2025
Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.
Claire A. Dubin, Chunyu Zhao, Katherine S. Pollard, Tomiko Oskotsky, Jonathan L. Golob, Marina Sirota.
Microbiota effects and predictors of Lactobacillus crispatus colonization after treatment with a vaginal live biotherapeutic: results from a randomized, double-blinded, placebo-controlled trial.
Seth M. Bloom, Laura Symul, Joseph Elsherbini, Jiawu Xu, Salina Hussain, Johnathan Shih, Ashley Sango, Caroline M. Mitchell, Anke Hemmerling, Thomas P. Parks, Aditi Kannan, Fatima A. Hussain, Craig R. Cohen, Susan P. Holmes, Douglas S. Kwon.
Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci.
KeAndreya M. Morrison, Rupesh Agarwal, Haley E. Stubbs, Hai Yu, Stefan Ruhl, Xi Chen, Paul M. Sullam, Barbara A. Bensing, Jeremy C. Smith, and T. M. Iverson.
A20's linear ubiquitin-binding motif restrains pathogenic activation of Th17 cells and IL-22-driven enteritis.
Christopher J. Bowman, Dorothea M. Stibor, Xiuofei Sun, Nika Lenci, Hiromichi Shimizu, Emily F. Tamashita, Rommel Advincula, Min Cheol Kim, Jessie A. Turnbaugh, Yang Sun, Bahram Razani, Peter J. Turnbaugh, Chun Jimmie Ye, Barbara A. Malynn, and Averil Ma.
Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.
Matthew Rendina, Peter J. Turnbaugh, Patrick H. Bradley.
Global consensus statement on the management of pregnancy in inflammatory bowel disease.
Uma Mahadevan, Cynthia H. Seow, Edward L. Barnes, Maria Chaparro, Emma Flanagan, Sonia Friedman, Mette Julsgaard, Sunanda Kane, Siew Ng, Joana Torres, Gillian Watermeyer, Jesus Yamamoto-Furusho, Christopher Robinson, Susan Fisher, Phil Anderson, Richard Gearry, Dana Duricova, Marla Dubinski, Millie Long.
Fecal microbiota transplantation in mice improves bone properties through altered mineral quality.
Bowen Wang, Samuel J. Stephen, Erika L Cyphert, Chongshan Liu, Christopher J. Hernandez, Deepak Vashishth.
Inflammatory Markers and Microbiome Dysbiosis in Hematopoietic cell transplant recipients with lung graft-versus-host disease.
Victoria Brehm, Ziyi Wang, Lius Rocha, Breanna Jones, Robert R. Jenq, Chia-Chi Chang, Guang-Shing Cheng, Joe Hsu, Husham Sharifi, Gregory Yanik, Luis Luna, Anum Waqar, Jhankruti Zaveri, Burton F. Dickey, Lara Bachoura, Elizabeth J. Shpall, Matt Zinter, David O'Dwyer, Richard E. Champlin, George Chen...Ajay Sheshadri.
Higher circulating short-chain fatty acids are associated with good neurologic outcome after cardiac arrest.
Ori J. Lieberman, Virginia Yao, Gerardo Velasquez, Matheus Otero, Kevin Bao, Katherine Peterson, Firas H. Kobeissy, Jonathan Z. Pan, Zhonghui Guan, H. E. Hinson, Sergio E. Baranzini, J. Claude Hemphill, Neel S. Singhal & Edilberto Amorim.
Host-microbe multiomic profiling predicts mortality in sepsis.
Natasha Spottiswoode, Lucile P. Neyton, Eran Mick, Katrina L. Kalantar, Samantha Hao, Emily C. Lydon, Rithwik Narendra, Paula Hayakawa Serpa, Saharai Caldera, Antonio Gomez, Carolyn Handrickson, Kirsten Kangelaris, Kathleen D. Liu, Pratik Sinha, Joseph L. DeRisi, Michael A. Matthay, Carolyn S. Calfee, Charles R. Langelier.
Microbiota and kidney disease: the road ahead.
