Self-trained citizen scientist, Martha Carlin, founds The BioCollective to accelerate microbiome research and therapies.

“Bad times have a scientific value. These are occasions a good learner would not miss.”
― Ralph Waldo Emerson

His vacant stare told Martha Carlin something was wrong with her 44-year-old husband. Many doctor’s visits later, the diagnosis – Parkinson’s Disease. A systems analyst and expert in turning around companies, Martha Carlin was determined to turn around the doctor’s prognosis that Parkinson’s would kill her husband. So for the next 15 years, she began pouring her energy, time, and disposable income into becoming a self-trained scientist. Starting with one of Michael J. Fox’s book, Martha read hundreds of books about nutrition, disease, and immunology.

With the help of a childhood friend who was a college librarian and Googling for unfamiliar terms, Martha read scientific journal articles. Slowly she put together a mind map of different potential genetic and environmental influences that might have led to her husband’s Parkinson’s disease. During Parkinson’s Disease, brain cells stop producing the chemical messages that allow for coordinated movement. Patients gradually lose control of their muscles. As she interviewed Parkinson’s patients, Martha noticed that many had frequently used antibiotics, had chronic strep or other infections, had chronic stress, and more. Parkinson’s is described as a disease of the body ecosystem. Martha realized Parkinson’s patients may also have a diseased microbial ecosystem. A 2014 paper published by Dr. Scheperjans [1] from Helsinki University correlated Parkinson’s disease to the lower abundance of specific gut bacteria. Reading Martin Blaser’s book, Missing Microbes, strengthened her belief in her hypothesis. Dr. Scheperjans put Martha in contact with Dr. Jack Gilbert, a leading microbiome expert at the University of Chicago, who analyzed the microbiome of stool samples from her and her husband. The more Martha read about the gut microbiome, the more she realized how she, as a system’s analyst, could help speed microbiome research and development of new therapies.

Turning Around Microbiome Science

Microbiome science is in a difficult place. We know that there’s a link between the microbiome and different diseases, but we still don’t have a good idea of what a “healthy” microbiome looks like.  We often don’t have an idea of HOW to fix problem “dysbiotic” microbiomes. Probiotic therapies have mixed results. Fecal transplants work >90% of the time for severe cases of Clostridium difficile [2, 3], but aren’t as successful with other digestive system disorders and other microbiome-related ailments [4-7]. Perhaps, like Martha suspects with Parkinson’s Disease, there is a microbiome ecosystem disease. We need to get rid of our 150+ year old habit of looking for a specific pathogen and start looking at the ENTIRE microbial community. What members are there and even more important – what are they doing?

In reading through the microbiome literature and talking to scientists, Martha realized that researchers were often focused on their one small part of the microbial ecosystem picture. Were researchers missing the bigger picture? Martha thought for microbiome research to be transferred from lab bench to a patient’s bedside quickly, a more holistic and efficient approach was needed.

• Microbiome datasets needed more human diversity as well as microbial (fungi, viruses, worm, archaea, and bacteria) diversity.
• The functions, the jobs that were and weren’t being done by the entire microbial ecosystem needed identifying.
• Microbes should be stored so they could be cultured for experiments and future therapeutics.
• TBC members should share in the profits that researchers make from their gut microbiome.

The BioCollective as a Solution

Martha, Dr. Jack Gilbert, and Dr. Suzanne Vernon came together to establish The BioCollective. Serving as a resource to collect, screen, and analyze gut microbiome communities, Martha envisions TBC as a “hypothesis generator” and “microbiome research accelerator”. Scientists can mine the database for microbes of interest and request samples to test their experiments. Jack Gilbert and his research team provide expertise in microbiome sequencing and analysis. Suzanne Vernon’s expertise in microbe culturing, allows for microbes of interest to be cultured from stool samples. This amazing trinity of lead “microbiome revolutionaries” are set to change science and medicine. See the post “7 ways The BioCollective is accelerating microbiome research and changing medicine” for details how TBC solves a variety of problems faced by stool donors and researchers.

Their Success Lies in Your Poop?

To succeed, TBC needs a large collection of stool samples from healthy and diseased individuals from around the world and throughout the social, economic, and cultural spectrum. Building a large database is essential for generating hypotheses. After collecting thousands of samples, one surprising result from the American Gut citizen science project was the influence of sleep (or lack thereof) on the bacterial microbiome community. TBC, with its broader sampling of microbes and use of WGS, is positioned to uncover many new hypotheses, see these ideas through testing, and help connect scientists to therapeutics companies. TBC is beginning by collaborating with the President’s Precision Medicine Initiative and National Microbiome Initiative, as well as researchers studying post-traumatic stress disorder, sickle-cell anemia, fecal transplants, Parkinson’s disease, autism, centenarians, and more. In working with a diversity of peoples, TBC will be able to identify and preserve our human microbial diversity. Interested in being part of TBC’s microbiome work? Sign up to become a TBC member. TBC is offering ~ 500 FREE kits of the microbiome community analysis and half-priced WGS (use code CAND50 at check-out) to begin to build the database. Functional data will also be generated on the initial microbiome community analysis kits. I ordered my kit! Join the microbiome “revolution”, help preserve human microbiome diversity, and advance science and medicine. Who knows, maybe every day you’ve been flushing a life-changing microbe down the toilet! Instead, let your poop help generate new hypotheses, new therapies, and maybe even a profit for you.

Additional Resources

https://www.the-scientist.com/notebook/a-citizen-scientist-makes-her-mark-in-microbiome-research-67580

Parkinson’s Disease May Start in the Gut – New Scientist

REFERENCES

1. Scheperjans F, Aho V, Pereira PAB, Koskinen K, Paulin L, Pekkonen E, Haapaniemi E, Kaakkola S, Eerola-Rautio J, Pohja M et al: Gut microbiota are related to Parkinson’s disease and clinical phenotype. Movement Disorders 2015, 30(3):350-358.
2. Fuentes S, van Nood E, Tims S, Heikamp-de Jong I, ter Braak C, Keller J: Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection. ISME J 2014, 8:1621 – 1633.
3. Gough E, Shaikh H, Manges AR: Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection. Clin Infect Dis 2011, 53(10):994-1002.
4. Frye RE, Slattery J, MacFabe DF, Allen-Vercoe E, Parker W, Rodakis J, Adams JB, Krajmalnik-Brown R, Bolte E, Kahler S et al: Approaches to studying and manipulating the enteric microbiome to improve autism symptoms. 2015 2015, 26.
5. Hourigan SK, Oliva-Hemker M: Fecal microbiota transplantation in children: a brief review. Pediatr Res 2016, 80(1):2-6.
6. Cui B, Feng Q, Wang H, Wang M, Peng Z, Li P, Huang G, Liu Z, Wu P, Fan Z: Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: safety, feasibility, and efficacy trial results. J Gastroenterol Hepatol 2015, 30.
7. Cui B, Li P, Xu L, Zhao Y, Wang H, Peng Z, Xu He, Xiang J, He Z, Zhang T et al: Step-up fecal microbiota transplantation strategy: a pilot study for steroid-dependent ulcerative colitis. Journal of Translational Medicine 2015, 13(1):298.

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