Research Publications


Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization

Xiaofan Jin​, Feiqiao B. Yu​, Jia Yan, Allison M. Weakley, Veronika Dubinkina, Xiandong Meng, and Katherine S. Pollard. Nature Communications, 2023


Long-term tolerance to skin commensals is established neonatally through a specialized dendritic cell subgroup

Antonin Weckel,  Miqdad O. Dhariwala, Kevin Ly, Niroshana Anandasabapathy, Yosuke Kumamoto, and Tiffany C. Scharschmidt. Immunity, 2023



SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations

Annamarie E. BustionRenuka R. Nayak, Ayushi Agrawal, Peter J. Turnbaugh, and Katherine S. Pollard. eLife Science, 2023


Inflammatory bowel disease in pregnancy and breastfeeding

Max N. Brondfield and Uma Mahadevan. Nature, 2023


Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Cecilia Noecker, Juan Sanchez, Jordan E. Bisanz, Veronica Escalante, Margaret Alexander, Kai Trepka, Almut Heinken, Yuanyuan Liu, Dylan Dodd, Ines Thiele, Brian C. DeFelice, and Peter J. Turnbaugh. PLOS BIOLOGY, 2023


Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors

Than S. Kyaw, Vaibhav Upadhyay, Irina Tolstykh, Katherine Van Loon, Angela Laffan, Dalila Stanfield, Daryll Gempis, Stacey A. Kenfield, June M. Chan, Sorbarikor Piawah, Chloe E. Atreya, Kimmie Ng, Alan Venook, Wesley Kidder, Peter J. Turnbaugh, Erin L. Van Blarigan. The American Journal of Clinical Nutrition, 2023


Forging the microbiome to help us live long and prosper

Rachel R. Rock and Peter J. Turnbaugh. PLOS BIOLOGY, 2023



Mild SARS-CoV-2 infection results in long-lasting microbiota instability

Vaibhav Upadhyay, Rahul K. Suryawanshi, Preston Tasoff, Maria McCavitt-Malvido, Renuka G. Kumar, Victoria Wong Murray, Cecilia Noecker, Jordan E. Bisanz, Yulin Hswen, Connie W. Y. Ha, Bharath Sreekumar, Irene P. Chen, Susan V. Lynch, Melanie Ott, Sulggi Lee, and Peter J. Turnbaugh. mBio, 2023


Periodontal treatment and microbiome-targeted therapy in management of periodontitis-related nonalcoholic fatty liver disease with oral and gut dysbiosis

Ryutaro Kuraji, Takahiko Shiba, Tien S. Dong, Yukihiro Numabe, and Yvonne L. Kapila. World Journal of Gastroenterology, 2023



The global anaerobic metabolism regulator fnr is necessary for the degradation of food dyes and drugs by Escherichia coli

Lindsey M. Pieper, Peter Spanogiannopoulos, Regan F. Volk, Carson J. Miller, Aaron T. Wright, and Peter J. Turnbaugh. American Society for Microbiology, 2023


Interactions between host epigenetics and microbiota: Who does what to whom, when, and why?

Donata Vercelli and Susan V. Lynch. Science Direct, 2023


Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset

Vinicius A Schoeps, Xiaoyuan Zhou, Mary K Horton, Feng Zhu, Kathryn E McCauley, Zahra Nasr, Akash Virupakshaiah, Mark P Gorman, Leslie A Benson, Bianca Weinstock-Guttman, Amy Waldman, Brenda L Banwell, Amit Bar-Or, Gary van Domselaar, Julia O'Mahony, Ali I Mirza, Charles N Bernstein, E Ann Yeh, T Charles Casper, Susan V Lynch, Helen Tremlett, Sergio Baranzini, Emmanuelle Waubant, US Network of Pediatric MS Centers, Ann Clin Transl Neurol, 2023


Robust airway microbiome signatures in acute respiratory failure and hospital-acquired pneumonia

Emmanuel Montassier, Georgios D. Kitsios, Josiah E. Radder, Quentin Le Bastard, Brendan J. Kelly, Ariane Panzer, Susan V. Lynch, Carolyn S. Calfee, Robert P. Dickson, Antoine Roquilly, Nature Medicine, 2023


Contributions of the early-life microbiome to childhood atopy and asthma development

Holly Steininger, Jacqueline Moltzau-Anderson, Susan V. Lynch, Semmin Immunol, 2023



The impact of prenatal dog keeping on infant gut microbiota development

Ariane R Panzer, Alexandra R Sitarik, Doug Fadrosh, Suzanne L Havstad, Kyra Jones, Brent Davidson, Salvatore Finazzo, Ganesa R Wegienka, Kimberley Woodcroft, Nicholas W Lukacs, Albert M Levin, Dennis R Ownby, Christine C Johnson, Susan V Lynch, Edward M Zoratti Clin Exp Allergy, 2023


Early-life gut microbiota and attention deficit hyperactivity disorder in preadolescents

