Kyle Bittinger, PhD

Kyle Bittinger, PhD

Kyle Bittinger, PhD, is the Analytics Core Director of the Microbiome Center at the Children's Hospital of Philadelphia.

Locations: Main Campus
Appointments and Referrals: 1-800-TRY-CHOP (1-800-879-2467)

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

Publications

Papers

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.

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.

 

Abstracts

2016

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.

2015

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.

Posters and Presentations

Poster Presentations

2015

Pannaraj PS, Li F, Cerini C, Bender J, Bittinger K, Bailey A, Rollie A, Adisetiyo H, Santiskulvong C, Bushman FD, Sleasman J, Aldrovandi GM: Breastfeeding influences establishment and development of the infant microbiome. Infectious Diseases Society of America, Poster presentation Oct 2015 Notes: Session 129, poster 753.

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.

Chehoud C, Albenberg LG, Judge C, Hoffmann C, Grunberg S, Bittinger K, Baldassano RN, Lewis JD, Bushman FD, Wu GD: A Fungal Signature in the Gut Microbiota of Pediatric Patients with Inflammatory Bowel Disease. 5th International Human Microbiome Congress, Poster Presentation Mar 2015 Notes: Session Comp-017, poster 148.

2014

Albenberg L, Esipova TV, Judge C, Bittinger K, Chen J, Grunberg S, Baldassano R, Lewis JD, Li H, Bushman FD, Vinogradov S, Wu GD: Radial Partitioning of the Gut Microbiota Associated With Tolerance to Oxygen and Asaccharolytic Metabolism. Digestive Disease Week 2014, Poster presentation May 2014 Notes: Abstract Sa1983.

Albenberg L, Chehoud C, Judge C, Grunberg Se, Bittinger K, Baldassano R, Lewis JD, Bushman FD, Wu GD: ITS Gene Sequencing Reveals a Unique Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease. Digestive Disease Week 2014, Poster presentation May 2014 Notes: Abstract Sa1163.

Lectures by Invitation

2015

Bittinger K. Training in Bioinformatics Applied to the Biodiversity of Agro-Ecosystems [presentation]. Institut de Recherche et de Dévelopment en Agroenvironment; 2015 Sep; Quebec City, Canada.

2014

Bittinger K. Analyses of microbial community composition and metagenomics using QIIME [presentation]. American Society for Microbiology 114th General Meeting; 2014 May; Boston, MA.

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