Kyle Bittinger, PhD

2023

Firrman J, Liu L, Mahalak K, Hu W, Bittinger K, Moustafa A, Jones SM, Narrowe A, Tomasula P.: An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner. Front Nutr 9: 1040744, Jan 2023.

Mahalak KK, Firrman J, Narrowe AB, Hu W, Jones SM, Bittinger K, Moustafa AM, Liu L.: Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner. Front Nutr 9: 1058910, Jan 2023.

Zhang Y, Li Y, Barber AF, Noya SB, Williams JA, Li F, Daniel SG, Bittinger K, Fang J, Sehgal A: The microbiome stabilizes circadian rhythms in the gut. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 120(5): e2217532120, Jan 2023.

Hong G, Daniel SG, Lee JJ, Bittinger K, Glaser L, Mattei LM, Dorgan DJ, Hadjiliadis D, Kawut SM, Collman RG: Distinct community structures of the fungal microbiome and respiratory health in adults with cystic fibrosis. J Cyst Fibros Page: S1569-1993(23)00047-4, Feb 2023.

Xiang Z, Wakade RS, Ribeiro AA, Hu W, Bittinger K, Simon-Soro A, Kim D, Li J, Krysan DJ, Liu Y, Koo H: Human Tooth as a Fungal Niche: Candida albicans Traits in Dental Plaque Isolates. mBio 14(1): e0276922, Feb 2023.

Carr RM, Li Y, Chau L, Friedman ES, Lee JJ, Adorini L, Erickson M, Zaru L, Shringarpure R, MacConell L, Bittinger K, Li H, Wu GD: An integrated analysis of fecal microbiome and metabolomic features distinguish Non-cirrhotic NASH from healthy control populations. Hepatology May 2023 Notes: Epub ahead of print. doi: 10.1097/HEP.0000000000000474.

Conrey PE, Denu L, O'Boyle KC, Rozich I, Green J, Maslanka J, Lubin JB, Duranova T, Haltzman BL, Gianchetti L, Oldridge DA, De Luna N, Vella LA, Allman D, Spergel JM, Tanes C, Bittinger K, Henrickson SE, Silverman MA: IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation. Sci Immunol 8(83): eade2335, May 2023.

Liu L, Narrowe AB, Firrman JA, Mahalak KK, Bobokalonov JT, Lemons JMS, Bittinger K, Daniel S, Tanes C, Mattei L, Friedman ES, Soares JW, Kobori M, Zeng WB, Tomasula PM: Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME). Foods 12(11): 2105, May 2023.

Vizioli C, Jaime-Lara R, Daniel SG, Franks A, Diallo AF, Bittinger K, Tan TP, Merenstein DJ, Brooks B, Joseph PV, Maki KA: Administration of Bifidobacterium animalis subsp. lactis Strain BB-12 in Healthy Children: Characterization, Functional Composition, and Metabolism of the Gut Microbiome. Front Microbiol 14: 1165771, May 2023.

Williams PA, Naughton KE, Simon LA, Soto GE, Parham LR, Ma X, Danan CH, Hu W, Friedman ES, McMillan EA, Mehta H, Stoltz MA, Ocaña JS, Zackular JP, Bittinger K, Whelan KA, Karakasheva TA, Hamilton KE: Intestinal epithelial autophagy is required for the regenerative benefit of calorie restriction. Am J Physiol Gastrointest Liver Physiol 324(5): G354-G368, May 2023.

Liu Y, Daniel SG, Kim HE, Koo H, Korostoff J, Teles F, Bittinger K, Hwang G: Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities. Microbiome 11(1): 123, Jun 2023.

Redding LE, Habing GG, Tu V, Bittinger KL, O'Day J, Pancholi P, Wang SH, Alexander A, Kelly BJ, Weese JS, Stull JW: Infrequent intrahousehold transmission of Clostridioides difficile between pet owners and their pets. Zoonoses Public Health 70(4): 341-351, Jun 2023.

2022

Elgarten C, Tanes C, Lee JJ, Danziger Isakov LA, Grimley MS, Green M, Michaels MG, Barnum JL, Ardura MI, Auletta JJ, Blumenstock J, Sief AE, Bittinger K, Fisher BT: Early stool microbiome and metabolome signatures in pediatric patients undergoing allogeneic hematopoietic cell transplantation.  Pediatr Blood Cancer 69: e29384, Jan 2022.

Ferro LE, Crowley LN, Bittinger K, Freidman ES, Decker, JE, Russel K, Katz S, Kim JK, Trabulsi JC: Effects of prebiotics, probiotics, and synbiotics on the infant gut microbiota and other health outcomes: A systematic review. Critical Review in Food Science and Nutrition 159(2): 67-480, Jan 2022.

Breton J, Tanes C, Tu V, Albenberg L, Rowley S, Devas N, Hwang R, Kachelries K, Wu GD, Baldassano RN, Bittinger K, Mattei P: A microbial signature for pediatric perianal Crohn's Disease. J Crohn's Colitis 15: jjac032, Feb 2022.

Nashed L, Mani J, Hazrati S, Stern DB, Subramanian P, Mattei L, Bittinger K, Hu W, Levy S, Maxwell GL, Hourigan SK: Gut microbiota changes are detected in asymptomatic very young children with SARS-CoV-2 infection. Gut 71(11): 2371-2373, Feb 2022.

