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-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
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 microbiome axis in health and respiratory diseases
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
Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research
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
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
Effects 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 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 from 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
Effects of long-term high dose aspartame on body mass, bone strength, femoral geometry, and microbiota composition in a young and aged cohort of male and female 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. bioRxiv [Preprint]. 2024
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 R Abate. bioRxiv [Preprint]. 2024
Biomedical knowledge graph-optimized prompt generation for large language models
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
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, 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
Staphylococcus aureus-specific skin resident memory T cells protect against bacteria colonization but exacerbate atopic dermatitis-like flares in mice
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
Preclinical Atopic Dermatitis Skin in Infants: An Emerging Research Area
Amy S Paller, Tiffany C Scharschmidt, Sanja Kezic, Alan D Irvine. J Invest Dermatol. 2024
Molecular Insights into O-Linked Sialoglycans Recognition by the Siglec-Like SLBR-N (SLBRUB10712) of Streptococcus gordonii
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
An Enterobacteriaceae bloom in aging animals is restrained by the gut microbiome
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
Chlamydia suis undergoes interclade recombination promoting Tet-island exchange
Helena Seth-Smith, Sankhya Bommana, Deborah Dean, Timothy D Read, Hanna Marti. BMC Genomics. 2024
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. 2024
Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains
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
Vaginal fungi are associated with treatment-induced shifts in the vaginal microbiota and with a distinct genital immune profile
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
Vaginal Lactobacillus crispatus persistence following application of a live biotherapeutic product: colonization phenotypes and genital immune impact
Eric Armstrong, Anke Hemmerling, Steve Miller, Sanja Huibner, Maria Kulikova, Emily Crawford, Gloria R Castañeda, Bryan Coburn, Craig R Cohen, Rupert Kaul. Microbiome. 2024
Microbiome-induced increases and decreases in bone matrix strength can be initiated after skeletal maturity
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
Activation of fetal-like molecular programs during regeneration in the intestine and beyond
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
The impact of the human gut microbiome on the treatment of autoimmune disease
Renuka R Nayak, Diego A Orellana. Immunol Rev. 2024
Functional genomic analysis of genes important for Candida albicans fitness in diverse environmental conditions
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
Deep mutational scanning of EccD3 reveals the molecular basis of its essentiality in the mycobacterium ESX secretion system
Donovan D Trinidad, Christian B Macdonald, Oren S Rosenberg, James S Fraser, Willow Coyote-Maestas. bioRxiv [Preprint]. 2024
Bioorthogonal Radiolabeling of Azide-Modified Bacteria Using [18F]FB-sulfo-DBCO
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
Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing
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
Microbial dynamics and pulmonary immune responses in COVID-19 secondary bacterial pneumonia
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
Toxigenic Clostridium perfringens Isolated from At-Risk Paediatric Inflammatory Bowel Disease Patients
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
Mediterranean diet and associations with the gut microbiota and pediatric-onset multiple sclerosis using trivariate analysis
