About

Nikhil Pai is an Associate Professor of Pediatrics at the Children's Hospital of Philadelphia and a faculty member at the University of Pennsylvania Perelman School of Medicine. His clinical expertise spans pediatric intestinal failure, complex nutritional disorders, inflammatory bowel disease, and metabolic liver diseases, with formal training in pediatric gastroenterology and obesity medicine. He is a double board-certified pediatric gastroenterologist, certified in both general pediatrics and pediatric gastroenterology by the Royal College of Physicians and Surgeons of Canada and the American Board of Pediatrics, respectively. Pai has extensive experience in diagnostic and therapeutic pediatric endoscopy and non-invasive liver assessment using FibroScan®. His clinical work includes providing comprehensive nutrition support and leading programs such as the Pediatric Fecal Microbiota Transplant Stool Bank at CHOP, the first of its kind in the United States. His research focuses on microbiome-host interactions, metabolic liver diseases, and microbiome-based therapeutics for chronic gastrointestinal disorders in children. He leads translational research combining clinical trials and multi-omics diagnostics to discover novel biomarkers and therapeutic targets, with significant contributions to fecal microbiota transplantation research, including the development of pediatric stool banks and conducting multicenter randomized controlled trials. Pai's work has been supported by over $23 million in grants and has earned multiple awards, including the ASPEN Stanley J. Dudrick Mid-Career Research Scholar Award and the CNS Young Investigator Award.

Research topics

• Bioinformatics
• Oncology
• Internal medicine
• Medicine

Selected publications

• Poster Session I - A133 REAL WORLD EFFICACY OF GLP-2 AGONISTS IN PEDIATRIC INTESTINAL FAILURE: CANADIAN NATIONAL MULTICENTRE CASE SERIES

  Journal of the Canadian Association of Gastroenterology · 2026-02-01

  articleOpen access

  Abstract Background Glucagon-like peptide-2 (GLP-2) analogues, particularly teduglutide, have shown promise in enhancing intestinal adaptation and reducing parenteral nutrition (PN) dependence among pediatric patients with short bowel syndrome (SBS). Despite growing clinical use, real-world evidence in children remains limited. Aims To evaluate clinical outcomes and institutional experiences with teduglutide therapy in pediatric SBS across multiple Canadian centers. Methods A cross-sectional, questionnaire-based study was conducted among pediatric gastroenterology and intestinal rehabilitation programs across Canada between January and September 2025. The survey collected data on patient demographics, indications for teduglutide initiation, duration of therapy, PN requirements before and after treatment, markers of intestinal adaptation, and adverse events. Results Data was obtained from five Canadian centers, representing 15 pediatric SBS patients treated with teduglutide. The median age at initiation was 61 months, and the median duration of therapy was 21 months. PN outcomes: 33% achieved complete PN independence, while 53% demonstrated a marked reduction (>/=20% decrease) in PN volume. 7% had minimal response (8.5% reduction) and 7% had no response. Intestinal adaptation: 67% showed improved enteral tolerance and stool consistency. Safety: Reported adverse events included catheter-related infections (20%) and injection-site reactions (7%). No gastrointestinal symptoms, neoplasia, or intestinal obstruction were observed. Of the 27% with an intact ileocecal valve, 50% achieved complete PN independence. Ethnicity was not included as a factor in the analysis, as the study population was largely homogeneous (∼ 75% of participants from the same racial background), limiting meaningful comparison across groups. Conclusions Teduglutide appears to be a valuable adjunct in the management of pediatric SBS within the Canadian context, contributing to reduced PN dependence and improved intestinal adaptation. The therapy was generally well tolerated, with few complications reported. These findings support broader access to teduglutide and highlight the need for standardized protocols and continued multicenter collaboration to optimize outcomes in this population. Funding Agencies C-CIRN

  PublisherDOI

• Smart Factory Evolution: Emerging IoT Manufacturing Trends with CPS and Robotic Automation