Simon-Soro A, Ren Z, Krom B, Hoogenkamp M, Cabello-Yeves P, Daniel S, Bittinger K, Tomas I, Koo H, Mira A: Polymicrobial aggregates in human saliva build the oral biofilm. mBio 13: e0013122, Feb 2022.

Mennella JA, Li Y, Bittinger K, Friedman ES, Zhao C, Li H, Wu GD, Trabulsi JC: The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status. Nutrients 14: 1241, Mar 2022.

Redding LE, Tu V, Abbas A, Alvarez M, Zackular JP, Gu C, Bushman FD, Kelly DJ, Barnhart D, Lee JJ, Bittinger K: Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations. Anaerobe 74: 102539, Apr 2022.

Firrman J, Liu L, Mahalak K, Tanes C, Bittinger K, Tu V, Bobokalonov J, Mattei L, Zhang H, Van den Abbeele P: The impact of environmental pH on the gut microbiota community structure and short chain fatty acid production. FEMS Microbiol Ecol 98(5): fiac038, May 2022.

Kastl A, Zong W, Gershuni VM, Friedman ES, Tanes C, Boateng A, Mitchell WJ, O'Connor K, Bittinger K, Terry NA, Bales C, Albenberg L, Wu GD: Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease. Gut Microbes 14(1): 2083417, May 2022.

Bartolo L, Afroz S, Pan YG, Xu R, Williams L, Lin CF, Tanes C, Bittinger K, Friedman ES, Gimotty PA, Wu GD, Su LF: SARS-CoV-2-specific T cells in unexposed adults display broad trafficking potential and cross-react with commensal antigens. Sci Immunol 7(76): eabn3127, Jul 2022.

Lee IK, Jacome DA, Cho JK, Tu V, Young AJ, Dominguez T, Northrup JD, Etersque JM, Lee HS, Ruff A, Aklilu O, Bittinger K, Glaser LJ, Dorgan D, Hadjiliadis D, Kohli RM, Mach RH, Mankoff DA, Doot RK, Sellmyer MA: Imaging sensitive and drug-resistant bacterial infection with [11C]-trimethoprim. J Clin Invest 132(18): e156679, Sep 2022.

Mahalak KK, Firrman J, Bobokalonov J, Narrowe AB, Bittinger K, Daniel S, Tanes C, Mattei LM, Zeng WB, Soares JW, Kobori M, Lemons JMS, Tomasula PM, Liu L.: Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome. Int J Mol Sci 23(21): 12973, Oct 2022.

Tenvooren I, Marquez DM, Schroeder AW, Cohen JN, Fassett MS, Lee J, Daniel SG, Bittinger K, Díaz RE, Fraser JS, Ali N, Ansel KM, Spitzer MH, Liang HE, Locksley RM: Innate type 2 immunity controls hair follicle commensalism by Demodex mites. Immunity 55(10): 1891-1908.e12, Oct 2022.

Stein R, Daniel SG, Baldassano RN, Feigenbaum K, Kachelries K, Sigall-Boneh R, Weston S, Levine A, Bittinger K: Outcomes and Predictors of Sustained Remission After Drug Withdrawal in Pediatric Crohn Disease. J Pediatr Gastroenterol Nutr 75(5): 608-615, Nov 2022.

Firrman J, Mahalak K, Bobokalonov J, Liu L, Lee JJ, Bittinger K, Mattei LM, Gadaingan R, Narrowe AB, Lemons JMS: Modulation of the gut microbiota structure and function by two structurally different lemon pectins. Foods 11(23): 3877, Dec 2022.

Mukhopadhyay S, Lee JJ, Hartman E, Woodford E, Dhudasia MB, Mattei LM, Daniel SG, Wade KC, Underwood MA, Bittinger K: Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly. Gut Microbes 14(1): 2154091, Dec 2022.

2021

Simon-Soro A, Kim D, Li Y, Liu Y, Ito T, Sims KR Jr, Benoit DSW, Bittinger K, Koo H: Impact of the repurposed drug thonzonium bromide on host oral-gut microbiomes. NPJ Biofilms Microbiomes 7: 7, Jan 2021 Notes: Co-senior author with Koo H.

Vajravelu ME, Lee JJ, Mitteer L, Zemel BS, Bittinger K, De León DD: Gut Microbiome Profile After Pancreatectomy in Infants With Congenital Hyperinsulinism. Pancreas 50: 89, Jan 2021.

Littmann ER, Lee JJ, Denny JE, Alam Z, Maslanka JR, Zarin I, Matsuda R, Carter RA, Susac B, Saffern MS, Fett B, Mattei LM, Bittinger K, Abt MC.: Host immunity modulates the efficacy of microbiota transplantation for treatment of Clostridioides difficile infection. Nat Commun 12: 755, Feb 2021.

Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD: Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe 29: 394, Mar 2021.

87. Weiss SL, Bittinger K, Lee JJ, Friedman ES, Mattei LM, Graham K, Zhang D, Bush J, Balamuth F, McGowan FX Jr, Bushman FD, Baldassano RN, Wu GD, Wallace DC, Collman RG.: Decreased Intestinal Microbiome Diversity in Pediatric Sepsis: A Conceptual Framework for Intestinal Dysbiosis to Influence Immunometabolic Function. Crit Care Explor 3: e0360, Mar 2021.

