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Nikhil Pai, BSc, MD, CNSC, FRCPC, FAAP
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Associate Professor of Pediatrics (Gastroenterology, Hepatology and Nutrition) at the Children's Hospital of Philadelphia
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Attending Physician, Division of GI, Hepatology, and Nutrition, Children's Hospital of Philadelphia
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Member, Metabolism, Nutrition and Physical Development Research Affinity Group, Children's Hospital of Philadelphia
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Member, Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine
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Member, Research Institute, Children's Hospital of Philadelphia
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Core Faculty, Clinical Futures, Children's Hospital of Philadelphia
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Director, Pediatric Fecal Microbiota Transplant Stool Bank, Children's Hospital of Philadelphia
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Founding Director, Clinical Trials Division, Center for Microbial Medicine, Children's Hospital of Philadelphia
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Department: Pediatrics
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Contact information
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Children's Hospital of Philadelphia
3e Division of Gastroenterology, Hepatology and Nutrition
2d Roberts Center for Pediatric Research
40 2716 South Street, Room 14321
Philadelphia, PA 19146
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3e Division of Gastroenterology, Hepatology and Nutrition
2d Roberts Center for Pediatric Research
40 2716 South Street, Room 14321
Philadelphia, PA 19146
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Office: 215-590-2997
32 Fax: 215-590-2799
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32 Fax: 215-590-2799
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Publications
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Education:
21 8 BSc 14 (Biology) c
36 University of Western Ontario, 2004.
21 7 MD 15 (Medicine) c
3f McMaster University School of Medicine, 2007.
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Permanent link21 8 BSc 14 (Biology) c
36 University of Western Ontario, 2004.
21 7 MD 15 (Medicine) c
3f McMaster University School of Medicine, 2007.
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233 My clinical expertise spans pediatric intestinal failure/short bowel syndrome (SBS), complex pediatric nutritional disorders, inflammatory bowel disease (IBD), and metabolic dysfunction-associated steatotic liver disease (MASLD). I have experience in both diagnostic and therapeutic pediatric endoscopy and have received formal training in the use of FibroScan® for non-invasive liver stiffness assessment. I provide comprehensive enteral and parenteral nutrition support, including advanced nutrition care in hospitalized and medically complex children.
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11a I completed my pediatric gastroenterology fellowship through the physician-scientist track at Boston Children’s Hospital and additional training in pediatric obesity medicine through the Obesity, Metabolism and Nutrition Institute (OMNI) at Massachusetts General Hospital.
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2b5 During my 9.5 years as an attending pediatric gastroenterologist at McMaster Children’s Hospital in Hamilton, Ontario, I provided broad-based pediatric GI care across the spectrum of pediatric gastrointestinal diseases. I served as the medical lead of the hospital’s Intestinal Rehabilitation Program (IRP) and helped develop the institution’s pediatric nutrition service through combined administrative leadership and clinical service delivery, including founding the hospital's first multi-disciplinary Pediatric Nutrition Advisory Committee (PNAC). My clinical interests include pediatric nutrition, intestinal failure, general pediatric gastroenterology and obesity medicine.
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279 At the Children's Hospital of Philadelphia (CHOP), I currently practice in both inpatient and outpatient settings within the Division of Gastroenterology, Hepatology & Nutrition. My clinical responsibilities include covering the general pediatric GI ambulatory and inpatient services, endoscopy, nutrition support, MASLD, and IRP coverage. I also lead the development of CHOP’s pediatric donor stool bank—the first of its kind in the United States—supporting clinical and investigational use of fecal microbiota transplant (FMT) for clinical (recurrent Clostridioides difficile colitis) and research-based applications.
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fc I am committed to delivering multidisciplinary, evidence-based care to children with complex gastrointestinal and nutritional conditions, integrating clinical excellence with a strong foundation in translational research and clinical innovation.
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299 I lead a translational research program focused on microbiome-host interactions, metabolic dysfunction-associated steatotic liver disease (MASLD), and novel microbiome-based therapeutics for chronic gastrointestinal disorders in children. My work combines clinical trials and multi-omics diagnostics - including urine metabolomics, radiologic imaging, and serum proteomics - to help discover novel biomarkers and therapeutic targets across a range of chronic gastrointestinal and nutritional disorders. These include: MASLD, inflammatory bowel diseases (IBD), anorexia nervosa, and small intestinal bacterial overgrowth (SIBO) in short bowel syndrome (SBS).
