uBiome is a biotechnology company based in San Francisco that gives individuals and organizations access to sequencing technology to sequence their microbiomes with a sampling kit and website. The company was founded by Jessica Richman and Zachary Apte in November 2012,
uBiome plans to announce a collaboration with the Centers for Disease Control and Prevention to analyze over 10,000 stool samples from hospital patients.
As research into the importance of the bacteria living in people’s guts—the microbiome—has become more common, the potential in turning the genetic sequences of those intestinal critters into a useful tool for doctors is obvious—problem is, it’s only potential. No one has quite figured out how. A healthy community of gut microbes isn’t easily reduced to a single metric, like blood sugar or cholesterol levels. So uBiome and the CDC have set out to develop something a “Microbiome Disruption Index”to track how treatments, like antibiotics, alter gut microbes.
CDC will collect the samples, and uBiome will sequence them.
Sequence: uBiome extracts the bacterial DNA out of the sample and identify each of the bacteria that the DNA came from. It’s a little like dusting a scene for fingerprints. *1
The San Francisco-based startup currently sells microbiome sampling kits directly to consumers, who mail the kits back to uBiome for analysis—much like 23andMe with its DNA sequencing kits. uBiome recently started offering grants in the form of $100,000 worth of kits to researchers. The CDC, which has microbiome on the brain (so to speak), decided to apply. “Working with companies developing expertise in this area is something we’re interested in,” says Alison Halpin, a CDC epidemiologist. “And CDC is always looking for partnerships.”
The collaboration, which will begin early next year, is still fairly open-ended. The CDC has only just started thinking about the Microbiome Disruption Index and how to use it to predict things like whether a patient might be at risk for infections that hang out in hospitals. But if sequencing costs continue to fall says Halpin, “It’s possible for [microbiome sequencing] to become a standard tool. We’re trying to anticipate that by understanding how you interpret that information.”
How to interpret sequencing information is a challenge for uBiome, too, which is expanding its business from direct-to-consumer kits to clinical tests ordered by doctors. “We’re moving into the clinical space in a number of ways,” says cofounder and CEO Jessica Richman. “This collaboration helps us figure out what the problems are.” In other words, this is all very early-days. Richman says that uBiome plans to announce its first clinical test next year, but she declined to give details.
Researchers have linked the makeup of the gut microbiome—with varying degree of certainty—to big things like obesity, cancer, and mental illness. But uBiome is more likely to start smaller, with clearer-cut tests like looking for the presence of nasty bugs such as the Clostridium difficile bacteria. (It causes all sorts of nasty gut problems, and can turn pathogenic when a person’s normal, healthy gut flora get wiped out by a course of antibiotics.) The advantage of microbiome sequencing is that uBiome could look test for several different pathogens at once without having to grow any of them in a petri dish first.
uBiome’s lab is currently certified under the Clinical Laboratory Improvement Amendments, which allows approved labs to develop new tests without getting individual approval for each one. That could feel like a red flag. Recent controversy over the blood testing company Theranos has highlighted the sometimes loose regulations, and the Food and Drug Administration has it wants to regulate lab tests more strictly.
For now, says Daniel Almonacid, a senior scientist at uBiome, “We assume we’re in good standing because the CLIA requirements are already met.”1
23andMe famously had a big battle with the FDA over the medical information it offered as results for its genetic tests. If uBiome wants to go in that direction, it may end up running into regulation, too. But in the meantime, 10,000 plus samples could be a significant conversion of poop into data. 1 UPDATE: Correction 8:50pm ET 11/30/2015 This quote has been corrected to more accurately reflect uBiome’s CLIA status.
2015 International Raising C. diff. Awareness Conference & Health EXPO
Boston, MA, USA ~ November 9th
7:30 a.m – 5:00 p.m
Join us at our 3rd annual International Raising C. diff. Awareness Conference and Health EXPO on November 9th. Not just another educational conference but one that pairs
world-renowned topic experts with presentations on state-of-the-art health care topics pertaining to a leading Healthcare-Associated Infection (HAI); C. difficile
*Prevention and Treatment Clinical trials and studies
*Fecal Microbiota Restoration and Transplants
……………………..and much more.
The panel of world-renowned topic experts will also discuss the burden of C. diff. the risk factors pertaining to current and emerging treatment options along with the importance of applying evidence-based clinical approaches to the prevention of a C. diff. infection (CDI), one of the leading Hospital-Acquired Infections.
