2025
Coordinated Variation in the Immune Systems and Microbiomes of Healthy Humans is Linked to Tonic Interferon States
Joel Babdor, Ravi K. Patel, Brittany Davidson, Cecilia Noecker, Maha Rahim, Jordan E. Bisanz, Iliana Tenvooren, Diana Marquez, Maria Calvo, Vrinda Johri, Elizabeth McCarthy, Avneet Shaheed, Christina Ekstrand, Allison M. Weakley, Feiqiao B. Yu, Oliver Fiehn, Peter H. Turnbaugh, Alexis J. Combes, Gabriella K. Fragiadakis, Matthew H. Spitzer. BioRxiv preprint, 2025
The Barancik Award Lecture: Multi-disciplinary Research Will be the Key to Stop, Restore, and End MS.
Sergio E. Baranzini. Multiple Sclerosis Journal, 2025
Racial and Ethnic Differences in Prenatal Exposure to Environmental Phenols and Parabens in the ECHO Cohort.
Michael S. Bloom, Sudhi Upadhyaya, Adaeze W. Nzegwu, Jordan R. Kulper, Jessie P. Buddley, Judy Aschner, Dana Barr, Emily S. Barrett, Deborah H. Bennett, Dana Dabelea, Anna L. Dunlop, Alma Fuller, Margaret Karagas, Doughal Llang, John Meeker, Rachel Miller, Thomas G. O'Connor, Megan E. Romano, Sheela Sathyanarayana, Anne P. Starling, Annemarie Stroustrup, Deborah J. Watkins, and for the ECHO Cohort Consortium. J Expo Sci Environ Epidemiol, 2025
Restoring the Multiple Sclerosis Associated Imbalance of Gut Indole Metabolites Promotes Remyelination and Suppresses Neuroinflammation
Larissa Jank, Saumira S. Singh, Judy Lee, Asmita Dhukhwa, Fatemeh Siavoshi, Deepika Joshi, Veronica Minney, Kanak Gupta, Sudeep Ghimire, Pradney Deme, Vinicius A. Shoeps, Karthik Soman, Dimitrios Ladakis, Matthew Smith, Kamil Borkowski, John Newman, Sergio E. Baranzini, Emmanuelle L. Waubant, Kathryn C. Fitzgerald, Ashutosh Mangalam, Norman Haughey, Michael Kornberg, Xitiz Chamling, Peter A. Calabresi, Pavan Bhargava. BioRxiv preprint, 2025
Skin Microbiome and Dermatologic Disorders
Tiffany C. Scharschmidt and Julia A. Segre. J Clin Invest, 2025
Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis
Jennifer D. Claytor, Din L. Lin, Kevin M. Magnaye, Tanedth Sanchez Guerrero, Charles R. Langelier, Susan V. Lynch, Najwa El-Nachef. Dig Dis Sci, 2025
Artificial Intelligence in Food and Nutrition Evidence: The Challenges and Opportunities
Regan L. Bailey, Amanda J. MacFarlane, Martha S. Field, Ilias Tagkopoulos, Sergio E. Baranzini, Kristen M. Edwards, Christopher J. Rose, Nicholas J. Schork, Akshat Singhal, Byron C. Wallace, Kelly P. Fisher, Konstantinos Markakis, and Patrick J. Stover. PNAS Nexus, 2025
The Emerging Fungal Pathogen Candida auris Induces IFNgamma to Colonize Mammalian Hair Follicles
Eric Dean Merrill, Victoria Prudent, Parna Modhadam, Abram Rodriguez, Charlotte Hurabielle, Elina K. C. Wells, Pauline Basso, Tiffany C. Scharschmidt, Michael D. Rosenblum, Ari B. Molofsky, Suzanne M. Noble. BioRxiv preprint, 2025
Exclusive Enteral Nutrition Initiates Individual Protective Microbiome Changes to Induce Remission in Pediatric Crohn's Disease
Deborah Häcker, Kolja Siebert, Byron J. Smith, Nikolai Köhler, Alessandra Riva, Aritra Mahapatra, Helena Haimes, Jiatong Nie, Amira Metwaly, Hannes Hölz, Quirin Manz, Federica DeZen, Jeannine Heetmeyer, Katharina Socas, Giang LeThi, Chen Meng, Karin Kleigrewe, Josch K. Pauling, Klaus Neuhaus, Markus List, Katherine S. Pollard, Tobias Schwerd, Dirk Haller. Cell Host Micr, 2025
Human Xenobiotic Metabolism Proteins Have Full-Length and Split Homologs in the Gut Microbiome
Matthew Rendina, Peter J. Turnbaugh, Patrick H. Bradley. BioRxiv preprint, 2025
The Fungal Gut Microbiota in Pediatric-Onset Multiple Sclerosis
Nelson Mok, Natalie C. Knox, Feng Zhu, Douglas L. Arnold, Amit Bar-Or, Charles Noah Bernstein, Christine Bonner, Jessica D. Forbes, Morag Graham, Ruth Ann Marie, Julia O'Mahony, E. Ann Yeh, Yinshan Zhao, Gary Van Domselaar, Brenda Banwell, Emmanuelle Waubant, and Helen L. Tremlett. Front Microbiol, 2025
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, Ganase Wegeinka, Edward M. Zoratti, Suzan V. Lynch, Christine C. Johnson, and Albert M. Levin. J All Clin Immunol, 2025
Topological Segregation of Stress Sensors Along the Gut Crypt-Villus Axis
Kould K. Touhara, Nathan D. Rosson, Fei Dong, Joel Castro, Andrea M. Harrington, Tifany Chu, Sonla Garcia-Caraballo, Marlana Brtzuela, Tracey O'Donnell, Jinhao Xu, Onur Cil, Stuart M. Brierley, Yulong Li & David Julius. Nature, 2025
Host-Microbe Multiomics Profiling Identifies Distinct COVID-19 Immune Dysregulation in Solid Organ Transplant Recipients
Harry Pickering, Joanna Schaenman, Hoang Van Phan, Cole Maguire, Alexandra Tsitsiklis, Nadine Rouphael, Nelson Ivan Agudelo Higuita, Mark A. Atkinson, Scott Brakenridge, Monica Fung, William Messer, IMPACC Network, Ramin Salehi-rad, Mathew C. Altman, Patrice M. Becker, Steven E. Bosinger, Walter Eckalbar, Annmarie Hoch, Naresh Doni Jayavelu, Seunghee Kim-Schulze, Meagan Jenkins, Steven H. Kleinstein, Florian Krammer, Holden T. Maecker, Charles R. Langelier. Nat Commun, 2025
Impact of Doxycycline Post-Exposure Prophylaxis for Sexually Transmitted Infections on the Gut Microbiome and Antimicrobial Resistome
Victoria T. Chu, Abigail Glascock, Deborah Donnell, Cole Grabow, Clare E. Brown, Ryan Ward, Christina Love, Katrina L. Kalantar, Stephanie E. Cohen, Chase Cannon, Michael H. Woodworth, Colleen F. Kelley, Connie Celum, Anne F. Leutkameyer & Charles R. Langelier. Nat Med, 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. BioRxiv preprint, 2025
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. MedRxiv preprint, 2025
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. J Bact Chem, 2025
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. J Clin Invest, 2025
Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.
Matthew Rendina, Peter J. Turnbaugh, Patrick H. Bradley. G3 (Bethesda), 2025
