Josephine Ni, M.D., is an Assistant Professor in the Departments of Internal Medicine and Microbiology at UT Southwestern Medical Center. She is a member of the Division of Digestive and Liver Diseases and focuses on the treatment of inflammatory bowel diseases.

She graduated from the University of California, Berkeley in 2005, then earned her medical degree at Northwestern University. She completed a residency in internal medicine at New York University where she served as a chief resident. She received advanced training in gastroenterology through a T-32 funded fellowship at the University of Pennsylvania, where she continued as faculty until 2021.

Board certified in internal medicine and gastroenterology, she joined the UT Southwestern faculty in 2021.

Dr. Ni is a physician-scientist. Her research explores bacterial colonization of the healthy and inflamed intestinal tract with the goal of modulating the gut microbiota to treat intestinal diseases. She is a recipient of the American Gastroenterological Association-Takeda Research Scholar Award in Inflammatory Bowel Disease, and her current research is funded by the NIH as well as a Career Award for Medical Scientists from the Burroughs Wellcome Fund. She is the author of multiple publications and has been invited to speak both nationally and internationally on her research.

Dr. Ni is a member of the American Gastroenterological Association and the Crohn’s and Colitis Foundation.


Medical School
Northwestern University Feinberg School of Medicine (2009)
New York University School of Medicine (2013), Internal Medicine
University of Pennsylvania Perelman School of Medicine (2016), Gastroenterology

Research Interest

  • E. coli
  • Inflammatory bowel disease
  • Microbiome


Featured Publications LegendFeatured Publications

Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome.
Chassaing B, Compher C, Bonhomme B, Liu Q, Tian Y, Walters W, Nessel L, Delaroque C, Hao F, Gershuni V, Chau L, Ni J, Bewtra M, Albenberg L, Bretin A, McKeever L, Ley RE, Patterson AD, Wu GD, Gewirtz AT, Lewis JD, Gastroenterology 2021 Nov
Risk for Post-Colonoscopy Irritable Bowel Syndrome in Patients With and Without Antibiotic Exposure: A Retrospective Cohort Study.
Vajravelu RK, Shapiro JM, Ni J, Thanawala SU, Lewis JD, El-Serag HB, Clin Gastroenterol Hepatol 2021 Sep
Bacterial colonization reprograms the neonatal gut metabolome.
Bittinger K, Zhao C, Li Y, Ford E, Friedman ES, Ni J, Kulkarni CV, Cai J, Tian Y, Liu Q, Patterson AD, Sarkar D, Chan SHJ, Maranas C, Saha-Shah A, Lund P, Garcia BA, Mattei LM, Gerber JS, Elovitz MA, Kelly A, DeRusso P, Kim D, Hofstaedter CE, Goulian M, Li H, Bushman FD, Zemel BS, Wu GD, Nat Microbiol 2020 06 5 6 838-847
A role for bacterial urease in gut dysbiosis and Crohn's disease.
Ni J, Shen TD, 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 L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD Sci Transl Med 2017 Nov 9 416
Gut microbiota and IBD: causation or correlation?
Ni J, Wu GD, Albenberg L, Tomov VT, Nat Rev Gastroenterol Hepatol 2017 Oct 14 10 573-584
Improved Long-term Outcomes of Patients With Inflammatory Bowel Disease Receiving Proactive Compared With Reactive Monitoring of Serum Concentrations of Infliximab.
Papamichael K, Chachu KA, Vajravelu RK, Vaughn BP, Ni J, Osterman MT, Cheifetz AS, Clin Gastroenterol Hepatol 2017 Oct 15 10 1580-1588.e3
Dietary Regulation of the Gut Microbiota Engineered by a Minimal Defined Bacterial Consortium.
Shen TC, Chehoud C, Ni J, Hsu E, Chen YY, Bailey A, Laughlin A, Bittinger K, Bushman FD, Wu GD, PLoS One 2016 11 5 e0155620
Engineering the gut microbiota to treat hyperammonemia.
Shen TC, Albenberg L, Bittinger K, Chehoud C, Chen YY, Judge CA, Chau L, Ni J, Sheng M, Lin A, Wilkins BJ, Buza EL, Lewis JD, Daikhin Y, Nissim I, Yudkoff M, Bushman FD, Wu GD, J Clin Invest 2015 Jul 125 7 2841-50
Intubation difficulties in a patient with an esophageal foreign body.
Goudra BG, Kronish K, Wong S, Ni J, J Clin Anesth 2014 Mar 26 2 160-1

Honors & Awards

  • Burroughs Wellcome Fund Career Awards for Medical Scientists

Professional Associations/Affiliations

  • American Gastroenterological Association
  • CrohnÂ’s and Colitis Foundation