Clostridium difficile (also known as C. diff.) is an important cause of infectious disease death in the United States. Nearly half a million Americans suffered from Clostridium difficile (C. diff.) infections in a single year according to a study released February 25, 2015 by the Centers for Disease Control and Prevention (CDC). • More than 100,000 of these infections developed among residents of U.S. nursing homes alone.* Approximately 29,000 patients died within 30 days of the initial diagnosis of a C. diff. infection. Of these 29,000 – 15,000 deaths were estimated to be directly related to a C. diff. infection. Therefore; C. diff. is an important cause of infectious disease death in the U.S. (Source: CDC)
Double Tree Suites Hotel – Boston – Cambridge 400 Soldiers Field Road, Boston, MA 02134 USA 1-617-783-0090 For Hotel Accommodations * * There are hotel accommodations available for Sunday evening offered at a special event rate for guests of the C Diff Foundation. Please inform the DoubleTree representative at the time of creating a reservation to receive the special event room rate.
Exclusive Admission: $75.00
Student Admission: $50.00
Each exclusive and student ticket includes admission to all presentations, formal and informal Q&A sessions, introductions to fellow healthcare professionals, continental breakfast (7:30 a.m.) , a plated four course luncheon with the choice of Chicken Florentine or Petite Filet Mignon main entree, Access to the Health EXPO, a conference book, a educational DVD, and formal conference program.
To Register and obtain tickets, please click on the following link
NOTE: *Presentations should not be recorded audio or video or published without prior written and signed permission from the guest speaker and addressed by each attendee seeking publication of said presentations.
Key Speaker and Conference Chair: Professor Mark Wilcox; Professor of Medical Microbiology, Leeds Institute of Biomedical and Clinical Sciences, UK. Professor Mark Wilcox is a Consultant Microbiologist, Head of Microbiology and Academic Lead of Pathology at the Leeds Teaching Hospitals, Professor of Medical Microbiology at the University of Leeds, and is the Lead on Clostridium difficile for the Public Health England. He has formerly been the Director of Infection Prevention, Infection Control Doctor and Clinical Director of Pathology at Leeds Teaching Hospitals.
Dr. John Bartlett, MD; Assistant Professor Medicine, UCLA/Sepulveda Veterans Admin Hospital 1972-5, Associate Professor and Professor of Medicine, Tufts University School of Medicine, Boston, 1975-80, Professor of Medicine and Chair Division of Infectious Diseases Division, Johns Hopkins University School of Medicine 1980 – 2006; Professor of Medicine, 2006 – 13; Professor of Medicine emeritus, Johns Hopkins University School of Medicine, 2013.Dominant research interests: anaerobic infections and pulmonary infections 1968 – 74; community acquired pneumonia and diagnostic methods, 1974-1980; Bowel prep for elective colon surgery; Protected bronchoscopy brush catheter-1977; Clostridium difficile 1977 – 84, HIV 1983 – 2014; bioterrorism 1999 –2004; Clostridium difficile infection, HIV/AIDS and antibiotic resistance 2006-2013 with Major current interests: Clostridium difficile infection, HIV infection, antibiotic resistance, careers in infectious diseases. Presentation Topic:“The discovery of Clostridium difficile as the cause of antibiotic-associated colitis.”
Professor Simon M. Cutting, Professor of Molecular Microbiology at Royal Holloway, University of London is a bacterial geneticist with over 25 years of experience with Bacillus since graduating from Oxford University with a D. Phil in 1986. His D.Phil was on understanding the genetic control of spore formation in Bacillus. After spending 7 years in the renowned laboratory of Professor Richard Losick at Harvard University Biological Laboratories (USA) he spent 3 years as an Assistant Professor at the University of Pennsylvania Medical School in Philadelphia. He returned to the UK in 1996 and since then has worked on developing bacterial spores as novel oral vaccines at
Royal Holloway, University of London. The Cutting lab has developed a number of prototype oral vaccines and is now entering a ‘first in man’ phase 1/IIa clinical trial of a prototype oral vaccine to Clostridium difficile (see www.cdvax.org). His other expertise is in the use of Bacillus spores as probiotics and has a number of contracts and consultancies with European and US companies in the food and feed sectors (see SporeGen.com). Presentation Topic: “Mucosal Vaccination: Decolonisation is Essential to Full Protection Against C. difficile“
Dr. Sadeq A. Quraishi, MD, MHA, MMSc Anesthesiologist/Intensive Care physician in the Department of Anesthesia, Critical Care and Pain Medicine at the Massachusetts General Hospital in Boston, MA. He is also Assistant Professor of Anaesthesia at Harvard Medical School in Boston, MA. Dr. Quraishi’s overall research goal is to better define how macro- and micro-nutrient status influence outcomes during acute stress and critical illness. In particular, his research group has focused on the immunomodulatory effects of vitamin D in the perioperative setting, during acute care hospitalization, and for patients in the intensive care unit. Recently, Dr. Quraishi’s group has identified vitamin D status as a potentially modifiable risk factor for hospital acquired C. diff infections and that the severity of C. Diff infections may also be related to vitamin D status . Presentation Topic: “Vitamin D as nutritional immunomodulation
for Clostridium difficile infections.”