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. Clin Gastroenterol Hepatol, 2025
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. J Bone Min Res, 2025
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. Transplant Cell Ther, 2025
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. Crit Care, 2025
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. Am J Respir Crit Care Med, 2025
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. Nature, 2025
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. Hepatol, 2025
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. Plast Reconstr Surg Glob Open, 2025
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. Clin Transl Sci, 2025
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. BioRxiv preprint, 2025
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. Adv Sci, 2025
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. Nat Comm, 2025
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. BioRxiv preprint, 2205
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. Res Sq preprint, 2025
Mining microbial metabolites of GPCR-targeted drugs.
Chen Zhang, Peter J. Turnbaugh. Trends Pharmacol Sci, 2025
Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (micoSLAM).
Miriam Goldman, Chunyu Zhao, Katherine S. Pollard. Comp Biol, 2025
Linkage of nucleotides and functional diversity varies across gut bacteria.
Veronika Dubinkina, Byron Smith, Chunyu Zhao, Cindy Pino, Katherine S. Pollard. BioRxiv preprint, 2025
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. BioRxiv preprint, 2025
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. J Nutr, 2025
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. Genom Med, 2025
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. Can Epi Biomark Prev, 2025
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. Sust Microbiol, 2025
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. Gen Res, 2025
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. Am J Obst Gyn, 2025
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. Lanc Micr, 2025
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. Mol Cell, 2025
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. MBio, 2025
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. Pediatr, 2025
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. BioRxiv preprint, 2025
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. Cell Biomat, 2025
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. Imm Infl, 2025
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. Gen Res, 2025
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. J Nutr, 2025
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. Nature, 2025
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. BioRxiv preprint, 2025
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. Lanc Micr, 2025
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. J All Clin Immunol, 2025
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. BioRxiv preprint, 2025
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. Nat Med, 2025
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
Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients
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-Nachev, Susan V Lynch. Sci Rep 2024
12, 13-diHOME promotes inflammatory macrophages and epigenetically modifies their capacity to respond to microbes and allergens
Din L Lin, Kevin M Magnaye, Cara E Porsche, Sophia R Levan, Elze Rackaityte, Mustafa Özçam, Susan V Lynch. J Immunol Res 2024
Clinical and molecular analysis of longitudinal rhinitis phenotypes in an urban birth cohort
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
The gut-airway axis in health and respiratory disease
Mustafa Özçam, Susan V Lynch. Nat Rev Microbiol 2024
Fecal microbiota is associated with extraintestinal manifestations in inflammatory bowel disease
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
Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy
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
Early-life nasal microbiota dynamics relate to longitudinal respiratory phenotypes in urban children
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
Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity
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
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. 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
Effect of early life exposures to the aryl hydrocarbon receptor ligand TCDF on gut microbiota and host metabolic homeostasis in C57BL/6J mice
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
Effects of high dose aspartame-based sweetener on the gut microbiota and bone strength in young and aged mice
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
Digesting the complex metabolic effects of diet on the host and microbiome
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
Human gut Actinobacteria boost drug absorption by secreting P-glycoprotein ATPase inhibitors
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
Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas
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
A diet-dependent metabolite shapes the gut microbiota to protect from autoimmunity
A diet-dependent host metabolite shapes the gut microbiota to protect from autoimmunity
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
High fat intake sustains sorbitol intolerance after antibiotic-mediated Clostridia depletion for the gut microbiota
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
Short-chain fatty acid producers in the gut are associated with pediatric multiple sclerosis onset
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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