Andrea E Cassidy-Bushrow, Alexandra R Sitarik, Christine Cole Johnson, Tisa M Johnson-Hooper, Zeinab Kassem, Albert M Levin, Susan V Lynch, Dennis R Ownby, Jannel M Phillips, Germaine J M Yong, Ganesa Wegienka, Jennifer K Straughen, Pediatr Res 2023



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 2023



Microbiome single cell atlases generated with a commercial instrument

Adam Abate, Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan Bisanz, Daniel Weisgerber, Cyrus Modavi, Peter Turnbaugh, Res Sq 2023



Associations between the Gut Microbiota, Race, and Ethnicity of Patients with Colorectal Cancer: A Pilot and Feasibility Study

Sorbarikor Piawah, Than S Kyaw, Kai Trepka, Anita L Stewart, Rosa V Mora, Dalila Stanfield, Kendall Levine, Erin L Van Blarigan, Alan Venook, Peter J Turnbaugh, Tung Nguyen, Chloe E Atreya, Cancers 2023


Simvastatin induces human gut bacterial cell surface genes

Veronica Escalante, Renuka R Nayak, Cecilia Noecker, Joel Babdor, Matthew Spitzer, Adam M Deutschbauer, Peter J Turnbaugh, Mol Microbiol 2023





Specific Oral Microbial Differences in Proteobacteria and Bacteroidetes Are Associated with Distinct Sites When Moving from Healthy Mucosa to Oral Dysplasia-A Microbiome and Gene Profiling Study and Focused Review

Allan Radaic, Eliah R Shamir, Kyle Jones, Alessandro Villa, Nandita R Garud, Aaron D Tward, Pachiyappan Kamarajan, Yvonne L Kapila, Microorganisms 2023


Nisin a probiotic bacteriocin mitigates brain microbiome dysbiosis and Alzheimer's disease-like neuroinflammation triggered by periodontal disease

Chuanjiang Zhao, Ryutaro Kuraji, Changchang Ye, Li Gao, Allan Radaic, Pachiyappan Kamarajan, Yoshimasa Taketani, Yvonne L Kapila, J Neuroinflammation 2023


Peptide YY: A Paneth cell antimicrobial peptide that maintains Candida gut commensalism

Joseph F Pierre, Brian M Peters, Diana La Torre, Ashley M Sidebottom, Yun Tao, Xiaorong Zhu, Candace M Cham, Ling Wang, Amal Kambal, Katharine G Harris, Julian F Silva, Olga Zaborina, John C Alverdy, Herbert Herzog, Jessica Witchley, Suzanne M Noble, Vanessa A Leone, Eugene B Chang, Science 2023



Pitfalls of genotyping microbial communities with rapidly growing genome collections

Chunyu Zhao, Zhou Jason Shi, Katherine S Pollard, Cell Syst 2023



MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies

Samuel S Minot, Bailey Garb, Alennie Roldan, Alice S Tang, Tomiko T Oskotsky, Christopher Rosenthal, Noah G Hoffman, Marina Sirota, Jonathan L Golob, Cell Rep Methods 2023


Personalised azithromycin+metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn's disease (CD): protocol of a pilot study

Charlotte M Verburgt, Katherine A Dunn, Anthony Otley, Melvin B Heyman, Sofia Verstraete, Withney Sunseri, Francisco Sylvester, Tim de Meij, Andre Comeau, Morgan Langille, Wouter J de Jonge, Marc A Benninga, Johan E Van Limbergen, BMJ Open 2023


Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer

Mohammed Muzamil Khan, Jennifer Frustino, Alessandro Villa, Bach-Cuc Nguyen, Sook-Bin Woo, William Evan Johnson, Xaralabos Varelas, Maria Kukuruzinska, Stefano Monti, Hum Genomics 2023



Perturbations of the ocular surface microbiome and their effect on host immune function

Chih-Chiun Jamie Chang, Bryan J Winn, Curr Opin Ophthamol 2023



Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji

Sankhya Bommana, Yi-Juan Hu, Mike Kama, Ruohong Wang, Reshma Kodimerla, Kenan Jijakli, Timothy D Read, Deborah Dean, mBio 2023



Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet

Hannah C Wastyk, Dalia Perelman, Madeline Topf, Gabriela K Fragiadakis, Jennifer L Robinson, Justin L Sonnenburg, Christopher D Gardner, Erica D Sonnenburg, Gut Microbes 2023


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. ScharschmidtJournal of Investigative Dermatology, 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

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 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. TurnbaughNature 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.
O¨ zc¸ am et al., 2022, Cell Host & Microbe 2022

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


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. LynchPLOS 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.DhariwalaTiffany C.ScharschmidtTrends in Immunology, 2021


Human gut bacterial metabolism drives Th17 activation and colitis

Margaret AlexanderQi Yan AngRenuka R.NayakAnnamarie E.BustionMoriah SandyBing ZhangVaibhav UpadhyayKatherine S.PollardSusan V. LynchPeter J.TurnbaughCell 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 LiKathryn 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. TurnbaughNature, 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. GonzalezGeil R. MeranaTiffany 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


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. PollardBioinformatics, 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 SVNature 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 PJNature Microbiology, 2020


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 TCCell 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. PollardTrends 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 PJNature 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 PJCell 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