Feres M, Retamal-Valdes B, Fermaino D, Faveri, M, Figueiredo LC, Mayer MPA, Lee JJ, Bittinger K, Teles F: Microbiome changes in young periodontitis patients treated with adjunctive metronidazole and amoxicillin. Journal of Periodontology 92: 467, Apr 2021.

Firrman J, Liu L, Mahalak K, Tanes C, Bittinger K, Bobokalonov J, Mattei L, Zhang H, Van den Abbeele P.: Comparative analysis of the gut microbiota cultured in vitro using a single colon versus a 3-stage colon experimental design. Appl Microbiol Biotechnol 105: 3353, Apr 2021.

Roy Paladhi U, Harb AH, Daniel SG, Dawwas GK, Schnellinger EM, Wollack C, Aberra FN, Bewtra M, Green JA, Klaproth JA, Lichtenstein GR, Saxena A, Berera S, Buchner A, Mehta SJ, Osterman MT, Rashid F, Tomov V, Caldera F, Sumona S, Mahadevan U, Roy A, Nessel L, Wu GD, Bittinger K, Lewis JD.: The Impact of Introducing Patient-Reported Inflammatory Bowel Disease Symptoms via Electronic Survey on Clinic Visit Length, Patient and Provider Satisfaction, and the Environment Microbiome. Inflamm Bowel Dis 27: 746, Apr 2021 Notes: Co-senior author with Lewis JD.

Benitez A, Tanes C, Mattei LM, Hofstaedter CE, Kim DK, Gross J, Ruffner MA, Albenberg L, Spergel J, Bittinger K, Muir AB: Effect of topical swallowed steroids on the bacterial and fungal esophageal microbiota in eosinophilic esophagitis. Allergy 76: 1549, May 2021.

Lewis JD, Sandler R, Brotherton C, Brensinger C, Li H, Kappelman MD, Daniel SG, Bittinger K, Albenberg L, Valentine JF, Hanson J, Suskind D, Meyer A, Compher CW, Bewtra M, Saxena A, Dobes A, Cohen B, Flynn AD, Fischer M, Saha S, Swaminath A, Yacyshyn B, Scherl E, Horst S, Curtis JR, Braly K, Nessel L, McCauley M, McKeever L, Herfarth H; DINE-CD Study Group: A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults with Crohn's Disease. Gastroenterology 161: 837, May 2021.

Alemán JO, Henderson WA, Walker JM, Ronning A, Jones DR, Walter PJ, Daniel SG, Bittinger K, Vaughan R, MacArthur R, Chen K, Breslow JL, Holt PR: Excess dietary fructose does not alter gut microbiota or permeability in humans: A pilot randomized controlled study. J Clin Transl Sci 5: e143, Jun 2021.

Tang SY, Meng H, Anderson ST, Sarantopoulou D, Ghosh S, Lahens NF, Theken KN, Ricciotti E, Hennessy EJ, Tu V, Bittinger K, Weljie AM, Grant GR, FitzGerald GA: Sex-dependent compensatory mechanisms preserve blood pressure homeostasis in prostacyclin receptor deficient mice. J Clin Invest 131: e136310, Jul 2021.

Merenstein C, Liang G, Whiteside SA, Cobián-Güemes AG, Merlino MS, Taylor LJ, Glascock A, Bittinger K, Tanes C, Graham-Wooten J, Khatib LA, Fitzgerald AS, Reddy S, Baxter AE, Giles JR, Oldridge DA, Meyer NJ, Wherry EJ, McGinniss JE, Bushman FD, Collman RG: Signatures of COVID-19 Severity and Immune Response in the Respiratory Tract Microbiome. mBio 12: e0177721, Aug 2021.

Rangu S, Lee JJ, Hu W, Bittinger K, Castelo-Soccio L: Understanding the Gut Microbiota in Pediatric Patients with Alopecia Areata and their Siblings: A Pilot Study. JID Innov 1: 100051, Aug 2021.

Tanes C, Walker EM, Slisarenko N, Gerrets GL, Grasperge BF, Qin X, Jazwinski SM, Bushman FD, Bittinger K, Rout N: Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection. Viruses 13: 1567, Aug 2021.

Byeon J, Blizinsky KD, Persaud A, Findley K, Lee JJ, Buscetta AJ, You S, Bittinger K, Minniti CP, Bonham VL, Grice EA: Insights into the skin microbiome of sickle cell disease leg ulcers. Wound Repair Regen 29: 801, Sep 2021.

Rhee RL, Lu J, Bittinger K, Lee JJ, Mattei LM, Sreih AG, Chou S, Miner JJ, Cohen NA, Kelly BJ, Lee H, Grayson PC, Collman RG, Merkel PA: Dynamic Changes in the Nasal Microbiome Associated with Disease Activity in Patients with Granulomatosis with Polyangiitis. Arthritis Rheumatol 73: 1703, Sep 2021.

Payne E, Harrington K, Richard P, Brackin R, Davis R, Couture S, Liff J, Asmus F, Mutina E, Fisher A, Giuvelis D, Sannajust S, Rostama B, King T, Mattei LM, Lee JJ, Friedman ES, Bittinger K, May M, Stevenson GW: Effects of Vancomycin on Persistent Pain-Stimulated and Pain-Depressed Behaviors in Female Fischer Rats With or Without Voluntary Access to Running Wheels. J Pain 22: 1530, Nov 2021.

