2025

Figure from a manuscript

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.

figure from a manuscript

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. 

figure from a manuscript

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.

 

 

figure from a manuscript

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.

figure from a manuscript

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.

Matthew Rendina, Peter J. Turnbaugh, Patrick H. Bradley.

figure from a manuscript

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.

figure from a manuscript

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.

figur from a manuscript

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.

a figure from a manuscript

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.

a figure from a manuscript

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.

manuscript figure

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.

manuscript figure

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.

title

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 LynchdRxiv [Preprint]. 2024

 

Din L Lin, Kevin M Magnaye, Cara E Porsche, Sophia R Levan, Elze Rackaityte, Mustafa Özçam, Susan V LynchJ 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 TurnbaughbioRxiv [Preprint]. 2024

 

Veronica Escalante, Renuka R Nayak, Cecilia Noecker, Joel Babdor, Matthew Spitzer, Adam M Deutschbauer, Peter J TurnbaughMol 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 HernandezJBMR Plus. 2024

 

Rachel N Carmody, Krista Varady, Peter J TurnbaughCell. 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 TurnbaughiScience 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 TurnbaughCell 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 BaranziniBioinformatics. 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 DeanmBio. 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 KleinNat 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 HernandezJ 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

 

Feng Zhu, Yinshan Zhao, Douglas L Arnold, Amit Bar-Or, Charles N Bernstein, Christine Bonner, Morag Graham, Janace Hart, Natalie Knox, Ruth Ann Marrie, Ali I Mirza, Julia O’Mahony, Gary Van Domselaar, E Ann Yeh, Brenda Banwell, Emmanuelle Waubant, Helen Tremlett, US Network of Pediatric MS Centers, the Canadian Pediatric Demyelinating Disease Network. Ann Clin Transl Neurol. 2024

 

Soumaya Zlitni, Sierra Bowden, Hila Sberro, Marcelo D T Torres, Joan M Vaughan, Antonio F M Pinto, Yishay Pinto, Daniel Fernandez, Hannes Röst, Alan Saghatelian, Cesar de la Fuente-Nunez, Ami S Bhatt. bioRxiv [Preprint]. 2024

 

Elias R Gerrick, Soumaya Zlitni, Patrick T West, Matthew M Carter, Claire M Mechler, Matthew R Olm, Elisa B Caffrey, Jessica A Li, Steven K Higginbottom, Christopher J Severyn, Frauke Kracke, Alfred M Spormann, Justin L Sonnenburg, Ami S Bhatt, Michael R Howitt. Cell. 2024

 

Minwoo Bae, Chi Le, Raaj S Mehta, Xueyang Dong, Lindsey M Pieper, Lorenzo Ramirez, Margaret Alexander, Sina Kiamehr, Peter J Turnbaugh, Curtis Huttenhower, Andrew T Chan, Emily P Balskus. Cell Host Microbe. 2024

 

2023

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


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. 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


 

https://www.sciencedirect.com/science/article/pii/S2666379122002567?via%3DihubHeritable 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


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. 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.

Document

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.

Allan Radaic, Yvonne L.Kapila. Computational and Structural Biotechnology Journal, 2021

Miqdad O.DhariwalaTiffany C.ScharschmidtTrends in Immunology, 2021

 

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

Kathy N. Lam, Peter Spanogiannopoulos, Paola Soto-Perez​, Allison M. Weakley, Feiqiao B. Yu, Peter J. Turnbaugh. Cell Reports, 2021 

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

 

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


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. 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
 


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 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