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522 I developed the first pediatric donor fecal microbiota transplant (FMT) stool bank in Canada, and am now leading the development of CHOP’s pediatric FMT stool bank—the first of its kind in the United States. My research has included the first pilot multicenter randomized controlled trial (RCT) of the study of FMT in pediatric ulcerative colitis (UC), and my group has completed one of the first RCTs of FMT in pediatric Crohn's disease (CD). My work has received support through multiple regional and national funding agencies, with over $23 million in grant support as principal investigator, or co-investigator to date. I have also received multiple awards recognizing my contributions to pediatric nutrition and microbiome research, including the American Society for Parenteral and Enteral Nutrition (ASPEN) Stanley J. Dudrick Mid-Career Research Scholar Award and Canadian Nutrition Society (CNS) Young Investigator Award. I hold academic, research, and leadership distinctions from the Canadian Institutes of Health Research (CIHR), the American Gastroenterological Association (AGA), and North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN), and serve as an Associate Editor for the Journal of Pediatric Gastroenterology, Hepatology and Nutrition (JPGN).
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159 Through cross-disciplinary collaborations across diverse specialties, and centers in Canada and the United States, my work will continue to focus on advancing microbiome-based therapeutics, precision nutrition strategies, and biomarker discovery to identify novel approaches to managing chronic gastrointestinal and nutritional disorders.
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Description of Clinical Expertise
1c2 I am a double board-certified pediatric gastroenterologist, certified in both general pediatrics and pediatric gastroenterology by the Royal College of Physicians and Surgeons of Canada (RCPSC) and the American Board of Pediatrics (ABP). I have also received my certification as a Nutrition Support Clinician (CNSC), and am a Fellow of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN-F).8
233 My clinical expertise spans pediatric intestinal failure/short bowel syndrome (SBS), complex pediatric nutritional disorders, inflammatory bowel disease (IBD), and metabolic dysfunction-associated steatotic liver disease (MASLD). I have experience in both diagnostic and therapeutic pediatric endoscopy and have received formal training in the use of FibroScan® for non-invasive liver stiffness assessment. I provide comprehensive enteral and parenteral nutrition support, including advanced nutrition care in hospitalized and medically complex children.
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11a I completed my pediatric gastroenterology fellowship through the physician-scientist track at Boston Children’s Hospital and additional training in pediatric obesity medicine through the Obesity, Metabolism and Nutrition Institute (OMNI) at Massachusetts General Hospital.
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2b5 During my 9.5 years as an attending pediatric gastroenterologist at McMaster Children’s Hospital in Hamilton, Ontario, I provided broad-based pediatric GI care across the spectrum of pediatric gastrointestinal diseases. I served as the medical lead of the hospital’s Intestinal Rehabilitation Program (IRP) and helped develop the institution’s pediatric nutrition service through combined administrative leadership and clinical service delivery, including founding the hospital's first multi-disciplinary Pediatric Nutrition Advisory Committee (PNAC). My clinical interests include pediatric nutrition, intestinal failure, general pediatric gastroenterology and obesity medicine.
8
279 At the Children's Hospital of Philadelphia (CHOP), I currently practice in both inpatient and outpatient settings within the Division of Gastroenterology, Hepatology & Nutrition. My clinical responsibilities include covering the general pediatric GI ambulatory and inpatient services, endoscopy, nutrition support, MASLD, and IRP coverage. I also lead the development of CHOP’s pediatric donor stool bank—the first of its kind in the United States—supporting clinical and investigational use of fecal microbiota transplant (FMT) for clinical (recurrent Clostridioides difficile colitis) and research-based applications.
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fc I am committed to delivering multidisciplinary, evidence-based care to children with complex gastrointestinal and nutritional conditions, integrating clinical excellence with a strong foundation in translational research and clinical innovation.
