Lyalina, Peter Spanogiannopoulos, Qi Yan Ang, Jingwei Cai, Sophia Dickmann, Marie Friedrich, Su-Yang Liu, Stephanie L. Collins, Danielle Ingebrigtsen, Steve Miller, Jessie A. Turnbaugh, Andrew D. Patterson, Katherine S. Pollard, Knut Mai, Joachim Spranger & Peter J. Turnbaugh. Nature, 2021
Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses
Aline Dionizio, Dawud Abduweli Uyghurturk, Carina Guimarães Souza Melo, Isabela Tomazini Sabino-Arias, Tamara Teodoro Araujo, Talita Mendes Silva Ventura, Juliana Vanessa Colombo Martins Perles, Jacqueline Nelisis Zanoni, Pamela Den Besten, Marília Afonso Rabelo Buzalaf. Chemosphere, 2021.
Hair of the mouse: A skin bacteria “cocktail” gets follicles back on their feet
Jeanmarie R. Gonzalez, Geil R. Merana, Tiffany C. Scharschmidt. Cell Host and Microbe, 2021
The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury
Matt S Zinter, Caroline A Lindemans, Birgitta A Versluys, Madeline Y Mayday, Sara Sunshine, Gustavo Reyes, Marina Sirota, Anil Sapru, Michael A Matthay, Sandhya Kharbanda, Christopher C Dvorak, Jaap J Boelens, Joseph L DeRisi. Blood, 2021
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic and Yvonne L. Kapila. Computational and Structural Biotechnology Journal, 2021
Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood
Susan V. Lynch and Donata Vercelli. American Journal of Respiratory and Critical Care Medicine, 2021
2020
Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis
AK Pröbstel, X Zhou, R Baumann, S Wischnewski, M Kutza, OL Rojas, K Sellrie, A Bischof, K Kim, A Ramesh, R Dandekar, AL Greenfield, RD Schubert, JE Bisanz, S Vistnes, K Khaleghi, J Landefeld, G Kirkish, F Liesche-Starnecker, V Ramaglia, S Singh, EB Tran, P Barba, K Zorn, J Oechtering, K Forsberg, LR Shiow, RG Henry, J Graves, BAC Cree, SL Hauser, J Kuhle, JM Gelfand, PM Andersen, J Schlege, PJ Turnbaugh, PH Seeberger, JL Gommerman, MR Wilson, L Schirmer, SE Baranzini. Science Immunology, 2020.
Periodontal pathogens promote cancer aggressivity via TLR/MyD88 triggered activation of Integrin/FAK signaling that is therapeutically reversible by a probiotic bacteriocin
P Kamarajan, I Ateia, JM Shin, JC Fenno, C Le, L Zhan, A Chang, R Darveau, YL Kapila. PLOS Pathogens, 2020
Modulation of pathogenic oral biofilms towards health with nisin probiotic
Radaic A, Ye C, Parks B, Gao L, Kuraji R, Malone E, Kamarajan P, Zhan L, Kapila YL. J Oral Microbiol. 2020
Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions
Margaret Alexander, Peter J.Turnbaugh. Immunity, 2020
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis
The iMSMS Consortium (SE Baranzini). Multiple Sclerosis Journal, 2020.
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome
Li Gao, Misun Kang, Martin Jinye Zhang, M. Reza Sailani, Ryutaro Kuraji, April Martinez, Changchang Ye, Pachiyappan Kamarajan, Charles Le, Ling Zhan, Hélène Rangé, Sunita P. Ho & Yvonne L. Kapila. npj Biofilms and Microbiomes, 2020
Probing the tumor micro(b)environment
Chloe E. Atreya, Peter J. Turnbaugh. Science, 2020
Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells
Qi Yan Ang, Margaret Alexander, John C. Newman, Yuan Tian, Jingwei Cai, Vaibhav Upadhyay, Jessie A.Turnbaugh, Eric Verdin, Kevin D. Hall, Rudolph L.Leibel, Eric Ravussin, Michael Rosenbaum, Andrew D.Patterson, Peter J.Turnbaugh. Cell, 2020
Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives
Ling Zou, Peter Spanogiannopoulos, Lindsey M. Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K. Shoichet, Kathleen M. Giacomini, and Peter J. Turnbaugh. Proceedings of the National Academy of Sciences, 2020
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
JE Bisanz, P Soto-Perez, C Noecker, AA Aksenov, KN Lam, GE Kenney, EN Bess, HJ Haiser, TS Kyaw, FB Yu, VM Rekdal, CWY Ha, S Devkota, EP Balskus, PC Dorrestein, E Allen-Vercoe, PJ Turnbaugh. Cell Host and Microbe, 2020
Phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
P.H. Bradley, K.S. Pollard. Bioinformatics, 2020
Viable bacterial colonization is highly limited in the human intestine in utero.
Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Nature Medicine, 2020
Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.
Bess EN, Bisanz JE, Yarza F, Bustion A, Rich BE, Li X, Kitamura S, Waligurski E, Ang QY, Alba DL, Spanogiannopoulos P, Nayfach S, Koliwad SK, Wolan DW, Franke AA, Turnbaugh PJ. Nature Microbiology, 2020
2019
Toxin-Triggered Interleukin-1 Receptor Signaling Enables Early-Life Discrimination of Pathogenic versus Commensal Skin Bacteria.
Leech JM, Dhariwala MO, Lowe MM, Chu K, Merana GR, Cornuot C, Weckel A, Ma JM, Leitner EG, Gonzalez JR, Vasquez KS, Diep BA, Scharschmidt TC. Cell Host & Microbe, 2019
Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.
Levan, S.R., Stamnes, K.A., Lin, D.L., Panzer A.R., Fukui E., McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV. Nature Microbiology, 2019
Population Genetics in the Human Microbiome
N.G. Garud and K.S. Pollard. Trends in Genetics, 2019
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
A. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, Z.J. Shi, K.S. Pollard, D.H. Parks, P. Hugenholtz, N. Segata, N.C. Kyrpides, R.D. Finn. BioRxiv, 2019
Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
M. Roodgar, B.H. Good, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K.S. Pollard, M.P. Snyder. BioRxiv, 2019
Cooking shapes the structure and function of the gut microbiome
Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ. Nature Microbiology, 2019
CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog
Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. Cell Host Microbe, 2019
Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, Burrows K, Robinson HG, Allanach JR, Yam J, Luck H, Campbell DJ, Allman D, Brooks DG, Tomura M, Baumann R, Zamvil SS, Bar-Or A, Horwitz MS, Winer DA, Mortha A, Mackay F, Prat A, Osborne LC, Robbins C, Baranzini SE, Gommerman JL. Cell, 2019