Dr. Mary Beth Dorr , Phd, studied Pharmacy at the University of the Sciences in Philadelphia and received a PhD in pharmacokinetics and drug metabolism from the University of North Carolina. For the last 28 years Dr. Dorr has worked in the pharmaceutical industry in various capacities, with the majority of the time devoted to the design and implementation of Phase 1 to 4 clinical trials, primarily for anti-infective products. Prior to joining Merck, Dr. Dorr directed several large, international clinical studies of the efficacy and safety of two IV antibiotics, Synercid and dalbavancin. She also directed clinical research programs for gastrointestinal and women’s health products. Mary Beth joined Merck in February 2011 and is currently a Clinical Director in the Late Stage Clinical Development Department as the Clinical Monitor directing 2 large pivotal Phase 3 trials investigating the safety and efficacy of the monoclonal antibodies actoxumab and bezlotoxumab as adjunctive therapy for the prevention of C. difficile recurrence. Presentation Topic:Bezlotoxumab for Prevention of Recurrent C. difficile Infection in Patients on Standard of Care Antibiotics: Results of Phase 3 Trials (MODIFY I and MODIFY II)
Dr. Hudson Garrett, Jr., PhD, MSN, MPH, FNP, CSRN, VA-BC, CDONA,FACONA,DON-CLTC
Dr. Hudson Garrett is currently employed as the VP, Clinical Affairs for PDI and NIce-Pak, and is responsible for the global Clinical Affairs program and also the Medical Science Liaison program for all divisions within the company. He holds a Bachelor of Science degree in Biology/Chemistry and Nursing, a dual Masters in Nursing and Public Health, Post-Masters Certificate as a Family Nurse Practitioner, a Post-Masters Certificate in Infection Prevention and Infection Control and a PhD in Healthcare Administration and Policy. He has completed the Johns Hopkins Fellows Program in Hospital Epidemiology and Infection Control, and the CDC Fundamentals of Healthcare Epidemiology program, and is board certified in family practice, critical care, vascular assess, moderate sedation, legal nurse consulting, and a director of nursing in long term care. Dr. Garrett is also a Fellow in the Academy of National Associations of Directors of Nursing Administration in Long Term Care. Presentation Topic: Preventing Clostridium difficile thru Antibiotic Stewardship
Dr. David Cook, PhD; A scientist and entrepreneur who has held senior operating and management positions in the biotechnology industry over his 20-year career. Before joining Seres Therapeutics, he was the chief operating officer for the International AIDS Vaccine Initiative, a global R&D organization whose mission is to develop a safe, globally accessible vaccine for HIV. Prior to IAVI, David was the founding CEO at Anza Therapeutics, a biotechnology start-up developing a novel microbial vaccine platform to induce cellular immune responses to fight or prevent diseases such as cancer, hepatitis C, malaria and tuberculosis. He is also a co-inventor on over twenty-five patents. He received his undergraduate degree from Harvard College and his PhD in chemistry from the University of California, Berkeley. Dr Cook is presently Executive Vice President of R&D, Chief Scientific Officer with Seres Therapeutics, Inc.. Presentation Topic: “The role of the microbiome in resisting C. difficile infection and the mechanism of Ecobiotic drugs.”
