Education and Training

Undergraduate Degree

BS in Chemistry - University of Pittsburgh, Pittsburgh, PA

Graduate Degree

PhD in Physical Chemistry - Massachusetts Institute of Technology, Cambridge, MA

Titles and Academic Titles

Analytics Core Director, Microbiome Center

Assistant Professor of Pediatrics, Perelman School of Medicine at the University of Pennsylvania

Departments and Services




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.

Bolyen E, Rideout JR, Dillion M, Bokulich N…Bittinger K, et al.: Reproducible, interactive, scalable, and extensible microbiome data science using QIIME 2. Nature Biotechnology 37(9), Sept 2019.

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

Clarke EL, Taylor LJ, Zhao Chunyu, Connell A, Lee JJ, Fett B, Bushman FD, Bittinger K: Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments. Microbiome 7(1): 46, Mar 2019.

Bhatnagar S, Pearson-Leary J ,Zhao C, Bittinger K, Eacret D, Luz S, Vigderman A, Dayanim, G: The gut microbiome regulates the increases in depressive-type behaviors and in inflammatory processes in the ventral hippocampus of stress vulnerable rats. Molecular Psychiatry Mar 2019.


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.


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.


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.


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.


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.




Conrad MA, Dawany N, Bittinger K, Baldassano RN, Piccoli D, Bushman FD, Devoto M, Kelsen JR: Characterization of the Intestinal Microbiome in Very Early Onset Inflammatory Bowel Disease. Digestive Disease Week Annual Meeting, San Diego, CA May 2016.


Shen Ting-Chin D, Albenberg L, Bittinger K, Chehoud C, Chen Y-Y, Judge C, Chau L, Sheng M, Lin A, Wilkins BJ, Lewis J, Daikhin YI, Nissim I, Yudkoff M, Bushman FD, Wu GD: Engineering the Gut Microbiota to Treat Hyperammonemia. Digestive Disease Week 2015, Poster presentation Apr 2015 Notes: Abstract 346.

Awards and Honors

2001-2002, DuPont Graduate Fellow, MIT

2001, Mary Louise Theodore Award, University of Pittsburgh

2000, Carrie T. Holland Scholarship, University of Pittsburgh