Patricia P. Bloom, Wendy S. garrett, Kristina L. Penniston, Mari-Karolina H. Winker, Stanley L. Hazen, Jose Agudelo, Mangesh Suryavanshi, Ahmed Babiker, Dylan Dodd, Michael A. Fischbach, Kerwyn Casey Huang, Curtis Huttenhower, Bina Joe, Kamyar Kalantar-Zadeh, Rob Knight, Aaron W. Miller, Hamid Rabb, Anvesha Srivastava, W. H. Wilson Tang, Peter J. Turnbaugh, Alan W. Walker, Nicola Wilck, Jiaojiao Xu, Tao Yang...Jennifer L. Pluznick.
Salivary microbiome and serum metabolomics add to clinical biomarkers to predict 6-month hospitalizations in a multicenter cirrhosis outpatient cohort.
Jasmohan S. Bajaj, Rajender K. Reddy, Puneeta Tandon, Jennifer C. Lai, Jacqueline G. O'Leary, Florence Wong, Guadalupe Garcia-Tsao, Hugo E. Vargas, Patrick S. Kamath, Scott W. Biggins, Phillip Vutien, Jawaid Shaw, Anna Teresa Miro Limon, Chinmay Bera, Joseph P. McGinley, Masoumah Sikaroodi, Brian J. Bush, Leroy R. Thacker, Patrick M. Gillevet.
Pilot study: Investigating the local breast microbiome in implant-based breast reconstruction using 16S rRNA sequencing.
Laura L. Barnes, Nisha Parmeshwar, Michael Campbell, Laura Esserman, Merisa Piper.
Announcing the biomedical data translator: Initial public release.
Karamarie Fecho, Gwenlyn Glusman, Sergio E. Baranzini, Chris Bizon, Matthew Brush, William Byrd, Lawrence Chung, Andrew Crouse, Eric Deutsch, Michel Dumontier, Aleksandra Foksinska, Jennifer Hadlock, Kaiwen He, Sui Huang, Robert Hubal, Gregory M. Hyde, Sharat Israni, Kelyne Kenmogne, David Koslicki, Jana D. Marcette, Ewy A. Mathe, Abrar Mesbah, Sierra A. T. Moxon, Christopher J. Mungall, John Osborne, Carrie Pasfield, Guangrong Qin, Stephen A. Ramsey, Justin Reese, Jared C. Roach, Reese Rose, Karthin Soman, Andrew I. Su, Casey Ta, Gaurav Vaidya, Rosina Weber, Qi Wei, Mark Williams, Chunlei Wu, Colleen Xu, Chase Yakaboski, The biomedical data translator consortium.
Comprehensive Cross-domain classification of microbiotas using partitioned amplification multiplexed amplicon sequencing (PAMA-seq).
Xiangpeng Li, Kai R. Trepka, Fangchao Song, Than S. Kyaw, Peter J. Tunbaugh, Adam R. Abate.
Microbiome single cell atlases generated with a commercial instrument.
Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan E. Bisanz, Daniel W. Weisgerber, Cyrus Modavi, Peter J. Turnbaugh, Adam ER. Abate.
Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure.
Mustafa Ozcam, Din L. Lin, Chhedi L. Gupta, Alison Li, J. Carlos Gomez, Lisa M. Wheathey, Carolyn H. Baloh, Srinath Sanda, Stacie M. Jones & Susan V. Lynch.
The gut microbiome shapes pharmacology and treatment outcomes for a key anti-inflammatory therapy.
Vanya Sofia Villa Sotto, Alexandra L. Degraeve, Chloe M. Heath, Diego A. Orellana, Erin R. Reilly, Mohana Mukherjee, Jacob G. Brockert, Darren S. Dumlao, Rebecca B. Blank, Noah Perlmutter, Steven Yu, Judith Ashouri, Jose U. Scher, Andrew D. Patterson, Peter J. Turnbaugh, Renuka R. Nayak.
Empiric azithromycin in Covid-19 impacts the respiratory microbiome and antimicrobial resistome without anti-inflammatory benefit.
Charles Langelier, Abigail Glascock, Cole Maguire, Hoang Van Phan, and 50 more.
Mining microbial metabolites of GPCR-targeted drugs.
Chen Zhang, Peter J. Turnbaugh.
Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (micoSLAM).
Miriam Goldman, Chunyu Zhao, Katherine S. Pollard.
Linkage of nucleotides and functional diversity varies across gut bacteria.
Veronika Dubinkina, Byron Smith, Chunyu Zhao, Cindy Pino, Katherine S. Pollard.
A cellular basis for heightened gut sensitivity in females.
