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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
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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
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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
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Holly Steininger, Jacqueline Moltzau-Anderson, Susan V. Lynch, Semmin Immunol, 2023
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FLG Deficiency in Mice Alters the Early-Life CD4+ T-Cell Response to Skin Commensal Bacteria
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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
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Simvastatin induces human gut bacterial cell surface genes
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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
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Nisin a probiotic bacteriocin mitigates brain microbiome dysbiosis and Alzheimer's disease-like neuroinflammation triggered by periodontal disease
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Peptide YY: A Paneth cell antimicrobial peptide that maintains Candida gut commensalism
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Pitfalls of genotyping microbial communities with rapidly growing genome collections
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MaLiAmPi enables generalizable and taxonomy-independent microbiome features from technically diverse 16S-based microbiome studies
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Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer
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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
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Randomized controlled trial demonstrates response to a probiotic intervention for metabolic syndrome that may correspond to diet
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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,
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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
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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
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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
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Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
Eric Armstrong, Anke Hemmerling, Steve Miller, Kerianne E Burke, Sara J Newmann, Sheldon R Morris, Hilary Reno, Sanja Huibner, Maria Kulikova, Nico Nagelkerke, Bryan Coburn, Craig R Cohen, Rupert Kaul. The Lancet Microbe, 2022
A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation
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Sustained effect of LACTIN-V (Lactobacillus crispatus CTV-05) on genital immunology following standard bacterial vaginosis treatment: results from a randomised, placebo-controlled trial
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Microbial stsueijignals, MyD88, and lymphotoxin drive TNF-independent intestinal epithelial tissue damage
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DART takes aim at community editing
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2021
Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis
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The impact of environmental mycobiomes on geographic variation in COVID-19 mortality
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
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Periodontal Disease: The Good, The Bad, and The Unknown
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The oralome and its dysbiosis: New insights into oral microbiome-host interactions
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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
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Black In Immuno: harnessing social media and digital platforms to connect the dots
Joel Babdor, Amy C. Fan, Madina Wane, Berenice Mbiribindi, Alexis S. Mobley, Justine C. Noel & Elaine Kouame. Nature Reviews Immunology, 2021
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
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Maternal gut microbiome regulates immunity to RSV infection in offspring
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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
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Caloric restriction disrupts the microbiota and colonization resistance
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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
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Microbiota, Epigenetics, and Trained Immunity. Convergent Drivers and Mediators of the Asthma Trajectory from Pregnancy to Childhood
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2020
Gut microbiota-specific IgA+ B cells traffic to the CNS in active multiple sclerosis
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
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Polymicrobial periodontal disease triggers a wide radius of effect and unique virome
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Probing the tumor micro(b)environment
Chloe E. Atreya, Peter J. Turnbaugh. Science, 2020
Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells
Qi Yan Ang, Margaret Alexander, John C. Newman, Yuan Tian, Jingwei Cai, Vaibhav Upadhyay, Jessie A.Turnbaugh, Eric Verdin, Kevin D. Hall, Rudolph L.Leibel, Eric Ravussin, Michael Rosenbaum, Andrew D.Patterson, Peter J.Turnbaugh. Cell, 2020
Bacterial metabolism rescues the inhibition of intestinal drug absorption by food and drug additives
Ling Zou, Peter Spanogiannopoulos, Lindsey M. Pieper, Huan-Chieh Chien, Wenlong Cai, Natalia Khuri, Joshua Pottel, Bianca Vora, Zhanglin Ni, Eleftheria Tsakalozou, Wenjun Zhang, Brian K. Shoichet, Kathleen M. Giacomini, and Peter J. Turnbaugh. Proceedings of the National Academy of Sciences, 2020
A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria
JE Bisanz, P Soto-Perez, C Noecker, AA Aksenov, KN Lam, GE Kenney, EN Bess, HJ Haiser, TS Kyaw, FB Yu, VM Rekdal, CWY Ha, S Devkota, EP Balskus, PC Dorrestein, E Allen-Vercoe, PJ Turnbaugh. Cell Host and Microbe, 2020
Phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
P.H. Bradley, K.S. Pollard. Bioinformatics, 2020
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
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M. Roodgar, B.H. Good, N.R. Garud, S. Martis, M. Avula, W. Zhou, S. Lancaster, H. Lee, A. Babveyh, S. Nesamoney, K.S. Pollard, M.P. Snyder. BioRxiv, 2019
Cooking shapes the structure and function of the gut microbiome
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CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog
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Recirculating Intestinal IgA-Producing Cells Regulate Neuroinflammation via IL-10.
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