  International Journal of Scientific Research in Computer Science Engineering and Information Technology · 2026-03-25

  articleOpen access1st authorCorresponding

  Smart manufacturing is the product of rapid convergence in several fields, including Cyber-Physical Systems (CPS), robotics, Digital Twin (DT) technology, and the quickly developing Internet of Things (IoT). Various CPS architectures are discussed in the study, including the 5C model and layered systems of intelligent manufacturing systems. The paper also covers their roles in real-time data acquisition, analytics, cognition, and self-configuration. The paper also delves into the CPS integration with IoT, which focuses on coordinated control, interoperability and scalable connectivity. Real-time aligning of physical and virtual resources enhanced the management of the lifecycle, predictive maintenance and optimization of processes because of the introduction of Digital twins. Additionally, as robotics and collaboration between humans and robots evolve further, autonomous, flexible, and secure industrial environment based on the principles of the Industry 4.0 can be achieved. The new trends in the IoT, which include edge computing, the integration of AI and machine learning, 5G connectivity, blockchain, sustainable, and remote monitoring, are transforming the industrial automation. The combination of these technologies forms intelligent and adaptive and data-driven manufacturing ecosystems that make processes more productive and resilient, efficient in operations, and globally competitive.

  PublisherOA PDFDOI

• Protocol for a pilot feasibility randomised controlled trial of fecal microbiota transplantation for adolescent anorexia nervosa

  BMJ Open · 2026-04-01

  articleOpen accessSenior author

  INTRODUCTION: Despite its serious impact, anorexia nervosa (AN) remains one of the least understood mental illnesses, with significant gaps in effective treatment options. No medications have been deemed effective and only 50% of individuals respond to conventional psychotherapies. Gastrointestinal (GI) bacteria have been found to be altered in individuals with AN. While, Fecal microbiota transplantation (FMT) has shown potential for alleviating anxiety and depression, its effects remain understudied for individuals with AN. This study aims to determine whether oral capsular FMT is acceptable to adolescents with AN and results in clinical improvement in weight and/or psychological symptoms. METHODS: This study will randomise 20 adolescents with AN, ages 12-17 years, to receive either FMT or placebo capsules. These 20 youth, as well as an additional 10 youth who decline trial enrolment, will participate in qualitative interviews. We will track recruitment rates and collect psychological and biological measures (blood, stool, urine and saliva) at multiple timepoints to assess how gut microbiota and their metabolites may influence the symptoms of AN. Interviews with participants and caregivers will explore their experiences and views on FMT as a treatment approach. ETHICS AND DISSEMINATION: This study has received ethics approval by the Hamilton Integrated Research Ethics Board (#17493) and investigational drug approval by Health Canada (Dossier ID: c292423). Informed consent will be obtained by research staff from all participants. Findings will be disseminated through academic conferences, clinical forums and partnerships with advocacy organisations to reach clinicians, researchers and individuals with lived experience. TRIAL REGISTRATION NUMBER: NCT06593366.

  PublisherOA PDFDOI

• Balancing safety and effectiveness: parent preferences for fecal microbiota transplant and established therapies in pediatric inflammatory bowel disease-results of a multicenter Canadian study.

  PubMed · 2026-01-01

  articleOpen access

  Background and Aims: Treatment decision-making in pediatric inflammatory bowel disease (IBD) is complex, with many existing and emerging options. However, little is known about parent preferences for these therapies. This multi-center Canadian study provides the first quantitative data on parent preferences for pediatric IBD treatments and explores characteristics associated with differing preferences. Methods: We conducted a cross-sectional survey including a discrete choice experiment (DCE) with Canadian parents (n = 159) of children diagnosed with UC/IBD-U, recruited from four pediatric IBD clinics. The DCE assessed preferences across four treatment attributes: chance of clinical remission, severity and chance of known side effects, severity of rare unknown side effects, and mode of treatment delivery. Latent class modeling was used to explore preference heterogeneity. Results: Parents prioritized safety, particularly the risk of rare unknown side effects, followed by likelihood of remission. Latent class analysis identified two distinct groups: one most concerned about rare unknown side effects, and another prioritizing treatment effectiveness. Thirty-eight percent of parents were open to fecal microbiota transplant (FMT), an emerging therapy that uses donor stool to help restore gut microbiome health. Younger parents and those with children experiencing more severe disease and on multiple medications were more likely to accept FMT. Across the cohort, many parents were willing to trade off less desirable delivery modes or increased risk in exchange for better treatment outcomes. Conclusions: Parents value both safety and effectiveness in IBD treatment decisions. Recognizing these preferences may support shared decision-making, particularly when discussing novel therapies like FMT.

  PublisherOA PDFDOI

• The Gut Microbiome as a Therapeutic Target in Alopecia Areata: Not Yet Part of the Patient Treatment Plan

  International Journal of Dermatology · 2026-04-17

  articleOpen access

  Interest in the gut microbiome as a therapeutic target for treating alopecia areata (AA) has grown considerably. However, existing evidence remains limited and inconsistent. Currently, there is insufficient evidence to recommend microbiome-directed testing and therapies to patients with AA. Rigorous longitudinal studies are needed before such interventions can be recommended.

  PublisherDOI

• Evidence‐based review of the nutritional treatment of obesity and metabolic dysfunction‐associated steatotic liver disease in children and adolescents

  Journal of Pediatric Gastroenterology and Nutrition · 2025-06-17 · 3 citations

  review

  The growing pediatric obesity epidemic has paralleled the surge in metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis. It develops due to nutritional imbalances, microbiome dysbiosis, gene regulation, hormonal changes, and environmental factors like food deserts, low activity level, and an unhealthy lifestyle. The prevalence of MASLD and obesity is rising every year. Lifestyle changes remain the mainstay treatment for obesity and MASLD. Per the 2023 American Association for the Study of Liver Diseases Practice Guidance on MASLD, achieving ≥5% weight loss can reduce hepatic steatosis, ≥7% weight loss can reduce hepatic inflammation, and ≥10% weight loss can reduce liver fibrosis. Therefore, nutritional interventions can be a powerful tool to help correct metabolic dysfunction and promote healthy weight loss. Current endorsed nutritional interventions for weight loss or MASLD include the Mediterranean diet, low glycemic/low carbohydrate diet, plant-based diet/anti-inflammatory diet, ketogenic diet, and intermittent fasting. This review provides evidence-based insights into current nutritional interventions for children and adolescents with obesity and MASLD to help guide pediatric gastroenterologists in making the best dietary-based recommendations in clinical practice.

  PublisherDOI

• Fecal Microbial Community Profiling Allows Discrimination of Phenotype and Treatment Response in Pediatric Crohn’s Disease and Ulcerative Colitis—An International Meta-Analysis

  Inflammatory Bowel Diseases · 2025-06-28 · 2 citations

  articleOpen access

  BACKGROUND AND AIMS: The pathophysiology of pediatric inflammatory bowel disease (PIBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is not entirely understood. Dysregulation of the intestinal microbiome is recognized as both a disease-driving and a potential therapeutic target. This study aimed to systematically analyze gut microbiome compositions and its applicability as a biomarker for disease progress and treatment response. METHODS: Bibliographic and nucleotide databases were searched. Raw 16S-rRNA sequencing reads were subjected to a uniform downstream dada2/phyloseq pipeline to extract taxonomy, community structure, and abundance information. Patient metadata were extracted from publications, and study authors were contacted for further details if required. RESULTS: Twenty-six studies comprising 3956 stool samples (CD 41%, UC 36%, 23% healthy) were included in the analyses. Median age of individuals was 12 (interquartile range 4). Sex distribution was comparable. Alpha diversity was reduced between the healthy and both UC and CD treatment-naïve groups (P < .001) and further reduced with increasing clinical disease activity. Beta diversity revealed altered community structure in treatment-naïve children with PIBD (P < .001). This alteration remained in patients in clinical remission (P < .001). Machine learning models discriminated between treatment-naïve patients with CD or UC with an area under the receiver operating characteristics curve (AUROC) of 98%. Microbial communities differed between patient responders versus nonresponders to treatment (P < .001). Further, microbial community profiling distinguished treatment response (eg, steroid, nutrition, or TNFα) with AUROCs of 82%-90%. CONCLUSIONS: Gut microbial community structure is substantially altered in active and inactive PIBD and may be utilized as a biomarker for differentiating PIBD subtype and predicting treatment response.