Archana Venkataraman, Eric E. Figueroa, Joel Castro, Fernanda M. Castro Navarro, Deepanshu Soota, Stuart M. Brierley, David Julius, Holly A. Ingraham.
The association of prenatal dietary factors with child autism diagnosis and autism-related traits using a mixture approach: results from the environmental influences on child health outcomes cohort.
Megan E. Bragg, Juliette Rando, Kecia N. Carroll, Stephanie M. Eick, Margaret R. Karagas, Pi-I Lin, Rebecca Schmidt, Kristin Lyall, ECHO cohort consortium.
Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID platform.
Dan Lu, Katrina L. Kalantar, Abigail L. Glascock, Victoria T. Chu, Estella S. Guerrero, Nina Bernick, Xochitl Butcher, Kristy Ewing, Elizabeth Fahsbender, Olivia Holmes, Erin Hoops, Ann E. Jones, Ryan Lim, Suzette McCanny, Lucia Reynoso, Karyna Rosario, Jennifer Tang, Omar Valenzuela, Peter M. Mourani, Amy J. Pickering, Amogelang R. Raphenya, Brian P. Alcock, Andrew G. McArthur, Charles R. Langelier.
Stability and variability of the human fecal microbiome over 2 years in the multiethnic cohort study: a metagenomic analysis.
Darya Moosavi, Keith R. Curtis, Timothy W. Randolph, Orsalem J. Kahsai, Hamza Ammar, Un-hee Lim, Iona Cheng, Lynne R. Wilkens, Loic Le Marchand, Johanna W. Lampe, Meredith A. J. Hullar.
Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster beds.
Erika L. Cyphert, Sanjiev Nand, Gabriela Franco, Michel Hajkowski, Luzmaria Soto, Danica Marvi Lee, Mettew C. Ferner, Chela J. Zabin, Jeffrey Blumenthal, Anna K. Deck, Katharyn E. Boyer, Laura W. Burrus, Christopher J. Hernandez, Archana Anand.
Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.
Abigail L. Lind, Nathan A. McDonald, Elias R. Gerrick, Ami S. Bhatt, Katherine S. Pollard.
Single-cell omics technologies - Fundamentals on how to create single-cell looking glasses for reproductive health.
Maigane Diop, Brittany R. Davidson, Gabriella K. Fragiadakis, Marina Sirota, Brice Gaudilliere, Alexis J. Combes.
Pathogen aetiology and risk factors for death among neonates with bloodstream infections at lower-tier South African hospitals: a cross-sectional study.
Susan Meiring, Vanessa Quan, Rudzani Mashau, Olga Perovic, Rindidzani Magobo, Marshagne Smith, Ruth Mpembe, Anne von Gottberg, Linda de Gouveia, Sibongile Walaza, Cheryl Cohen, Constance Kapongo, Cheryl Mackay, Mphekwa Rhomas Mailula, Omphile Mekgoe, Lerato Motjala, Rose Phayane, Angela Dramowski, Nelesh Govender...Vanessa Pierce.
Activation of bacterial programmed cell death by phage inhibitors of host immunity.
Sukrit Silas, Heloisa Carlon, Kira S. Makarova, Eric S. Laderman, Thomas Todeschini, Pradeep Kumar, Matthew Johnson, Michael Bocek, Franklin L. Nobrega, Eugene V. Koonin, Joseph Bondy-Denomy.
Microbial vitamin biosynthesis links gut microbiota dynamics to chemotherapy toxicity.
Lars E. Hillege, Kai. R. Trepka, Benjamin G. H. Gurthie, Xueyan Fu, Romy Aarnoutse, Maia R. Paymar, Christine Olson...Peter J. Turnbaugh.
Maternal cardiometabolic risk factors in pregnancy and offspring blood pressure at age 2 to 18 years.
Zhongzheng Niu, Ako Adams, Sarah Dee Geiger, et al.
IL-25-induced memory ILC2s mediate long-term small intestinal adaptation.
Victor S. Cortez, Sara Viragova, Satoshi Koga, Meizi Liu, Claire O'Leary, Roberto R. Ricardo-Gonzalez, Andrew W. Schroeder, Nathan Kochhar, Ophir D. Klein, Hong-Erh Liang, Richard M. Locksley.
Engineered epithelial curvature controls Paneth cell localization in intestinal organoids.