Julie Gubb, PhD, CIC, has worked in the field of Infection Prevention in varying roles at healthcare facilities in multiple states for more than two decades. After graduating from the University of Detroit Mercy with a degree in Medical Technology, she began her career as Senior Clinical Microbiologist at an acute care hospital in Detroit, Michigan, where she developed an interest in Infection Control while managing the activities of a full-service microbiology laboratory. She was the Director of Infection Control at Mount Clemens Regional Medical Center in Michigan, and has also held positions in Infection Prevention at healthcare facilities in California and Nevada. As a Senior Infection Preventionist for Xenex, Julie works closely with hospitals throughout the United States to understand their infection prevention goals and develop strategies for attaining those goals. As an active member of the national organization Association for Professionals in Infection Control & Epidemiology (APIC), she has maintained Board Certification in Infection Control and Epidemiology since 1993 and speaks frequently at APIC chapter meetings. Presentation Topic: Stand Up for Cleanliness / Enhanced Room Disinfection
Dr. Patricia J. Freda Pietrobon, PhD: Associate Vice President, R&D,
Sanofi Pasteur, has over 25 years of experience in the Vaccine & Diagnostic industries and more then 20 years in leadership roles focusing on research & development of new vaccines. Patricia began her career in diagnostic assay development with a focus on validation and quality alignment to regulatory requirements and GXPs. Patricia has been with Sanofi Pasteur for over 25 years and has contributed to the development and licensure of new bacterial & viral vaccines for pediatric & adult populations worldwide.
Barley Chironda, Manager of Infection Prevention and Control (IPAC) and Medical Device Reprocessing Device at St. Joseph Health Centre in Toronto, Canada. He is certified in Infection prevention and control (CIC TM) and has worked extensively as an Infection Preventionist. Barely has been an integral to the successful decline in Clostridium difficile infections through implementing innovative technology and quality improvement behavioral changes. Barley’s presentation will show a behind the scenes account of the C. diff. management from the healthcare facilities perspective while providing a call to action.
Dr. Martha Clokie, PhD, Leicester UK, Professor in Microbiology. Dr. Cloakie’s research focuses on phages that infect bacterial pathogens of medical relevance and has published 41 papers in this area. Her major focus has been on Clostridium difficile where she has isolated a large phage collection. In vitro and in vivo data has shown that the viruses have therapeutic potential. A patent has been filed on these phages and working with AmpliPhi to develop a product. Dr. Cloakie has regular contact with the BBC and other media to talk about her work, and other phage projects, and has consulted with Science museum, London and Eden Project, UK to advise on bacteriophage displays.
Lee Jones, Founder, President and CEO of Rebiotix Inc, has over thirty years of experience in the medical technology industry in large and small companies and academia. Most recently Lee was Chief Administrative Officer of the Schulze Diabetes Institute at the University of Minnesota, Minneapolis, MN and is the former president and chief executive officer of Inlet Medical. Inlet Medical was sold to Cooper Surgical in 2006. Lee will introduce Rebiotix Inc., a biotechnology company founded in 2011 in Roseville, MN to revolutionize the treatment of challenging gastrointestinal diseases by harnessing the power of the human microbiome The company is developing an entirely new kind of biological drug designed to reverse pathogenic processes responsible for disease through the transplantation of live human-derived microbes into a sick person’s intestinal tract. Presentation Topic: Blazing a Trail with the Gut Microbiome
Professor Nancy Sheridan, a C. diff. Survivor and Associate Professor at the Fashion Institute of Technology and a winner of the prestigious SUNY Chancellor’s Award for Excellence in Teaching. Professor Sheridan will share her personal experience being treated for a painful and extended journey with a C. diff. infection (CDI). Professor Sheridan has been teaching since fall 2000 in the Fashion Merchandising Management Department within the School of Business and Technology. For the past seven years, she has also taught at the University of Pennsylvania, Wharton Business School to undergraduate and MBA students.