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Description of Other Expertise
161 I am a jazz saxophone player with over 25 years of experience. I have performed professionally with a jazz quartet, performed with small groups and big bands in Hamilton, Toronto and Boston, and have been a member of the Penn Jazz Ensembles. My primary style is jazz, with additional performance experience in bossa nova, funk, and rock.65
Description of Research Expertise
2fe I am an attending pediatric gastroenterologist in the Division of Gastroenterology, Hepatology & Nutrition at the Children's Hospital of Philadelphia (CHOP), clinician-scientist and supervisor of the Pai Lab, Director of the Clinical Trials Division for the CHOP Center for Microbial Medicine, and Associate Professor of Pediatrics at the University of Pennsylvania Perelman School of Medicine. I am affiliated with the CHOP Center for Microbial Medicine, the University of Pennsylvania Institute for Translational Medicine and Therapeutics, and the CHOP Research Institute. I am also an Associate Clinical Professor at McMaster University in the Faculty of Health Sciences, and Staff Gastroenterologist (Part-Time) at McMaster Children's Hospital.8
299 I lead a translational research program focused on microbiome-host interactions, metabolic dysfunction-associated steatotic liver disease (MASLD), and novel microbiome-based therapeutics for chronic gastrointestinal disorders in children. My work combines clinical trials and multi-omics diagnostics - including urine metabolomics, radiologic imaging, and serum proteomics - to help discover novel biomarkers and therapeutic targets across a range of chronic gastrointestinal and nutritional disorders. These include: MASLD, inflammatory bowel diseases (IBD), anorexia nervosa, and small intestinal bacterial overgrowth (SIBO) in short bowel syndrome (SBS).
8
522 I developed the first pediatric donor fecal microbiota transplant (FMT) stool bank in Canada, and am now leading the development of CHOP’s pediatric FMT stool bank—the first of its kind in the United States. My research has included the first pilot multicenter randomized controlled trial (RCT) of the study of FMT in pediatric ulcerative colitis (UC), and my group has completed one of the first RCTs of FMT in pediatric Crohn's disease (CD). My work has received support through multiple regional and national funding agencies, with over $23 million in grant support as principal investigator, or co-investigator to date. I have also received multiple awards recognizing my contributions to pediatric nutrition and microbiome research, including the American Society for Parenteral and Enteral Nutrition (ASPEN) Stanley J. Dudrick Mid-Career Research Scholar Award and Canadian Nutrition Society (CNS) Young Investigator Award. I hold academic, research, and leadership distinctions from the Canadian Institutes of Health Research (CIHR), the American Gastroenterological Association (AGA), and North American Society for Pediatric Gastroenterology, Hepatology and Nutrition (NASPGHAN), and serve as an Associate Editor for the Journal of Pediatric Gastroenterology, Hepatology and Nutrition (JPGN).
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159 Through cross-disciplinary collaborations across diverse specialties, and centers in Canada and the United States, my work will continue to focus on advancing microbiome-based therapeutics, precision nutrition strategies, and biomarker discovery to identify novel approaches to managing chronic gastrointestinal and nutritional disorders.
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124 Popov J, Hartung E, Hill L, Chauhan U, Pai N.: Pediatric patient and parent perceptions of fecal microbiota transplantation for the treatment of ulcerative colitis. J Pediatr Gastroenterol Nutr 73(6): 684-688, Dec 2021.
11f Yamamoto M, Shanmuganathan M, Hart L, Pai N, Britz-McKibbin P: Urinary metabolites enable differential diagnosis and therapeutic monitoring of pediatric inflammatory bowel disease. Metabolites 11(4): 245, Apr 2021.
188 Lemay JA, Yamamoto M, Kroezen Z, Shanmuganathan M, Ly R, Hart L, Pai N, Britz-McKibbin P.: Lyophilized fecal short-chain fatty acid and electrolyte determination by capillary electrophoresis with indirect UV detection for assessment of pediatric inflammatory bowel disease. J Pharm Biomed Anal 192(1): 113658, Jan 2021.
121 Popov J, Caputi V, Nandeesha N, Rodriguez DA, Pai N.: Microbiota-immune interactions in ulcerative colitis and colitis associated cancer and emerging microbiota-based therapies. Int J Mol Sci 22(21): 11365, Oct 2021.