Shen TD, Daniel SG, Patel S, Kaplan E, Phung L, Lemelle-Thomas K, Chau L, Herman L, Trisolini C, Stonelake A, Toal E, Khungar V, Bittinger K, Reddy KR, Wu GD: The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis. Gut Microbes 13: 1987781, Nov 2021.

2020

Mahalak KK, Firrman J, Tomasula PM, Nuñez A, Lee JJ, Bittinger K, Rinaldi W, Liu LS: Impact of steviol glycosides and erythritol on the human and gut microbiome. Journal of Agricultural and Food Chemistry Jan 2020.

Sinha Sidhartha R, Haileselassie Yeneneh, Nguyen Linh P, Tropini Carolina, Wang Min, Becker Laren S, Sim Davis, Jarr Karolin, Spear Estelle T, Singh Gulshan, Namkoong Hong, Bittinger Kyle, Fischbach Michael A, Sonnenburg Justin L, Habtezion Aida: Dysbiosis-induced secondary bile acid deficiency promotes intestinal inflammation. Cell host & microbe 27(4): 659-670.e5, Feb 2020.

Giron Leila B, Tanes Ceylan E, Schleimann Mariane H, Engen Phillip A, Mattei Lisa M, Anzurez Alitzel, Damra Mohammad, Zhang Huanjia, Bittinger Kyle, Bushman Frederic, Kossenkov Andrew, Denton Paul W, Tateno Hiroaki, Keshavarzian Ali, Landay Alan L, Abdel-Mohsen Mohamed: Sialylation and fucosylation modulate inflammasome-activating eIF2 Signaling and microbial translocation during HIV infection. Mucosal immunology Mar 2020.

Shi Zhenda, Zhao Chunyu, Mattei Lisa M, Bittinger Kyle, Jiang Baoming, Gewirtz Andrew T: Genome sequence of a segmented filamentous bacterium strain that confers a rotavirus resistance phenotype in mice. Microbiology resource announcements 9(10), Mar 2020.

Bittinger Kyle, Zhao Chunyu, Li Yun, Ford Eileen, Friedman Elliot S, Ni Josephine, Kulkarni Chiraag V, Cai Jingwei, Tian Yuan, Liu Qing, Patterson Andrew D, Sarkar Debolina, Chan Siu H J, Maranas Costas, Saha-Shah Anumita, Lund Peder, Garcia Benjamin A, Mattei Lisa M, Gerber Jeffrey S, Elovitz Michal A, Kelly Andrea, DeRusso Patricia, Kim Dorothy, Hofstaedter Casey E, Goulian Mark, Li Hongzhe, Bushman Frederic D, Zemel Babette S, Wu Gary D: Bacterial colonization reprograms the neonatal gut metabolome. Nature microbiology 5: 838-847, Apr 2020.

Liang G, Zhao C, Zhang H, Mattei L, Sherrill-Mix S, Bittinger K, Kessler LR, Wu GD, Baldassano RN, DeRusso P, Ford E, Elovitz MA, Kelly MS, Patel MZ, Mazhani T, Gerber JS, Kelly A, Zemel BS, Bushman FD.: The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 581: 470-474, May 2020.

Polster S, Sharma A, Tanes C, Tang A, Mericko P, Cao Y, Carrión-Penagos J, Girard R, Koskimäki J, Zhang D, Stadnik A, Romanos S, Lyne S, Shenkar R, Yan K, Lee C, Akers A, Morrison L, Robinson M, Zafar A, Bittinger K, Kim H, Gilbert J, Kahn M, Shen L, Awad I: Permissive microbiome characterizes human subjects with a neurovascular disease cavernous angioma. Nature Communications 11(2659): 2659, May 2020.

Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA.: Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biol 21: 122, May 2020.

Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K, Tasian GE.: Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease. J Am Soc Nephrol 31: 1358-1369, Jun 2020.

Mahalak KK, Firrman J, Lee JJ, Bittinger K, Nuñez A, Mattei LM, Zhang H, Fett B, Bobokalonov J, Arango-Argoty G, Zhang L, Zhang G, Liu LS: Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro. PLOS One 15(6), Jun 2020.

Bushman FD, Conrad M, Ren Y, Zhao C, Gu C, Petucci C, Kim MS, Abbas A, Downes KJ, Devas N, Mattei LM, Breton J, Kelsen J, Marakos S, Galgano A, Kachelries K, Erlichman J, Hart JL, Moraskie M, Kim D, Zhang H, Hofstaedter CE, Wu GD, Lewis JD, Zackular JP, Li H, Bittinger K, Baldassano R.: Multi-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease. Cell Host Microbe 28: 422-433, Sep 2020.

Gu C, Bushman FD, Zhao C, Hofstaedter C, Tebas P, Glaser L, Baldassano RN, Bittinger K, Mattei LM: Investigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly. PLOS One 15: e0236533, Nov 2020 Notes: Accepted Oct 21, 2020.

Liang G, Conrad MA, Kelsen JR, Kessler LR, Breton J, Albenberg LG, Marakos S, Galgano A, Devas N, Erlichman J, Zhang H, Mattei L, Bittinger K, Baldassano RN, Bushman FD.: Dynamics of the Stool Virome in Very Early-Onset Inflammatory Bowel Disease. J Crohns Colitis 14: 1600-1610, Nov 2020.