Max Yavitt, Alex Khang, Kaustav Bera, Delaney L. McNally, Michael R. Blatchley, Aaron P. Gallagher, Ophir D. Klein, David Castillo-Zaofeifa, Peter J. Dempsey, Kristi S. Anseth.
Multiple sclerosis and gut microbiota: Lachnospiraceae from the ileum of MS twins trigger MS-like disease in germfree transgenic mice - An unbiased functional study.
Hongsup Yoon, Lisa Anna Gerdes, Florian Beigel, +9, Anneli Peters.
Accurate estimation of interspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.
Byron J. Smith, Chunyu Zhao, Veronika Dubinkina, Xiaofan Jin, Lieon Zahavi, Saar Shoer, Jacqueline Moltzau-Anderson, Eran Segal, Katherine S. Pollard.
The effect of quintuply-fortified salt on the gut microbiome of nonpregnant women of reproductive age in Punjab, India: A substudy of a randomized, community-based trial.
Lauren Thompson, Yvonne E. Goh, Manu Jamwal, Bidhi L. Singh, Gurjinder Kaur Brar, Charles D. Arlond, Jamie Westcott, Nancy F. Krebs, Angela Zivkovic, Reena Das, Mona Duggal, Christine M. McDonald.
Topological segregation of stress sensors along the gut crypt-villus axis.
Kouki K. Touhara, Nathan D. Rossen, Fei Deng, Joel Castro, Andrea M. Harrington, Tifany Chu, Sonia Garcia-Caraballo, Mariana Brizuela, Tracey O'Donnell, Jinhao Xu, Onur Cil, Stuart M. Brierley, Yulong Li, David Julius.
Effect of azithromycin treatment on the microbial composition, functional dynamics and resistomes of endocervical, vaginal and rectal micobiomes of women in Fiji with Chlamydia trahomatis infection.
Sankhya Bommana, Olusola Olagoke, Yi-Juan Hu, Roselle Wang, Mike Kama, Morgan Dehdashti, Reshma Kodimerla, Timothy D. Read, Deborah Dean.
Effect of the vaginal live biotherapeutic LACTIN-V (Lactobacillus crispatus CTV-05) on vaginal microbiota and genital tract inflammation among women at high risk of HIV acquisition in South Africa: a phase 2, randomized, placebo-controlled trial.
Anke Hemmerling, Caroline M. Mitchell, Suuba Demby, Misue Ghebremichael, Joseph Elserbini, Jiawu Xu, Nondumiso Xulu, Jonathan Shih, Krista Dong, Vaneshree Govender, Vanessa Pillay, Nasreen Ismail, Gardenia Casillas, Jayajothi Moodley, Agnes Bergerat, Tess Brunner, Lenine Liebenberg, Sinaye Ngcapy, Ian Mbano, Laurel Lagenaur, Carig R. Cohen.
The Barancik award lecture: Multi-disciplinary research wil be the key to stop, retore, and end MS.
Sergio E. Baranzini.
The relationship between the early-life gastrointestinal microbiome and childhood nocturnal cough.
Amy A. Eapen, Tengfei Ma. Alexandra R. Sitarik, Ze Meng, Dennis R. Ownby, Andrea E. Cassidy-Bushrow, Ganesa Wegeinka, Edward M. Zoratti, Susan V. Lynch, Christine C. Johnson, Albert M. Levin.
Gut bacteria lactate stimulates lung epithelial mitochondria and exacerbates acute lung injury.
Vaibhav Upadhyay, Edwin F. Ortega, Luis A. Ramirez Hernandez, Margaret Alexander, Gagandeep Kaur, Kai Trepka, Rachel R. Rock, Rafaella T. Shima, Colby Cheshire, Narges Alipanah-Lechner, Carolyn S. Calfee, Michael A. Matthay, Joyce V. Lee, Andrei Goga, Isha H. Jain, Peter J. Turnbaugh.
Clinical translation of microbiome research.
Jack A. Gilbert, Meghan B. Azad, Martin J. Blaser, Mariana Byndloss, Charles Y. Chui, Hiutung Chu, Lara R. Dugas, Eran Elinav, Sean M. Gibbons, Katharine E. Gilbert, Matthew R. Henn, Suzanne L. Ishaq, Ruth E. Ley, Susan V. Lynch, Eran Segal, Tim D. Spector, Philip Strandwitz, Jotham Suez, Carolina Tropini, Katrina Whiteson, Rob Knight.