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
A cross-sectional study of MRI features and the gut microbiome in pediatric-onset multiple sclerosis
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
Dual quorum-sensing control of purine biosynthesis drives pathogenic fitness of Enterococcus faecalis
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
Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition
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
Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme
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. Bustion, Renuka 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. Scharschmidt. Journal 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
Heritable vaginal bacteria influence immune tolerance and relate to early-life markers of allergic sensitization in infancy
Kathryn E. McCauley, Elze Rackaityte, Brandon LaMere, Douglas W. Fadrosh, Kei E. Fujimura, Ariane R. Panzer, Din L. Lin, Kole V. Lynch, Joanna Halkias, Ventura F. Mendoza, Trevor D. Burt, Casper Bendixsen, Kathrine Barnes, Haejin Kim, Kyra Jones, Dennis R. Ownby, Christine C. Johnson, Christine M. Seroogy, James E. Gern 8, Homer A. Boushey, and Susan V. Lynch. Cell Reports Medicine, 2022
Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism
Peter Spanogiannopoulos, Than S. Kyaw, Ben G. H. Guthrie, Patrick H. Bradley, Joyce V. Lee, Jonathan Melamed, Ysabella Noelle Amora Malig, Kathy N. Lam, Daryll Gempis, Moriah Sandy, Wesley Kidder, Erin L. Van Blarigan, Chloe E. Atreya, Alan Venook, Roy R. Gerona, Andrei Goga, Katherine S. Pollard & Peter J. Turnbaugh. Nature Microbiology, 2022
Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course
Xiaoyuan Zhou, Ryan Baumann, Xiaohui Gao, Myra Mendoza, Sneha Singh, Ilana Katz Sand, Zongqi Xia, Laura M. Cox, Tanuja Chitnis, Hongsup Yoon, Laura Moles, Stacy J. Caillier, Adam Santaniello, Gail Ackermann, Adil Harroud, Robin Lincoln, Refujia Gomez, Antonio González Peña, Elise Digga, Daniel Joseph Hakim, Yoshiki Vazquez-Baeza, Karthik Soman, Shannon Warto, Greg Humphrey, Mauricio Farez, Lisa Ann Gerdes, Jorge R. Oksenberg, Scott S. Zamvil, Siddharthan Chandran, Peter Connick, David Otaegui, Tamara Castillo-Triviño, Stephen L. Hauser, Jeffrey M. Gelfand, Howard L. Weiner, Reinhard Hohlfeld, Hartmut Wekerle, Jennifer Graves, Amit Bar-Or, Bruce A.C. Cree, Jorge Correale, Rob Knight, Sergio E. Baranzini. Cell, 2022
Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
Eric Armstrong, Anke Hemmerling, Steve Miller, Kerianne E Burke, Sara J Newmann, Sheldon R Morris, Hilary Reno, Sanja Huibner, Maria Kulikova, Nico Nagelkerke, Bryan Coburn, Craig R Cohen, Rupert Kaul. The Lancet Microbe, 2022
A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation
Mustafa O¨ zcam, Jee-Hwan Oh, Restituto Tocmo, Tim S. Bugni, Jens Walter, Jan-Peter van Pijkeren.
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. Lynch. PLOS One, 2021.
The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
Joshua Ladau, Katrina Abuabara, Angelica M. Walker, Marcin P. Joachimiak, Ishan Bansal, Yulun Wu, Elijah B. Hoffman, Chaincy Kuo, Nicola Falco, Jared Streich, Mark J. van der Laan, Haruko M. Wainwright, Eoin L. Brodie, Matthias Hess, Daniel Jacobson, and James B. Brown. MedRXiv (preprint), 2021.
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro
Zhou Jason Shi, Boris Dimitrov, Chunyu Zhao, Stephen Nayfach & Katherine S. Pollard. Nature Biotechnology, 2021.
Periodontal Disease: The Good, The Bad, and The Unknown
Lea M. Sedghi, Margot Bacino and Yvonne Lorraine Kapila.. Front. Cell. Infect. Microbiol., 2021.
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic, Yvonne L.Kapila. Computational and Structural Biotechnology Journal, 2021
Baby’s skin bacteria: first impressions are long-lasting
Miqdad O.Dhariwala, Tiffany C.Scharschmidt, Trends in Immunology, 2021
Human gut bacterial metabolism drives Th17 activation and colitis
Margaret Alexander, Qi Yan Ang, Renuka R.Nayak, Annamarie E.Bustion, Moriah Sandy, Bing Zhang, Vaibhav Upadhyay, Katherine S.Pollard, Susan V. Lynch, Peter J.Turnbaugh. Cell Host & Microbe, 2021.