2019

Weaver Lehn K, Minichino Danielle, Biswas Chhanda, Chu Niansheng, Lee Jung-Jin, Bittinger Kyle, Albeituni Sabrin, Nichols Kim E, Behrens Edward M: Microbiota-dependent signals are required to sustain TLR-mediated immune responses. JCI Insight 4(1), Jan 2019.

Firrman J, Liu L, Van den Abbeele, P, Tanes C, Bittinger K, Tomasula P : Applying advanced in vitro culturing technology to study the human gut microbiota  JoVE  144, Feb 2019.

Firrman Jenni, Liu LinShu, Van den Abbeele Pieter, Tanes Ceylan, Bittinger Kyle, Tomasula Peggy: Applying advanced in vitro culturing technology to study the human gut microbiota. Journal of visualized experiments : JoVE(144), Feb 2019.

Clarke Erik L, Taylor Louis J, Zhao Chunyu, Connell Andrew, Lee Jung-Jin, Fett Bryton, Bushman Frederic D, Bittinger Kyle: Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome 7(1): 46, Mar 2019.

Pearson-Leary Jiah, Zhao Chunyu, Bittinger Kyle, Eacret Darrell, Luz Sandra, Vigderman Abigail S, Dayanim Gabriel, Bhatnagar Seema: The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Molecular psychiatry 25(5): 1068-1079, Mar 2019.

Melo-Gonzalez Felipe, Kammoun Hana, Evren Elza, Dutton Emma E, Papadopoulou Markella, Bradford Barry M, Tanes Ceylan, Fardus-Reid Fahmina, Swann Jonathan R, Bittinger Kyle, Mabbott Neil A, Vallance Bruce A, Willinger Tim, Withers David R, Hepworth Matthew R: Antigen-presenting ILC3 regulate T cell-dependent IgA responses to colonic mucosal bacteria. The Journal of experimental medicine 216(4): 728-742, Apr 2019.

Firrman J, LinShu L, Tanes C, Bittinger K, Mahalak K, Rinaldi W. : Metagenomic assessment of the Cebus apella gut microbiota. American Journal of Primatology 81(10-11): e23023, May 2019.

Yardeni T, Tanes C, Bittinger K, Mattei LM, Schaefer P, Signh LN, Wu G, Murdock D, Wallace DC: Host mitochondria influence gut microbiome diversity: A role for ROS. Science Signaling 12(588): eaaw3159, July 2019.

Bolyen Evan, Rideout Jai Ram, Dillon Matthew R, Bokulich Nicholas A, Abnet Christian C, Al-Ghalith Gabriel A, Alexander Harriet, Alm Eric J, Arumugam Manimozhiyan, Asnicar Francesco, Bai Yang, Bisanz Jordan E, Bittinger Kyle, Brejnrod Asker, Brislawn Colin J, Brown C Titus, Callahan Benjamin J, Caraballo-Rodríguez Andrés Mauricio, Chase John, Cope Emily K, Da Silva Ricardo, Diener Christian, Dorrestein Pieter C, Douglas Gavin M, Durall Daniel M, Duvallet Claire, Edwardson Christian F, Ernst Madeleine, Estaki Mehrbod, Fouquier Jennifer, Gauglitz Julia M, Gibbons Sean M, Gibson Deanna L, Gonzalez Antonio, Gorlick Kestrel, Guo Jiarong, Hillmann Benjamin, Holmes Susan, Holste Hannes, Huttenhower Curtis, Huttley Gavin A, Janssen Stefan, Jarmusch Alan K, Jiang Lingjing, Kaehler Benjamin D, Kang Kyo Bin, Keefe Christopher R, Keim Paul, Kelley Scott T, Knights Dan, Koester Irina, Kosciolek Tomasz, Kreps Jorden, Langille Morgan G I, Lee Joslynn, Ley Ruth, Liu Yong-Xin, Loftfield Erikka, Lozupone Catherine, Maher Massoud, Marotz Clarisse, Martin Bryan D, McDonald Daniel, McIver Lauren J, Melnik Alexey V, Metcalf Jessica L, Morgan Sydney C, Morton Jamie T, Naimey Ahmad Turan, Navas-Molina Jose A, Nothias Louis Felix, Orchanian Stephanie B, Pearson Talima, Peoples Samuel L, Petras Daniel, Preuss Mary Lai, Pruesse Elmar, Rasmussen Lasse Buur, Rivers Adam, Robeson Michael S, Rosenthal Patrick, Segata Nicola, Shaffer Michael, Shiffer Arron, Sinha Rashmi, Song Se Jin, Spear John R, Swafford Austin D, Thompson Luke R, Torres Pedro J, Trinh Pauline, Tripathi Anupriya, Turnbaugh Peter J, Ul-Hasan Sabah, van der Hooft Justin J J, Vargas Fernando, Vázquez-Baeza Yoshiki, Vogtmann Emily, von Hippel Max, Walters William, Wan Yunhu, Wang Mingxun, Warren Jonathan, Weber Kyle C, Williamson Charles H D, Willis Amy D, Xu Zhenjiang Zech, Zaneveld Jesse R, Zhang Yilong, Zhu Qiyun, Knight Rob, Caporaso J Gregory: Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2. Nature biotechnology 37(9): 1091, Sep 2019.

Graf EH, Elkan M, Fink JS, Zhao C, Bittinger K, Hopkins S, Ulloa ER, Rajagopalan R, Mitchell S, Darcy C: Association of enterovirus D68 with acute flaccid myelitis, Philadelphia, Pennsylvania, USA, 2009-2018. Emerging Infectious Diseases 25(9), Sept 2019 Notes: Note, Accepted June 26, 2019.