2024
VMAP: Vaginal Microbiome Atlas during Pregnancy
Antonio Parraga-Leo, Tomiko T Oskotsky, Boris Oskotsky, Camilla Wibrand, Alennie Roldan, Alice S Tang, Connie W Y Ha, Ronald J Wong, Samuel S Minot, Gaia Andreoletti, Idit Kosti, Kevin R Theis, Sherrianne Ng, Yun S Lee, Patricia Diaz-Gimeno, Phillip R Bennett, David A MacIntyre, Susan V Lynch, Roberto Romero, Adi L Tarca, David K Stevenson, Nima Aghaeepour, Jonathan L Golob, Marina Sirota. JAMIA Open. 2024 Sep
Bing Zhang, Kevin M Magnaye, Emily Stryker, Jacqueline Moltzau-Anderson, Cara E Porsche, Sandra Hertz, Kathryn E McCauley, Byron J Smith, Martin Zydek, Katherine S Pollard, Averil Ma, Najwa El-Nachef, Susan V Lynch. Sci Rep 2024.
Enhanced Gut Microbiome Capacity for Amino Acid Metabolism is associated with Peanut Oral Immunotherapy Failure
Mustafa Özçam, Din L Lin, Chhedi L Gupta, Allison Li, Lisa M Wheatley, Carolyn H Baloh, Srinath Sanda, Stacie M Jones, Susan V Lynch. dRxiv [Preprint]. 2024
Din L Lin, Kevin M Magnaye, Cara E Porsche, Sophia R Levan, Elze Rackaityte, Mustafa Özçam, Susan V Lynch. J Immunol Res 2024
Sima K Ramratnam, Molly Johnson, Cynthia M Visness, Agustin Calatroni, Mathew C Altman, Tomasz Janczyk, Kathryn E McCauley, Claire Schachtschneider, Kei E Fujimura, Douglas W Fadrosh, Susan V Lynch, Leonard B Bacharier, George T O'Connor, Megan T Sandel, Meyer Kattan, Robert A Wood, Peter J Gergen, Daniel J Jackson, Alkis Togias, James E Gern, Childhood Asthma in Urban Settings (CAUSE) network. J Allergy Clin Immunol. 2024
Mustafa Özçam, Susan V Lynch. Nat Rev Microbiol 2024
Sandra Hertz, Jacqueline Moltzau Anderson, Hans Linde Nielsen, Claire Schachtschneider, Kathryn E McCauley, Mustafa Özçam, Lone Larsen, Susan V Lynch, Henrik Nielsen. Ann Med 2024
Karin C Wu, Kathryn E McCauley, Susan V Lynch, Renuka R Nayak, Nicole J King, Sheena Patel, Tiffany Y Kim, Katherine Condra, Doug Fadrosh, Dat Nguyen, Din L Lin, Kole Lynch, Stanley J Rogers, Jonathan T Carter, Andrew M Posselt, Lygia Stewart, Anne L Schafer. J Bone Miner Res. 2024
Kathryn E McCauley, Juliana Durack, Kole V Lynch, Douglas W Fadrosh, Kei E Fujimura, Faith Vundla,Mustafa Özçam, Petra LeBeau, Agustin Caltroni, Preston Burns, Hoang T Tran, Leonard B Bacharier, Meyer Kattan, George T O'Connor, Robert A Wood, Alkis Togias, Homer A Boushey, Daniel J Jackson, James E Gern, Susan V Lynch, National Institute of Allergy and Infectious Diseases–sponsored Childhood Asthma in Urban Settings Consortium. J Allergy Clin Immunol. 2024
Jonathan L Golob, Tomiko T Oskotsky, Alice S Tang, Alennie Roldan, Verena Chung, Connie W Y Ha, Ronald J Wong, Kaitlin J Flynn, Antonio Parraga-Leo, Camilla Wibrand, Samuel S Minot, Boris Oskotsky, Gaia Andreoletti, Idit Kosti, Julie Bletz, Amber Nelson, Jifan Gao, Zhoujingpeng Wei, Guanhua Chen, Zheng-Zheng Tang, Pierfrancesco Novielli, Donato Romano, Ester Pantaleo, Nicola Amoroso, Alfonso Monaco, Mirco Vacca, Maria De Angelis, Roberto Bellotti, Sabina Tangaro, Abigail Kuntzleman, Isaac Bigcraft, Stephen Techtmann, Daehun Bae, Eunyoung Kim, Jongbum Jeon, Soobok Joe, Preterm Birth DREAM Community, Kevin R Theis, Sherrianne Ng, Yun S Lee, Patricia Diaz-Gimeno, Phillip R Bennett, David A MacIntyre, Gustavo Stolovitzky, Susan V Lynch, Jake Albrecht, Nardhy Gomez-Lopez, Roberto Romero, David K Stevenson, Nima Aghaeepour, Adi L Tarca, James C Costello, Marina Sirota. Cell Rep Med. 2024
Kai R Trepka, Wesley A Kidder, Than S Kyaw, Taylor Halsey, Christine A Olson, Edwin F Ortega, Cecilia Noecker, Vaibhav Upadhyay, Dalila Stanfield, Paige Steiding, Benjamin G H Guthrie, Peter Spanogiannopoulos, Darren Dumlao, Jessie A Turnbaugh, Matthew D Stachler, Erin L Van Blarigan, Alan P Venook, Chloe E Atreya, Peter J Turnbaugh. bioRxiv [Preprint]. 2024