Black In Immuno: harnessing social media and digital platforms to connect the dots
Joel Babdor, Amy C. Fan, Madina Wane, Berenice Mbiribindi, Alexis S. Mobley, Justine C. Noel & Elaine Kouame. Nature Reviews Immunology, 2021
Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome
Kathy N. Lam, Peter Spanogiannopoulos, Paola Soto-Perez, Allison M. Weakley, Feiqiao B. Yu, Peter J. Turnbaugh. Cell Reports, 2021
The oral microbiome: Role of key organisms and complex networks in oral health and disease
Lea Sedghi, Vincent DiMassa, Anthony Harrington, Susan V. Lynch, Yvonne L. Kapila. Periodontology 2000, 2021
Maternal gut microbiome regulates immunity to RSV infection in offspring
Wendy Fonseca, Carrie-Anne Malinczak, Kei Fujimura, Danny Li, Kathryn McCauley, Jia L , Shannon K.K. Best, Diana Zhu, Andrew J. Rasky, Christine C. Johnson, Jennifer Bermick, Edward M. Zoratti, Dennis Ownby, Susan V. Lynch, Nicholas W. Lukacs, Catherine Ptaschinski. J Exp Med, 2021
Lung immune tone via gut-lung axis: gut-derived LPS and short-chain fatty acids’ immunometabolic regulation of lung IL-1β, FFAR2, and FFAR3 expression
Qing Liu, Xiaoli Tian, Daisuke Maruyama, Mehrdad Arjomandi, and Arun Prakash. Am J Physiol Lung Cell Mol Physiol, 2021
Caloric restriction disrupts the microbiota and colonization resistance
Reiner Jumpertz von Schwartzenberg, Jordan E. Bisanz, Svetlana Lyalina, Peter Spanogiannopoulos, Qi Yan Ang, Jingwei Cai, Sophia Dickmann, Marie Friedrich, Su-Yang Liu, Stephanie L. Collins, Danielle Ingebrigtsen, Steve Miller, Jessie A. Turnbaugh, Andrew D. Patterson, Katherine S. Pollard, Knut Mai, Joachim Spranger & Peter J. Turnbaugh. Nature, 2021
Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses
Aline Dionizio, Dawud Abduweli Uyghurturk, Carina Guimarães Souza Melo, Isabela Tomazini Sabino-Arias, Tamara Teodoro Araujo, Talita Mendes Silva Ventura, Juliana Vanessa Colombo Martins Perles, Jacqueline Nelisis Zanoni, Pamela Den Besten, Marília Afonso Rabelo Buzalaf. Chemosphere, 2021.
Hair of the mouse: A skin bacteria “cocktail” gets follicles back on their feet
Jeanmarie R. Gonzalez, Geil R. Merana, Tiffany C. Scharschmidt. Cell Host and Microbe, 2021
The pulmonary metatranscriptome prior to pediatric HCT identifies post-HCT lung injury
Matt S Zinter, Caroline A Lindemans, Birgitta A Versluys, Madeline Y Mayday, Sara Sunshine, Gustavo Reyes, Marina Sirota, Anil Sapru, Michael A Matthay, Sandhya Kharbanda, Christopher C Dvorak, Jaap J Boelens, Joseph L DeRisi. Blood, 2021
The oralome and its dysbiosis: New insights into oral microbiome-host interactions
Allan Radaic and Yvonne L. Kapila. Computational and Structural Biotechnology Journal, 2021
Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood
Susan V. Lynch and Donata Vercelli. American Journal of Respiratory and Critical Care Medicine, 2021
2020
Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis
AK Pröbstel, X Zhou, R Baumann, S Wischnewski, M Kutza, OL Rojas, K Sellrie, A Bischof, K Kim, A Ramesh, R Dandekar, AL Greenfield, RD Schubert, JE Bisanz, S Vistnes, K Khaleghi, J Landefeld, G Kirkish, F Liesche-Starnecker, V Ramaglia, S Singh, EB Tran, P Barba, K Zorn, J Oechtering, K Forsberg, LR Shiow, RG Henry, J Graves, BAC Cree, SL Hauser, J Kuhle, JM Gelfand, PM Andersen, J Schlege, PJ Turnbaugh, PH Seeberger, JL Gommerman, MR Wilson, L Schirmer, SE Baranzini. Science Immunology, 2020.
Periodontal pathogens promote cancer aggressivity via TLR/MyD88 triggered activation of Integrin/FAK signaling that is therapeutically reversible by a probiotic bacteriocin
P Kamarajan, I Ateia, JM Shin, JC Fenno, C Le, L Zhan, A Chang, R Darveau, YL Kapila. PLOS Pathogens, 2020
Modulation of pathogenic oral biofilms towards health with nisin probiotic
Radaic A, Ye C, Parks B, Gao L, Kuraji R, Malone E, Kamarajan P, Zhan L, Kapila YL. J Oral Microbiol. 2020
Deconstructing Mechanisms of Diet-Microbiome-Immune Interactions
Margaret Alexander, Peter J.Turnbaugh. Immunity, 2020
Household paired design reduces variance and increases power in multi-city gut microbiome study in multiple sclerosis
The iMSMS Consortium (SE Baranzini). Multiple Sclerosis Journal, 2020.