Shi Z, Zou J, Zhang Z, Zhao X, Noriega J, Zhang B, Zhao C, Ingle H, Bittinger K, Mattei LM, Pruijssers AJ, Plemper RK, Nice TJ, Baldridge M, Dermody TS, Chassaing B, Gewirtz AT: Segmented filamentous bacteria prevent and cure rotavirus infection. Cell Oct 2019 Notes: (Epub ahead of print).

Firrman Jenni, Liu Linshu, Tanes Ceylan, Friedman Elliot, Bittinger Kyle, Daniel Scott, van den Abbeele Pieter, Evans Bradley S: Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform. Journal of Agricultural and Food Chemistry Nov 2019.

Simon-Soro Aurea, Sohn Michael B, McGinniss John E, Imai Ize, Brown Melanie C, Knecht Vincent R, Bailey Aubrey, Clarke Erik L, Cantu Edward, Li Hongzhe, Bittinger Kyle, Diamond Joshua M, Christie Jason D, Bushman Frederic D, Collman Ronald G: Upper respiratory dysbiosis with a facultative-dominated ecotype in advanced lung disease and dynamic change after lung transplant. Annals of the American Thoracic Society 16(11): 1383-1391, Nov 2019.

Tang Alan T, Sullivan Katie R, Hong Courtney C, Goddard Lauren M, Mahadevan Aparna, Ren Aileen, Pardo Heidy, Peiper Amy, Griffin Erin, Tanes Ceylan, Mattei Lisa M, Yang Jisheng, Li Li, Mericko-Ishizuka Patricia, Shen Le, Hobson Nicholas, Girard Romuald, Lightle Rhonda, Moore Thomas, Shenkar Robert, Polster Sean P, Roedel Claudia J, Li Ning, Zhu Qin, Whitehead Kevin J, Zheng Xiangjian, Akers Amy, Morrison Leslie, Kim Helen, Bittinger Kyle, Lengner Christopher J, Schwaninger Markus, Velcich Anna, Augenlicht Leonard, Abdelilah-Seyfried Salim, Min Wang, Marchuk Douglas A, Awad Issam A, Kahn Mark L: Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation. Science Translational Medicine 11(520), Nov 2019.

Uribe-Herranz Mireia, Rafail Stavros, Beghi Silvia, Gil-de-Gómez Luis, Verginadis Ioannis, Bittinger Kyle, Pustylnikov Sergey, Pierini Stefano, Perales-Linares Renzo, Blair Ian A, Mesaros Clementina A, Snyder Nathaniel W, Bushman Frederic, Koumenis Constantinos, Facciabene Andrea: Gut microbiota modulate dendritic cell antigen presentation and radiotherapy-induced antitumor immune response. The Journal of clinical investigation 130(1): 466-479, Dec 2019.

2018

Leiby JS, McCormick K, Sherrill-Mix S, Clarke EL, Kessler LR, Taylor LJ, Hofstaedter CE, Roche AM, Mattei L, Bittinger K, Elovitz MA, Leite R, Parry S, Bushman FD: Lack of detection of a human placenta microbiome in samples from preterm and term deliveries. Microbiome 6(1): 196, Oct 2018.

Friedman ES, Bittinger K, Esipova TV, Hou L, Chau L, Jiang J, Mesaros C, Lund PJ, Liang X, FitzGerald GA, Goulian M, Lee D, Garcia BA, Blair IA, Vinogradov SA, Wu GD: Microbes vs. chemistry in the origin of the anaerobic gut lumen. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 115(16): 4170-4175, Apr 2018.

Uribe-Herranz M, Bittinger K, Rafail, S, Guedan S, Pierini S, Tanes C, Ganetsky A, Morgan MA, Gill S, Tanyi JL, Bushman FD, June CH, Facciabene A: Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12 JCI Insight 3(4): e94952, Feb 2018.

Clarke EL, Lauder AP, Hofstaedter CE, Hwang Y, Fitzgerald AS, Imai I, Biernat W, Bartłomiej R, Majewska H, Dubaniewicz A, Litzky LA, Feldman D, Bittinger K, Rossman MD, Patterson Karen C, Bushman FD, Collman RG: Microbial Lineages in Sarcoidosis: A Metagenomic Analysis Tailored for Low-Microbial Content Samples. American journal of respiratory and critical care medicine 197(2): 225-234, Jan 2018.

2017

Kim D, Hofstaedter CE, Zhao C, Mattei L, Tanes C, Clarke E, Lauder A, Sherrill-Mix S, Chehoud C, Kelsen J, Conrad M, Collman RG, Baldassano RN, Bushman FD, Bittinger K: Optimizing methods and dodging pitfalls in microbiome research. Microbiome 5(1): 52, May 2017.

Ni J, Shen Ting-Chin D, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg LG, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD: A role for bacterial urease in gut dysbiosis and Crohn's disease. Science translational medicine 9(416): doi: 10.1126, Nov 2017.

Silverman M, Kua L, Tanca A, Pala M, Palomba A, Tanes C, Bittinger K, Uzzau S, Benoist C, Mathis D: Protective major histocompatibility complex allele prevents type 1 diabetes by shaping the intestinal microbiota early in ontogeny. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 114(36): 9671-9676, Sep 2017.]