Veronica Escalante, Renuka R Nayak, Cecilia Noecker, Joel Babdor, Matthew Spitzer, Adam M Deutschbauer, Peter J Turnbaugh. Mol Microbiol. 2024
Pharma[e]cology: How the Gut Microbiome Contributes to Variations in Drug Response
Kai R Trepka, Christine A Olson, Vaibhav Upadhyay, Chen Zhang, Peter J Turnbaugh. Annu Rev Pharmacol Toxicol. 2024
Yuan Tian, Bipin Rimal, Jordan E Bisanz, Wei Gui, Trenton M Wolfe, Imhoi Koo, Iain A Murray, Shaneice K Nettleford, Shigetoshi Yokoyama, Fangcong Dong, Sergei Koshkin, K Sandeep Prabhu, Peter J Turnbaugh, Seth T Walk, Gary H Perdew, Andrew D Patterson. Environ Health Perspect. 2024
Erika L Cyphert, Chongshan Liu, Angie L Morales, Jacob C Nixon, Emily Blackford, Matthew Garcia, Nicolas Cevallos, Peter J Turnbaugh, Ilana L Brito, Sarah L Booth, Christopher J Hernandez. JBMR Plus. 2024
Rachel N Carmody, Krista Varady, Peter J Turnbaugh. Cell. 2024
Emerging tools and best practices for studying gut microbial community metabolism
Cecilia Noecker, Peter J Turnbaugh. Nat Metab 2024
Than S Kyaw, Chen Zhang, Moriah Sandy, Kai Trepka, Shenwei Zhang, Luis A Ramirez Hernandez, Lorenzo Ramirez, Janice J N Goh, Kristie Yu, Vincent Dimassa, Elizabeth N Bess, Jacob G Brockert, Darren S Dumlao, Jordan E Bisanz, Peter J Turnbaugh. iScience 2024
Megan D McCurry, Gabriel D D'Agostino, Jasmine T Walsh, Jordan E Bisanz, Ines Zalosnik, Xueyang Dong, David J Morris, Joshua R Korzenik, Andrea G Edlow, Emily P Balskus, Peter J Turnbaugh, Jun R Huh, A Sloan Devlin. Cell. 2024
Margaret Alexander, Vaibhav Upadhyay, Rachel Rock, Lorenzo Ramirez, Kai Trepka, Patrycja Puchalska, Diego Orellana, Qi Yan Ang, Caroline Whitty, Jessie A Turnbaugh, Yuan Tian, Darren Dumlao, Renuka Nayak, Andrew Patterson, John C Newman, Peter A Crawford, Peter J Turnbaugh. Cell Reports. 2024
Jee-Yon Lee, Connor R Tiffany, Scott P Mahan, Matthew Kellom, Andrew W L Rogers, Henry Nguyen, Eric T Stevens, Hugo L P Masson, Kohei Yamazaki, Maria L Marco, Emiley A Eloe-Fadrosh, Peter J Turnbaugh, Andreas J Bäumler. Cell. 2024
Erika L Cyphert, Chongshan Liu, Angie L Morales, Jacob C Nixon, Emily Blackford, Matthew Garcia, Nicolas Cevallos, Peter J Turnbaugh, Ilana L Brito, Sarah L Booth, Christopher J Hernandez. bioRxiv [Preprint]. 2024
Xiangpeng Li, Linfeng Xu, Benjamin Demaree, Cecilia Noecker, Jordan E Bisanz, Daniel W Weisgerber, Cyrus Modavi, Peter J Turnbaugh, Adam R Abate. bioRxiv [Preprint]. 2024
Karthik Soman, Peter W Rose, John H Morris, Rabia E Akbas, Brett Smith, Braian Peetoom, Catalina Villouta-Reyes, Gabriel Cerono, Yongmei Shi, Angela Rizk-Jackson, Sharat Israni, Charlotte A Nelson, Sui Huang, Sergio E Baranzini. Bioinformatics. 2024
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, Ruth Ann Marrie, 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. 2024
Camille Braun, Cédric Badiou, Aurélie Guironnet-Paquet, Masashi Iwata, Vanina Lenief, Amandine Mosnier, Charlotte Beauclair, Emilie Renucci, Pauline Bouschon, Roxane Cuzin, Yoann Briend, Vijaykumar Patra, Sabine Patot, Tiffany C Scharschmidt, Willem van Wamel, Nicole Lemmens, Saeko Nakajima, François Vandenesh, Jean-François Nicolas, Gérard Lina, Audrey Nosbaum, Marc Vocanson. J Allergy Clin Immunol.2024
Amy S Paller, Tiffany C Scharschmidt, Sanja Kezic, Alan D Irvine. J Invest Dermatol. 2024
Cristina Di Carluccio, Linda Cerofolini, Miguel Moreira, Frédéric Rosu, Luis Padilla-Cortés, Giulia Roxana Gheorghita, Zhuojia Xu, Abhishek Santra, Hai Yu, Shinji Yokoyama, Taylor E Gray, Chris D St Laurent, Yoshiyuki Manabe, Xi Chen, Koichi Fukase, Matthew S Macauley, Antonio Molinaro, Tiehai Li, Barbara A Bensing, Roberta Marchetti, Valérie Gabelica, Marco Fragai, Alba Silipo. ACS Cent Sci. 2024