Polymicrobial periodontal disease triggers a wide radius of effect and unique virome
Li Gao, Misun Kang, Martin Jinye Zhang, M. Reza Sailani, Ryutaro Kuraji, April Martinez, Changchang Ye, Pachiyappan Kamarajan, Charles Le, Ling Zhan, Hélène Rangé, Sunita P. Ho & Yvonne L. Kapila. npj Biofilms and Microbiomes, 2020
Probing the tumor micro(b)environment
Chloe E. Atreya, Peter J. Turnbaugh. Science, 2020
Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells
Qi Yan Ang, Margaret Alexander, John C. Newman, Yuan Tian, Jingwei Cai, Vaibhav Upadhyay, Jessie A.Turnbaugh, Eric Verdin, Kevin D. Hall, Rudolph L.Leibel, Eric Ravussin, Michael Rosenbaum, Andrew D.Patterson, Peter J.Turnbaugh. Cell, 2020
Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives
Ling Zou, Peter Spanogiannopoulos, Lindsey M. Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K. Shoichet, Kathleen M. Giacomini, and Peter J. Turnbaugh. Proceedings of the National Academy of Sciences, 2020
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
JE Bisanz, P Soto-Perez, C Noecker, AA Aksenov, KN Lam, GE Kenney, EN Bess, HJ Haiser, TS Kyaw, FB Yu, VM Rekdal, CWY Ha, S Devkota, EP Balskus, PC Dorrestein, E Allen-Vercoe, PJ Turnbaugh. Cell Host and Microbe, 2020
Phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
P.H. Bradley, K.S. Pollard. Bioinformatics, 2020
Viable bacterial colonization is highly limited in the human intestine in utero.
Rackaityte E, Halkias J, Fukui EM, Mendoza VF, Hayzelden C, Crawford ED, Fujimura KE, Burt TD, Lynch SV. Nature Medicine, 2020
Genetic basis for the cooperative bioactivation of plant lignans by Eggerthella lenta and other human gut bacteria.
Bess EN, Bisanz JE, Yarza F, Bustion A, Rich BE, Li X, Kitamura S, Waligurski E, Ang QY, Alba DL, Spanogiannopoulos P, Nayfach S, Koliwad SK, Wolan DW, Franke AA, Turnbaugh PJ. Nature Microbiology, 2020
2019
Toxin-Triggered Interleukin-1 Receptor Signaling Enables Early-Life Discrimination of Pathogenic versus Commensal Skin Bacteria.
Leech JM, Dhariwala MO, Lowe MM, Chu K, Merana GR, Cornuot C, Weckel A, Ma JM, Leitner EG, Gonzalez JR, Vasquez KS, Diep BA, Scharschmidt TC. Cell Host & Microbe, 2019
Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance.
Levan, S.R., Stamnes, K.A., Lin, D.L., Panzer A.R., Fukui E., McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV. Nature Microbiology, 2019
Population Genetics in the Human Microbiome
N.G. Garud and K.S. Pollard. Trends in Genetics, 2019
A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome
A. Almeida, S. Nayfach, M. Boland, F. Strozzi, M. Beracochea, Z.J. Shi, K.S. Pollard, D.H. Parks, P. Hugenholtz, N. Segata, N.C. Kyrpides, R.D. Finn. BioRxiv, 2019
Longitudinal linked read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment
M. Roodgar, B.H. Good, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K.S. Pollard, M.P. Snyder. BioRxiv, 2019
Cooking shapes the structure and function of the gut microbiome
Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, Northen TR, Turnbaugh PJ. Nature Microbiology, 2019
CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog
Soto-Perez P, Bisanz JE, Berry JD, Lam KN, Bondy-Denomy J, Turnbaugh PJ. Cell Host Microbe, 2019
Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
Rojas OL, Pröbstel AK, Porfilio EA, Wang AA, Charabati M, Sun T, Lee DSW, Galicia G, Ramaglia V, Ward LA, Leung LYT, Najafi G, Khaleghi K, Garcillán B, Li A, Besla R, Naouar I, Cao EY, Chiaranunt P, Burrows K, Robinson HG, Allanach JR, Yam J, Luck H, Campbell DJ, Allman D, Brooks DG, Tomura M, Baumann R, Zamvil SS, Bar-Or A, Horwitz MS, Winer DA, Mortha A, Mackay F, Prat A, Osborne LC, Robbins C, Baranzini SE, Gommerman JL. Cell, 2019