Xiao E, Mattos M, Vieira GHA, Chen S, Correa JD, Wu Y, Albieiro ML, Bittinger K, Graves DT.: Diabetes Enhances IL-17 Expression and Alters the Oral Microbiome to Increase its Pathogenicity. Cell Host & Microbe 22(1): 120-128, Jul 2017.

Pannaraj, PS, Li F, Cerini C, Bender JM, Yang S, Rollie A, Adisetiyo H, Zabih S, Lincez PJ, Bittinger K, Bailey A, Bushman FD, Sleasman JW, Aldrovandi, GM: Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome. JAMA Pediatrics 171(7): 647-654, Jul 2017.

2016

Lauder Abigail P, Roche Aoife M, Sherrill-Mix Scott, Bailey Aubrey, Laughlin Alice L, Bittinger Kyle, Leite Rita, Elovitz Michal A, Parry Samuel, Bushman Frederic D: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota. Microbiome 4(1): 29, Jun 2016.

Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD.: Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium. PLOS One 11(5): e0155620, May 2016.

Kelly Brendan J, Imai Ize, Bittinger Kyle, Laughlin Alice, Fuchs Barry D, Bushman Frederic D, and Collman Ronald G: Composition and dynamics of the respiratory tract microbiome in intubated patients. Microbiome 4(1): 7, Feb 2016.

Indugu Nagaraju, Bittinger Kyle, Kumar Sanjay, Vecchiarelli Bonnie, Pitta Dipti: A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms. PeerJ 4: e1599, Feb 2016.

Wu Gary D, Compher Charlene, Chen Eric Z, Smith Sarah A, Shah Rachana D, Bittinger Kyle, Chehoud Christel, Albenberg Lindsey G, Nessel Lisa, Gilroy Erin, Star Julie, Weljie Aalim M, Flint Harry J, Metz David C, Bennett Michael J, Li Hongzhe, Bushman Frederic D, Lewis James D: Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut 65(1): 63-72, Jan 2016.

2015

Liang Xue, Bittinger Kyle, Li Xuanwen, Abernethy Darrell R, Bushman Frederic D, FitzGerald Garret A: Bidirectional interactions between indomethacin and the murine intestinal microbiota. eLife 4: e08973, Dec 2015.

Kelsen Judith*, Bittinger Kyle*, Pauly-Hubbard Helen, Posivak Leah, Grunberg Stephanie, Baldassano Robert, Lewis James D, Wu Gary D, Bushman Frederic D: Alterations of the subgingival microbiota in pediatric Crohn's disease studied longitudinally in discovery and validation cohorts. Inflammatory Bowel Diseases 21(12): 2797-805, Dec 2015 Notes: * joint first authors.

Lewis James D, Chen Eric Z, Baldassano Robert N, Otley Anthony R, Griffiths Anne M, Lee Dale, Bittinger Kyle, Bailey Aubrey, Friedman Elliot S, Hoffmann Christian, Albenberg Lindsey, Sinha Rohini, Compher Charlene, Gilroy Erin, Nessel Lisa, Grant Amy, Chehoud Christel, Li Hongzhe, Wu Gary D, Bushman Frederic D: Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn's disease. Cell Host & Microbe 18(4): 489-500, Oct 2015.

Kelly Brendan J, Gross Robert, Bittinger Kyle, Sherrill-Mix Scott, Lewis James D, Collman Ronald G, Bushman Frederic D, Li Hongzhe: Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA. Bioinformatics 31(15): 2461-8, Aug 2015.

Chehoud Christel, Albenberg Lindsey G, Judge Colleen, Hoffmann Christian, Grunberg Stephanie, Bittinger Kyle, Baldassano Robert N, Lewis James D, Bushman Frederic D, Wu Gary D: Fungal signature in the gut microbiota of pediatric patients with inflammatory bowel disease. Inflammatory Bowel Diseases 21(8): 1948-56, Aug 2015.

Shen Ting-Chin David, Albenberg Lindsey, Bittinger Kyle, Chehoud Christel, Chen Ying-Yu, Judge Colleen A, Chau Lillian, Ni Josephine, Sheng Michael, Lin Andrew, Wilkins Benjamin J, Buza Elizabeth L, Lewis James D, Daikhin Yevgeny, Nissim Ilana, Yudkoff Marc, Bushman Frederic D, Wu Gary D: EngineBittinger Kyle, Charlson Emily S, Loy Elizabeth, Shirley David J, Haas Andrew R, Laughlin Alice, Yi Yanjie, Wu Gary D, Lewis James D, Frank Ian, Cantu Edward, Diamond Joshua M, Christie Jason D, Collman Ronald G, Bushman Frederic D: Improved characterization of medically relevant fungi in the human respiratory tract using next-generation sequencing. Genome Biology 15(10): 487, Oct 2014.y Aubrey, Diamond Joshua M, Cantu Edward, Haas Andrew R, Abbas Arwa, Frye Laura, Christie Jason D, Bushman Frederic D, Collman Ronald G: Viral metagenomics reveal blooms of anelloviruses in the respiratory tract of lung transplant recipients. American Journal of Transplantation 15(1): 200-9, Jan 2015.

2014

Albenberg Lindsey, Esipova Tatiana V, Judge Colleen P, Bittinger Kyle, Chen Jun, Laughlin Alice, Grunberg Stephanie, Baldassano Robert N, Lewis James D, Li Hongzhe, Thom Stephen R, Bushman Frederic D, Vinogradov Sergei A, Wu Gary D: Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology 147(5): 1055-63.e8, Nov 2014.