Rebecca Choi, Rahul Bodkhe, Barbara Pees, Dan Kim, Maureen Berg, David Monnin, Juhyun Cho, Vivek Narayan, Ethan Deller, Cathy Savage-Dunn, Michael Shapira. Aging Biol. 2024
Helena Seth-Smith, Sankhya Bommana, Deborah Dean, Timothy D Read, Hanna Marti. BMC Genomics. 2024
Sankhya Bommana, Yi-Juan Hu, Mike Kama, Ruohong Wang, Reshma Kodimerla, Kenan Jijakli, Timothy D Read, Deborah Dean. mBio. 2024
Rachel K Zwick, Petr Kasparek, Brisa Palikuqi, Sara Viragova, Laura Weichselbaum, Christopher S McGinnis, Kara L McKinley, Asoka Rathnayake, Dedeepya Vaka, Vinh Nguyen, Coralie Trentesaux, Efren Reyes, Alexander R Gupta, Zev J Gartner, Richard M Locksley, James M Gardner, Shalev Itzkovitz, Dario Boffelli, Ophir D Klein. Nat Cell Biol. 2024
Eric Armstrong, Anke Hemmerling, Steve Miller, Sanja Huibner, Maria Kulikova, Rachel Liu, Emily Crawford, Gloria R Castañeda, Bryan Coburn, Craig R Cohen, Rupert Kaul. Microbiol Spectr. 2024
Eric Armstrong, Anke Hemmerling, Steve Miller, Sanja Huibner, Maria Kulikova, Emily Crawford, Gloria R Castañeda, Bryan Coburn, Craig R Cohen, Rupert Kaul. Microbiome. 2024
Chongshan Liu, Erika L Cyphert, Samuel J Stephen, Bowen Wang, Angie L Morales, Jacob C Nixon, Nicholas R Natsoulas, Matthew Garcia, Pablo Blazquez Carmona, Albert C Vill, Eve Donnelly, Ilana L Brito, Deepak Vashishth, Christopher J Hernandez. J Bone Miner Res. 2024
Sara Viragova, Dong Li , Ophir D Klein. Stem Cell. 2024
Microbiome research in autoimmune and immune-mediated inflammatory diseases: lessons, advances and unmet needs
Jose U Scher, Renuka Nayak, Jose C Clemente. Ann Rheum Dis. 2024
Renuka R Nayak, Diego A Orellana. Immunol Rev. 2024
Emily H Xiong, Xiang Zhang, Huijuan Yan, Henry N Ward, Zhen-Yuan Lin, Cassandra J Wong, Ci Fu, Anne-Claude Gingras, Suzanne M Noble, Nicole Robbins, Chad L Myers, Leah E Cowen. Cell Rep. 2024
Donovan D Trinidad, Christian B Macdonald, Oren S Rosenberg, James S Fraser, Willow Coyote-Maestas. bioRxiv [Preprint]. 2024
Aryn A Alanizi, Alexandre M Sorlin, Matthew F L Parker, Marina López-Álvarez, Hecong Qin, Sang Hee Lee, Joseph Blecha, Oren S Rosenberg, Joanne Engel, Michael A Ohliger, Robert R Flavell, David M Wilson. Bioconjug Chem. 2024
Investigating Pseudomonas aeruginosa Gene Function During Pathogenesis Using Mobile-CRISPRi
Michelle A Yu, Amy B Banta, Ryan D Ward, Neha K Prasad, Michael S Kwon, Oren S Rosenberg, Jason M Peters. Methods Mol Biol. 2024
Mark Voorhies, Bastian Joehnk, Jessie Uehling, Keith Walcott, Claire Dubin, Heather L Mead, Christina M Homer, John N Galgiani, Bridget M Barker, Rachel B Brem, Anita Sil. bioRxiv [Preprint]. 2024
Natasha Spottiswoode, Alexandra Tsitsiklis, Victoria T Chu, Hoang Van Phan, Catherine DeVoe, Christina Love, Rajani Ghale, Joshua Bloomstein, Beth Shoshana Zha, Cole P Maguire, Abigail Glascock, Aartik Sarma, Peter M Mourani, Katrina L Kalantar, Angela Detweiler, Norma Neff, Sidney C Haller, COMET Consortium, Joseph L DeRisi, David J Erle, Carolyn M Hendrickson, Kirsten N Kangelaris, Matthew F Krummel, Michael A Matthay, Prescott G Woodruff, Carolyn S Calfee, Charles R Langelier. Nat Commun. 2024
James Kuo, Jasmina Uzunovic, Amanda Jacobson, Michelle Dourado, Sarah Gierke, Manohary Rajendram, Daniela Keilberg, Jordan Mar, Emily Stekol, Joanna Curry, Sofia Verstraete, Jessica Lund, Yuxin Liang, Fiona B Tamburini, Natalie S Omattage, Matthieu Masureel, Steven T Rutherford, David H Hackos, Man-Wah Tan, Allyson L Byrd, Mary E Keir, Elizabeth Skippington, Kelly M Storek. J Crohns Colitis. 2024