15f Pai N, Popov J, Hill L, Hartung E.: Protocol for a double-blind, randomised, placebo-controlled pilot study for assessing the feasibility and efficacy of faecal microbiota transplant in a paediatric Crohn's disease population: PediCRaFT Trial. BMJ Open 9(11): e030120, Nov 2019.
1cb Quirt J, Belza C, Pai N, Clause RF, Markovic F, Wong-Sterling S, Avitzur Y, Wales PW.: Reduction of central line-associated bloodstream infections and line occlusions in pediatric intestinal failure patients receiving long-term parenteral nutrition using an alternative locking solution, 4% Tetrasodium ethylenediamine-tetraacetic acid. J Parenter Enteral Nutr 45(6): 1286-92, Aug 2021.
de Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM.: Role of the microbiome in energy regulation and metabolism. Gastroenterology 146(6): 1525-33, May 2014.
ed Wang AY, Popov J, Pai N.: Fecal microbial transplant for the treatment of pediatric inflammatory bowel disease. World J Gastroenterol 22(47): 10304-10315, Dec 2016.
ec Pai N, Margolis KG: The microbiome in early biomarker discovery for neurodevelopmental disorders: A novel research roadmap? Gastroenterology 4(4): 813-4, Aug 2024.
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Selected Publications
19d Pai N, Popov J, Hill L, Hartung E, Grzywacz K, Moayyedi P; McMaster Pediatric Fecal Microbiota Transplant Research Collaboration.: Results of the first pilot randomized controlled trial of fecal microbiota transplant in pediatric ulcerative colitis: Lessons, limitations, and future prospects. Gastroenterology 161(2): 388-393.e3, Aug 2021.124 Popov J, Hartung E, Hill L, Chauhan U, Pai N.: Pediatric patient and parent perceptions of fecal microbiota transplantation for the treatment of ulcerative colitis. J Pediatr Gastroenterol Nutr 73(6): 684-688, Dec 2021.
11f Yamamoto M, Shanmuganathan M, Hart L, Pai N, Britz-McKibbin P: Urinary metabolites enable differential diagnosis and therapeutic monitoring of pediatric inflammatory bowel disease. Metabolites 11(4): 245, Apr 2021.
188 Lemay JA, Yamamoto M, Kroezen Z, Shanmuganathan M, Ly R, Hart L, Pai N, Britz-McKibbin P.: Lyophilized fecal short-chain fatty acid and electrolyte determination by capillary electrophoresis with indirect UV detection for assessment of pediatric inflammatory bowel disease. J Pharm Biomed Anal 192(1): 113658, Jan 2021.
121 Popov J, Caputi V, Nandeesha N, Rodriguez DA, Pai N.: Microbiota-immune interactions in ulcerative colitis and colitis associated cancer and emerging microbiota-based therapies. Int J Mol Sci 22(21): 11365, Oct 2021.
15f Pai N, Popov J, Hill L, Hartung E.: Protocol for a double-blind, randomised, placebo-controlled pilot study for assessing the feasibility and efficacy of faecal microbiota transplant in a paediatric Crohn's disease population: PediCRaFT Trial. BMJ Open 9(11): e030120, Nov 2019.
1cb Quirt J, Belza C, Pai N, Clause RF, Markovic F, Wong-Sterling S, Avitzur Y, Wales PW.: Reduction of central line-associated bloodstream infections and line occlusions in pediatric intestinal failure patients receiving long-term parenteral nutrition using an alternative locking solution, 4% Tetrasodium ethylenediamine-tetraacetic acid. J Parenter Enteral Nutr 45(6): 1286-92, Aug 2021.
de Nieuwdorp M, Gilijamse PW, Pai N, Kaplan LM.: Role of the microbiome in energy regulation and metabolism. Gastroenterology 146(6): 1525-33, May 2014.
ed Wang AY, Popov J, Pai N.: Fecal microbial transplant for the treatment of pediatric inflammatory bowel disease. World J Gastroenterol 22(47): 10304-10315, Dec 2016.
ec Pai N, Margolis KG: The microbiome in early biomarker discovery for neurodevelopmental disorders: A novel research roadmap? Gastroenterology 4(4): 813-4, Aug 2024.
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