Pitta Dipti W, Kumar Sanjay, Vecchiarelli Bonnie, Shirley David J, Bittinger Kyle, Baker Linda D, Ferguson James D, Thomsen Neal: Temporal dynamics in the ruminal microbiome of dairy cows during the transition period. Journal of Animal Science 92(9): 4014-22, Sep 2014.

Osborne Lisa C, Monticelli Laurel A, Nice Timothy J, Sutherland Tara E, Siracusa Mark C, Hepworth Matthew R, Tomov Vesselin T, Kobuley Dmytro, Tran Sara V, Bittinger Kyle, Bailey Aubrey G, Laughlin Alice L, Boucher Jean-Luc, Wherry E John, Bushman Frederic D, Allen Judith E, Virgin Herbert W, Artis David: Virus-helminth coinfection reveals a microbiota-independent mechanism of immunomodulation. Science 345(6196): 578-82, Aug 2014.

2023

Bittinger K, Hu W, Tanes C, Sistrunk JR, Friedman ES, Li H, Lewis JD, Bushman FD, Wu GD: Metabolomics distinguishes diet- and microbiome-derived metabolites during episodes of inflammatory bowel disease dysbiosis. Gastroenterology 164(6): S-204, May 2023.

Hecht A, Harling L, Lee J, Friedman ES, Tanes C, Bittinger K, Goulian M, Wu GD: Dietary carbohydrates regulate the colonization of Klebsiella pneumoniae and nitrogen composition in the gut. Gastrenterology 164(6): S-259, May 2023.

Katona BW, Tu V, Nyul T, Bittinger K, Ni J: Characterization of microbiome differences amongst patients with colonic polyposis with and without a known genetic driver. Gastroenterology 164(6): S-251, May 2023.

2022

Benitez A, Tanes C, Hu W, Friedman ES, Gerber J, Kelly A... Bittinger K, Zemel BS.: Impact of early life antibiotics on the gut microbiome, bile acids, and related gastrointestinal manifestations. Gastroenterology 167(2): S-1010, May 2022.

Kastl A, Zong W, Gershuni V, Friedman ES, Tanes C, Boateng A, O'Connor K, Bittinger K, Terry NA, Bales CB, Albenberg L, Wu GD.: Clinical phenotyping of patients with short bowel syndrome via effects of diet and the gut microbiota on bile acid metabolism.  Gastroenterology 162(7): S-653-S-654, May 2022.

Lemons JS, Conrad M, Tanes C, Friedman ES, Chau L, Ogawa SA, Curry D, Murphy D, Kachelries K, Bittinger K, Liu LS, Baldassano RN, Wu GD: Intestinal acylcarnitines as a biomarker of IBD and their role in bacterial metabolism. Gastroenterology 162(7): S-222, May 2022.

Paraskevopoulou M, Mayer LS, Krueger A, Pattekar A, Ramos A, ... Bittinger K, ... Tomov V,  Juarez J.: A single cell approach reveals immune cell dynamics in ulcerative colitis (UC) and highlights association of CD8 intraepithelial lymphocytes (IELS) with response to Vedolizumab treatment.  Gastroenterology 167(2): S-1093, May 2022.

Zong W, Allu SR, Friedman ES, Firrman J, Tu V, Bittinger K, Liu L, Vinogradov S, Wu GD.: Disruption of intestinal oxygen dynamics during acute colitis alters the gut microbiome. Gastroenterology 162(7): S-511, May 2022.

Bass R, Tanes C, Friedman E, Bittinger K, Wu G, Stallings V: Cystic fibrosis transmembrane conductance regulator potentiator (ivacaftor) has minimal effects on gut microbiome composition in people with cystic fibrosis and gating mutations. Journal of Cystic Fibrosis 21: S112, Oct 2022.

Hong G, Lipscombe C, Daniel S, O'Dea A, Bittinger K, Dorgan D, Hadjiliadis D.: CFTR modulation on the microbial environment in cystic fibrosis.  Blood 138: 3169, Nov 2022.

2021

Breton J, Baldassano RN, Albenberg L, Bittinger K, Conrad M, Compher CW, Tanes C, Tu V, Kachelries K: Dietary inflammatory potential and food patterns in relation to gut microbiome among children with Crohn's disease: a comparative study with healthy controls. DDW 2021, Virtual Conference May 2021 Notes: Abstract. May 21-23, 2021.

Wu GD, Li Y, Li H, Friedman ES, Carr RM, Bittinger K, Chau L, Murphy D, Lee JJ, Adronini L, Erickson M. : Fecal metabolomic signatures of bile and amino acids distinguish patients with NASH in the Regenerate study compared to healthy control population.  Hepatology 74: 956A-956A, Oct 2021.

2023

Bittinger K. "Metabolomics distinguishes diet- and microbiome-derived metabolites during episodes of inflammatory bowel disease dysbiosis." Digestive Disease Week (DDW). May 2023.

2021

Bittinger K. "New approaches to microbiome data analysis." Digestive Diseases Research Center, Vanderbilt University (virtual). Nov 2021.

Bittinger K. "Influencers of the neonatal microbiome." Pediatric Academic Societies (PAS) 2021 Conference (virtual). Apr 2021.