Ali I Mirza, Feng Zhu, Natalie Knox, Lucinda J Black, Alison Daly, Christine Bonner, Gary Van Domselaar, Charles N Bernstein, Ruth Ann Marrie, Janace Hart, E Ann Yeh, Amit Bar-Or, Julia O’Mahony, Yinshan Zhao, William Hsiao, Brenda Banwell, Emmanuelle Waubant, Helen Tremlett. Commun Med (Lond). 2024
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2022
Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT)
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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
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Microcosm cultures of a complex synthetic community reveal ecology and genetics of gut microbial organization
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Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome
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The best offense is a good beta-defensin
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Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
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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
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Microbial stsueijignals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage
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2021
Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis
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The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
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Periodontal Disease: The Good, The Bad, and The Unknown
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Allan Radaic, Yvonne L.Kapila. Computational and Structural Biotechnology Journal, 2021
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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
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Maternal gut microbiome regulates immunity to RSV infection in offspring
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Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses
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Hair of the mouse: A skin bacteria “cocktail” gets follicles back on their feet
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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
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Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood
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2020
Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis
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Periodontal pathogens promote cancer aggressivity via TLR/MyD88 triggered activation of Integrin/FAK signaling that is therapeutically reversible by a probiotic bacteriocin
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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
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Polymicrobial periodontal disease triggers a wide radius of effect and unique virome
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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
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Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Nature Medicine, 2020
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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
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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
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CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog
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