Dr Mel Thomson, PhD, completed her Honors degree in microbiology and immunology at the University of Melbourne . She then immigrated to the UK where she worked on various projects as diverse as allergy and cancer before undertaking further studies. She completed a Masters of Research in functional genomics before reading for a PhD in microbial genetic regulation in Neisseria species, both at University of York, UK. After the award of her PhD, Dr Thomson became interested the host-pathogen interactions at the Leeds Institute of Molecular Medicine, UK. Dr Thomson returned to Australia in 2011 to start her own research group studying host-pathogen interactions in the GI tract, at Deakin Medical School. A passionate science communicator, and has recently become a national ‘torch bearer’ for the concept of crowd funding academic research, which a track record of three successful ‘Pozible’ crowd funding campaigns, ‘Mighty Maggots’, ‘Hips 4 Hipsters’ and ‘No more Poo Taboo’ Presentation Topic: “All that glitters is C.diff awareness gold and Crowdfunding: The ‘No more poo taboo’ animation”
Dr Rahma Wehelie – LifeClean International AB – Sweden; LifeClean International AB is a Swedish company with an international orientation that conducts research, development, and production in the spore, bacteria, and virus eliminating industry. LifeClean was established in 2013 after many years of research and the headquarter lies in Uddevalla, Sweden. Presentation Topic: Dr Wehelie will be discussing LifeClean’s research, development and production eliminating Clostridium difficile, Norovirus, and other multidrug-resistant bacteria
Dr. Klaus Gottlieb, MD, FACG,Synthetic Biologics, Inc.,Vice President, Clinical;Regulatory Affairs Dr. Gottlieb is an experienced board-certified internist and gastroenterologist with a strong clinical science, business and drug development background. He joined Synthetic Biologics after serving as Senior Medical Director-Therapeutic Strategy Lead Gastroenterology of Quintiles, a Fortune 500 company and the world’s largest provider of biopharmaceutical development and commercial outsourcing services. At Quintiles, Dr. Gottlieb served as Global Medical Advisor for three separate large Phase 3 inflammatory bowel disease (IBD) trials and provided significant input on the shaping, design and evaluation of numerous IBD and other gastrointestinal (GI) clinical trials throughout all stages of development programs. Prior to joining Quintiles in 2013, he was with the FDA in Silver Spring, MD as a Senior Clinical Reviewer for the Division of Gastroenterology and Inborn Errors Products. Widely published, his academic contributions have been recognized by an appointment as Professor of Medicine (Clinical) at George Washington University and the following elected fellowships: Fellow American College of Physicians, Fellow American College of Gastroenterology, Fellow American Society of Gastrointestinal Endoscopy. Presentation Topic: Protecting the Gut Microbiome
For additional information contact the C Diff Foundation: (919) 201-1512 or email@example.com
To Register and obtain tickets, please click on the following link
The study will provide new insights on mechanics of fecal microbiota transplantation with patients being treated for a C. diff. infection.
uBiome and OpenBiome Partner for Microbiome Study in FMT Patients
Study will provide new insights on mechanics of fecal microbiota transplantation in patients treated for a C. difficile infection.
uBiome and OpenBiome announced a new partnership to study the microbiome of patients undergoing fecal microbiota transplantation (FMT) as a treatment for Clostridium difficile infections (C. diff).
Any patient undergoing clinical FMT treatment can request their complimentary mail-order microbiome testing kit at http://ubiome.com/pages/fmt. The kit allows them to swab a sample of their microbiome, which they send back to uBiome for analysis and sequencing. uBiome will use the collected data to conduct a study of FMT’s impact on the body’s microbiota. All study participants will also receive a detailed report on their personal microbiome.
“Because we will be looking at patients before, during, and after FMT we will be able to learn about how the microbiota adjusts to the treatment,” adds OpenBiome Co-Founder and President Dr. Mark Smith. “This has the potential to not only shed light on C. diff, but also open the door to using FMT with patients suffering other conditions.”
C. diff infections can occur when there is a severe imbalance of gut microbiota. Because of this imbalance, the bacterium thrives and causes extreme gastrointestinal distress.
This study will serve to increase awareness and understanding of how FMT affects the human microbiome, which could increase its acceptance in the medical community as a way to treat a potential variety of gastrointestinal conditions.
uBiome (ubiome.com) sequences the microbiome for citizen scientists, researchers, and clinicians, using microbial genomics to help patients benefit from new discoveries in scientific research. uBiome conducts research studies on the microbiome and develops clinical diagnostics based on microbiome research.
OpenBiome (openbiome.org) is a nonprofit stool bank dedicated to expanding safe access to fecal microbiota transplantation (FMT) therapies. Founded by a team of microbiologists, public health advocates, and concerned citizens, OpenBiome aims to significantly reduce the practical barriers for clinicians providing FMTs, while connecting scientists across studies and disciplines.
To read the article in its entirety please click on the following link: