The Biome Squad

The Biome Squad

This issue of Physician Outlook highlights just some of the exciting research that was presented at the historic and exclusive Malibu Microbiome Meeting in March of 2021, which brought together pioneering leaders from across the globe in the vast burgeoning field of Gut Microbiome Science.

The study of the human intestinal microbiome and the role that it plays in medicine is in its infancy. It is truly the next frontier of medicine.

We as physicians spend many years mastering the principles of basic science before we are granted the privilege of practicing medicine. Understanding the complexity of the microbiome requires a solid understanding of the fields of both cellular and molecular biology, and it is only fitting that we begin our journey at the very beginning, at the very core of basic science: the cell, the basic membrane-bound entity that houses the fundamental molecules from which ALL living things are composed.

Thomas Borody, M.D. The CRAPsuleTM

Father Of FMT

The Man From Down Under Who First Had Success With The Fecal Microbial Transplant.....

Thomas Borody, M.D. The CRAPsuleTM

Dr. Thomas Borody completed his BSc(Med) and later MBBS graduating in 1974 from the University of New South Wales in Sydney, Australia. He then completed his MD by thesis at the Garvan Institute of Medical Research and University of Sydney School of Veterinary Science. After having spent 3 years in clinical research at the Mayo Clinic, Rochester, Minnesota mentored by the late Sid Phillips, he gained his PhD at the University of Newcastle and his DSc at University of Technology. Given this rigorous background, Dr. Borody established the Centre for Digestive Diseases (CDD) in Sydney, Australia in 1984 and has overseen its growth into an active clinical research institute overseeing treatments for around 10,000 patients per year.

As Dr. Borody’s interests focus on solving clinical problems by developing novel treatments often infection-associated, his first patented and effective treatment was the Triple Therapy which cured H. pylori. He then went on to develop a Crohn’s disease triple anti-Mycobacterium treatment (AMAT) which completed two successful pivotal trials, and in a paper just published, individualized antibiotic treatment followed by microbiome restoration achieved Crohn’s disease cure for the first time. To date, the CDD has completed over 30,000 FMT treatments, naming Dr. Borody the ‘Father of FMT’ -likely the most experienced in the world.

Among emerging new treatments that involve the microbiome, Borody has developed an oral capsule of filtered, freeze-dried donor fecal microbiota, also known as the Crapsule™. In a joint venture with Finch Therapeutics, these refined lyophilised FMT capsules are approaching FDA approval for treatment of C. difficile infection and Autism Spectrum Disorder as a novel indication contingent on trials. At the Malibu Microbiome Meeting, Dr. Borody discussed how FMT is being applied to treat other conditions beyond C. diff focusing on Crohn’s disease and neurological conditions. 

Dr. Neil Stollman

GI Expert 

A Guy Who Knows His Sh!T, All The Way From New York To Northern California  

Dr. Neil Stollman

Dr. Neil Stollman received his medical degree from the New York University School of Medicine, completed his residencies in Internal Medicine at The College of Physicians and Surgeons of Columbia University, and fellowships in Gastroenterology and Advanced Therapeutic Endoscopy at Jackson Memorial Hospital and the University of Miami School of Medicine.   

Today, Dr. Stollman serves as an Associate Clinical Professor of Medicine at UCSF and Chief of the Division of Gastroenterology at Alta Bates Summit Medical Center in Oakland, CA. Also the Director of the East Bay Center for Digestive Health Research Center, Dr. Stollman conducts and publishes clinical research that can be identified in various journals such as The Lancet and The American Journal of Gastroenterology.   

As a recognized expert, Dr. Stollman has a comprehensive background in treatments of C. Difficile and Fecal Microbiota Transplant (FMT), diverticular disease, H pylori infection, acid reflux disease, GI bleeding, microscopic colitis, eosinophilic esophagitis, and Barrett’s esophagus.  

At the Microbiome Meeting, Dr. Stollman  introduced and explained the fundamentals of the human gut microbiome and its role in health, FMT as the proof-of-concept for bacteriotherapy, and gave insight on an emerging therapy that can positively influence a baby’s microbiome.  

Dr. Alexander Khoruts

The Pharm-er

Rooting A New Branch Of Medicine

Dr. Alexander Khoruts

Dr. Alexander Khoruts is a physician-scientist with a background in immunology and clinical specialty in gastroenterology. A product of the University of Minnesota, Dr. Khoruts was a Howard Hughes Physician Fellow whose early research focused on basic biology of T cells and autoimmunity, but subsequently has redirected his efforts into development of microbiota-based therapeutics.

Now serving as the Medical Director of the University of Minnesota Microbiota Therapeutics Program, Dr. Khoruts is leading the only academic institution that manufactures microbiota-based products under the current good manufacturing practice regulations enforced by the FDA. With an objective to develop the ‘pharmacology’ of microbiota-based therapeutics, Dr. Khoruts works to root this new branch of medicine by supporting clinical trials for a variety of potential indications in collaboration with investigators across the US.

At the Microbiome Meeting, Dr. Khoruts explored the impact of regulatory policies on the future of fecal microbiota transplantation and addressed how the FDA’s approval process impacts patients, research, and innovation in the field of health and science. Ultimately, his presentation explored the challenges in doing research to develop and make available the next-generation microbiota therapeutics and identified how we can help move this new branch of medicine forward. 

Scott Jackson, PhD

Standards Seeker

Making Moves In Measuring ‘Magic Poop’

Scott Jackson, PhD

Upon completing his PhD research at the University of Maryland and Johns Hopkins University, Scott Jackson served 11 years as a principal investigator with the FDA.

Now serving at the National Institute of Standards and Technology (NIST), Jackson leads the Complex Microbial Systems Group in the Biosystems and Biomaterials Division where he is dedicated to measurement research in emerging bioscience areas, including the microbiome. Jackson plays a vital role in improving measurement tools and reference materials that aid in analyzing microbiome DNA. 

At the Microbiome Meeting, Jackson described the importance of developing products and standards for microbiome research, and presented a 2020 pilot study that found storing and preservation methods to have impact on the biological attributes of the fecal material stored for FMTs.Additionally, he gave insight to this technology by exploring the challenges associated with the measurement of SARS-CoV-2 in human stool and wastewater. 

Dr. Colleen Kelly

Gastro Girl

Shifting Treatment Paradigms For Patients Who Suffer From Digestive Diseases

Dr. Colleen Kelly

Dr. Colleen Kelly is a gastroenterologist in the Center for Women’s Gastrointestinal Medicine at the Women’s Medicine Collaborative. She is an assistant professor of medicine at The Warren Alpert Medical School of Brown University and a faculty member in the fellowship pathway in women’s gastrointestinal diseases at Alpert Medical School.

Dr. Kelly’s passion for the microbiota and fecal matter transplant (FMT) has contributed to a shift in the treatment paradigm for patients who suffer from digestive diseases like recurrent C. diff, Irritable Bowel Syndrome (IBS)and Inflammatory Bowel Disease (IBD), naming her”Gastro Girl.” As the first in the Microbiome Movement to get an Investigational New Drug (IND) approval from the FDA for FMT, and the NIH to fund a randomized clinical trial, she has also collaborated on several studies investigating the impact of FMT on patients with IBD, Nonalcoholic Fatty Liver Disease, and Alopecia Areata.

With a major interest on in the long-term effects around the manipulation of gut microbiota, Dr. Kelly serves as the primary author for the forthcoming American College of Gastroenterology (ACG) 2019 C. difficile treatment guidelines. Additionally, she is one of the primary investigators for an NIH-funded FMT National Registry, which will answer important questions around the safety of FMT. At the Microbiome Meeting, Dr. Kelly reviewed evidence from randomized controlled trials and described the efficacy and safety of FMT in C. difficile infection. 

Dr. “Mimi” Wang

A Leading Lady  

Revitalizing Cancer Treatment With The Microbiome

Dr. “Mimi” Wang

Dr. Yinghong Wang has a strong academic background and profound clinical experience from world renowned medical programs of Johns Hopkins and Cleveland Clinic. She possesses extensive experience taking care of patients with complex Crohn’s Disease and Ulcerative Colitis and has been recognized for her expertise in managing cancer immunotherapy induced GI toxicities. She also plays a major role in developing management guidelines for immunotherapy induced colitis and works on building a detailed management algorithm at the institutional level.

Dr. Wang and her team have achieved a new breakthrough of successful treatment for immunotherapy induced colitis refractory to immunosuppressant by fecal microbiota transplant. The initiative Dr. Wang has taken in setting up an IBD clinic and FMT service available to patients is identical to that of a pioneer, putting Dr. Wang as one of the leading ladies in the Microbiome Movement.

With her specializing in areas such as Inflammatory Bowel Disease (IBD), fecal microbiota transplantation (FMT), and cancer immunotherapy induced gastrointestinal toxicities, Dr. Wang described how gut microorganisms impact the outcome of cancer and cancer therapy related gastrointestinal complications, and how microbial manipulation may transform patient care.


Follow Dr. Feuerstadt on Twitter at @DrPaulGastro and on his website

Professor GI

Educating The Next Generation On Microbiome-Based Therapies

Follow Dr. Feuerstadt on Twitter at @DrPaulGastro and on his website

Dr. Paul Feuerstadt attended the University of Pennsylvania where he earned his Bachelor of Arts degree graduating summa cum laude. He attended the Weill Medical College of Cornell University in New York where he earned his medical doctor degree and stayed at New York Presbyterian Hospital for his residency in internal medicine. His clinical gastroenterology training was completed at Montefiore Medical Center in the Bronx, New York.

Dr. Feuerstadt has been involved in research focusing on fecal microbiota transplantation (FMT), C. difficile infection, irritable bowel syndrome (IBS) and ischemic bowel disorders.

While he is an author and co-author of many manuscripts and textbook chapters, Dr. Feurerstadt can frequently be found educating and mentoring medical students, residents and fellows in the realm of research at the Divisionof Digestive Disease at Yale-New Haven Hospital where he serves as the Assistant Clinical Professor of Medicine.

At the Microbiome Meeting, Dr. Feuerstadt described the unique challenges to conducting clinical trials of microbiome-based therapies in C. difficile infections. 

Dr. Faming Zhang


An Advocate Of Maintaining Tradition In Practice To Evolve New Therapies

Dr. Faming Zhang

Dr. Faming Zhang is a doctor, Vice Chief, and researcher at the Institute for Digestive Endoscopy & Medical Center for Digestive Diseases at The Second Affiliated Hospital of Nanjing Medical University in Nanjing, China. He is also the Director of Intestinal Diseases whose perspective on the microbiome and disease is unique, taking on a holistic approach that most Western physicians do not consider. In a recent study, Dr. Zhang saw potential to utilize Traditional Chinese Medicine (TCM) philosophy and concluded that it was a helpful outlook to deeply investigate the complex ecosystem of gut microbiota.

Dr. Zhang believes that standardized procedures will move FMT into mainstream medicine, thus he’s developed a clinical flow for FMT procedures as well as an automatic system--GenFMTer, that auto-purifies isolated microbiota from the stool. His contribution to move microbiome procedures like FMT into the mainstream is simple, but necessary for standard of care practices. At the Microbiome Meeting,Dr. Zhang described the latest progress on methodology, safety, and benefits related to FMT in conditions beyond C. diff infection. 

James Adams, PhD

Super Dad

Raising Hopes For Family, Friends And Those With Autism

James Adams, PhD

Although an engineering professor, Dr. James B. Adams’ motivation to research autism spectrum disorders (ASD) began with the intention to understand and help his daughter, who was diagnosed with ASD at age 2.5. Today, Dr. Adams currently serves as the Director of the Autism/Asperger’s Research Program at Arizona State University. His research focuses on the medical causes of autism, how to treat and prevent as well as the areas of nutrition, oxidative stress, gut problems, gut bacteria, toxic metals, and seizures. In addition to having over 150 peer-reviewed articles published, with 50 of them being related to ASDs, Dr. Adams also serves as the President of the Autism Society of Greater Phoenix, President of the Autism Nutrition Research Center, is the co-leader of the Scientific Advisory Committee of the Autism Research Institute, and chairman of the Scientific Advisory Board of the Neurological Health Foundation. Recently, Dr. Adams and his collaborators Profs. Rosa Krajmanik-Brown and Dae-Wook Kang have demonstrated long-term beneficial effects for children diagnosed with ASD through a revolutionary technique known as Microbiota Transfer Therapy (MTT), originally pioneered by Australian Gastroenterologist, Dr. Thomas Borody for children with ASD with gastrointestinal disorders. Remarkably, they found that two years after treatment stopped there was a 59% improvement in gut symptoms and a 47% improvement in ASD symptoms compared to pre-treatment. Dr. Adams and colleagues are inspirationally breaking ground in autism research, and are raising new hope for the family and friends of an entire population that goes underserved. At the Microbiome Meeting, Dr. Adams dove deeper on the topic of Microbiota Transplant for Autism and reviewed a phase 1 clinical trial of MTT in children with autism. 

Andreas Papoutsis, PhD

Dr. Unknown

The Man Breaking Ground Behind Closed Doors

Andreas Papoutsis, PhD

Andreas Papoutsis is a bioinformatics scientist with extensive experience in oversight and execution of molecular clinical trial testing with rigorous quality systems programs. He has a deep understanding of methodologies and data analysis focusing on the human genome and microbiome profiling.

Dr. Papoutsis has researched and investigated new technologies for the analysis of genes associated with various types of cancer and is currently working with next generation sequencing technology to analyze and identify pathogens like SARS-COV-2 in stool samples.

At the Malibu Microbiome Meeting Dr. Papoutsis presented on the topic of metagenomics to enhance the understanding of the methods used to study the composition and function of the gut microbiome and went in depth on a clinical trial for gene sequencing in stool samples. Papoutsis’ insight on the hidden realm behind the analysis of the gut microbiome is not only foundational, but fascinating and extremely relevant for future medicine. 

Dr. Sahil Khanna

GI’s Tour-Guide

Guiding Professionals And Patients From Diagnosis To Treatment On Common Digestive Issues

Dr. Sahil Khanna

Dr. Sahil Khanna completed medical school at the All India Institute of Medical Sciences in New Delhi followed by Post-Doctoral Research at University of California San Diego, CA. Upon completion of his Masters in Clinical and Translational Sciences at the Mayo Clinic in Rochester, MN he now serves an Associate Professor of Medicine in the Division of Gastroenterology and Hepatology and directs the Comprehensive Gastroenterology Interest group, C. difficile Clinic, Fecal Microbiota Transplantation program, and C. difficile related clinical trials.

Dr. Khanna’s clinical interests include epidemiology and emerging therapeutics for C. difficile infection. He has contributed increasing awareness of the microbiome by developing an education module intended for healthcare professionals who care for patients with digestive issues that discusses the role of the microbiome and reviews the importance of a healthy microbiota and strategies to prevent dysbiosis and restore balance. His most recent book, Mayo Clinic on Digestive Health, contains content on the latest medical research on digestive health and serves as a fundamental guide for treating common digestive issues from diagnosis to treatment.

At the Microbiome Meeting, Dr. Sahil Khanna guided us through microbiome based therapies for recurrent urinary tract infections and examined the role of microbiome based therapy in chronic UTI.


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