  PublisherDOI

• Silent Struggles: Uncovering Mental Health Burdens in Adolescents with Inflammatory Bowel Disease and Juvenile Idiopathic Arthritis—A Retrospective Chart Review

  Children · 2025-07-29 · 2 citations

  articleOpen access

  BACKGROUND/OBJECTIVES: Juvenile idiopathic arthritis (JIA) and inflammatory bowel disease (IBD) are chronic autoimmune conditions that impact the physical and psychological well-being of pediatric patients. While previous studies have shown a high prevalence of mental health challenges among youth with chronic conditions, the prevalence of mental health issues in Canadian pediatric patients with JIA and IBD remains unclear. We aimed to estimate the prevalence of documented mental health disorders and related medication use of youth with JIA or IBD at a tertiary care centre. METHODS: We conducted a retrospective chart review of youths aged 12-17 diagnosed with JIA or IBD at McMaster Children's Hospital (MCH) to understand the prevalence of generalized anxiety disorder (GAD), separation anxiety disorder, social anxiety disorder (SAD), obsessive-compulsive disorders (OCD), eating disorders, major depressive disorder (MDD), adolescent adjustment disorder, suicide attempt/suicide ideation, self-harm behaviour, substance use disorder, and attention deficit disorders (ADD). RESULTS: We reviewed 429 patient charts, including 303 patients with IBD and 126 with JIA. Our findings identified 90 IBD patients and 20 JIA patients who had one or more documented mental health conditions. Proportionately, there was a higher prevalence of mental health conditions among IBD patients (30%) compared to JIA patients (16%). The most frequently observed conditions in both IBD and JIA patients were GAD (63%, 50%), ADD (33%, 35%), and MDD (29%, 15%). CONCLUSIONS: These findings highlight the critical need for early mental health screening and integrated care approaches that address both medical and psychosocial needs in adolescents with chronic illnesses. Future research should incorporate prospective study designs, include diverse geographic and demographic populations, and explore targeted interventions to improve mental and physical health outcomes in this vulnerable group.

  PublisherOA PDFDOI

• Diagnosis and Management of Small Intestinal Bacterial Overgrowth in Pediatric Short Bowel Syndrome

  Gastroenterology Clinics of North America · 2025-09-10

  article1st authorCorresponding
  PublisherDOI

• Call to action—Pediatric MASLD requires immediate attention to curb health crisis

  Hepatology · 2025-06-23 · 11 citations

  articleOpen access

  Pediatric metabolic dysfunction-associated steatotic liver disease (MASLD) has become more prevalent on a global scale over the last decades and is associated with significant comorbidities in childhood and a 40-fold higher risk of early mortality in young adulthood. MASLD has now become the leading indication for liver transplantation in young adults in the United States. However, pediatric MASLD is still perceived as an indolent condition by many patients, families, and clinicians. In this Call to Action, we aim to raise awareness of pediatric MASLD as a public health crisis. Herein, we describe insufficient screening and disease staging practices, and a lack of accurate non-invasive tests and effective pharmacotherapy, both stemming from a paucity of multicenter clinical trials in pediatric MASLD. We provide clear steps to address this public health emergency by promoting awareness campaigns, educating and empowering patients and families, addressing barriers including access to care, nutritional and exercise support programs, establishing multidisciplinary care, launching community initiatives, and conducting clinical trials in pediatric MASLD for an age-based evaluation of novel diagnostic and therapeutic options. We conclude by highlighting the urgent need for comprehensive public health policies to control the tide of pediatric MASLD and call upon stakeholders to act now.

  PublisherOA PDFDOI

Frequent coauthors

• Jelena Popov

  Boston Children's Hospital

  99 shared

• Lee Hill

  McGill University Health Centre

  73 shared

• Emily Hartung

  McMaster University

  34 shared

• Michal Moshkovich

  University of Toronto

  33 shared

• Lara Hart

  32 shared

• Mary Zachos

  McMaster University

  21 shared

• Melanie Figueiredo

  McMaster University

  18 shared

• Kanish Baskaran

  McMaster University

  17 shared

Labs

• Pai LabPI

Education

• FAAP, FRCPC (Pediatric Gastroenterology and Nutrition), Pediatric Gastroenterology, Nutrition and Hepatology (Boston Children's Hospital) (Physician-Scientist Stream)

  Harvard Medical School

  2014

• FAAP, FRCPC (Pediatrics), Pediatrics

  University of Toronto Faculty of Medicine, Hospital for Sick Children

  2011

• MD

  McMaster University Michael G DeGroote School of Medicine

  2007

Awards & honors

• American Society for Parenteral and Enteral Nutrition (ASPEN…
• Canadian Nutrition Society (CNS) Young Investigator Award