The BioCollective – transforming and accelerating microbiome research and novel therapies – while saving our human microbiome diversity and maybe you. Your poop is more than just waste.

If you think that microbiome research has changed medicine – you ain’t seen nothing yet. The BioCollective (TBC) is transforming citizen science microbiome research from sample collection to the potential for providing a return on your initial “deposit”. TBC is building a microbiome data and sample repository to help scientists accelerate their research and development of potential therapeutics. TBC’s unique approach to microbiome citizen science research is due to the perfect trinity of collaborators: Martha Carlin, Jack Gilbert, PhD, and Suzanne Vernon, PhD. TBC is the brainchild of self-trained citizen scientist Martha Carlin, a former systems analyst who “turned around” struggling companies. Martha realized that for microbiome research to aid or even cure microbiome-related diseases, a new, integrative, multi-pronged approach was needed and a wider diversity of people should be sampled.

The BioCollective provides solutions to many of the current issues with human microbiome research.

1. A clean poop sample

   • TBC Member issue: People are often totally “icked” out and may have trouble collecting high quality sample.
   • Researcher issue: TBC Members have difficulty collecting the sample, leading to potential contamination issues.
   • TBC solution: a unique collecting device that fits over your toilet ready for your deposit. Once your duty is done, you drop the device in a biohazard bag, expel the air from the bag, and stored on ice until shipped. (US and EU patents pending)

2. Getting beyond WEIRD Databases

   • TBC Member issue: Cost – most citizen science microbiome sites come with a hefty price tag ($90/sample), which certainly doesn’t fit in my family’s budget. Probably most families would pay a bill or buy groceries instead of having their poop microbial community identified. That poop, and potentially helpful microbes, are going to go on down the toilet. TBC founder, Martha Carlin sees that wasted waste as a wasted opportunity. The high cost means microbiome databases are full of WEIRD (Western, educated, industrialized, rich, and democratic) peoples. True solutions to our medical problems lie in examining the diversity of the microbial ecosystems of a diversity of peoples.
   • Researcher issue: Identifying and recruiting potential TBC Members for a microbiome research trial takes time, energy, and funds away from research. A diverse database of healthy and diseased microbiomes available for analysis means scientists form hypotheses from TBC data. Researchers may identify specific microbes that differ between healthy and sick or which compounds are missing from a sick person’s microbial ecosystem. Now time, energy, and funds are used testing hypotheses.
   • TBC solution: Provide ~ 500 microbial community diversity sampling kits for FREE to the interested public and reduced rate whole genome sequencing (WGS). TBC is donating ~1,000 kits to a collaboration with The Minority Health Ministries to examine sickle cell disease, microbiome communities, and stress in inner-city Baltimore.

3. Finding out the microbial cast

   • TBC Member issue: Since the majority of the microbiome research done is on bacteria, TBC Members may not realize that viruses, fungi, and even worms may be important members of the microbiome and human health.
   • Researcher issue: Researchers focus on what they know and what is being funded.  Currently, most funding is going to bacterial microbiome studies and the bacterial databases are more robust. In only focusing on bacteria, we may be missing some key players in the microbial ecosystem. For example, a community with both fungi and bacteria has been identified with people with Crohn’s disease [1].
   • TBC solution: Using methods to identify bacteria, archaea, viruses, fungi, and worms from each sample.  Perhaps an important, previously unknown phage, fungi, or other microbe may be found [2]. WGS data may reveal the jobs and functions of non-bacterial components of the gut microbiome.

     

4. The role(s) of each microbial member

   • TBC Member issue: Some diseases may not be caused by specific microbes, so knowing “who” is there may not be enough. We might need to know what these microbes are doing and how the whole microbial ecosystem is working or broken.
   • Researcher issue: “Healthy” is sometimes difficult to define due to different types of microbes doing the same jobs. Knowing what jobs are and are not being done in a given sample is much more helpful. However, it is expensive to collect and analyze this kind of data. Many studies do cheaper 16S rRNA studies to look for anything of interest, then apply for funding for functional work.
   • TBC solution: Sequence the genomes of the entire microbial community to identify what genes are present, what potential jobs are done by the microbes present, and if antibiotic resistant or other genes of interest are present. TBC is also looking into metabolomics to identify the chemistry and physics underlying host-microbe interactions.

5. Experimenting with the microbes

   • TBC Member issue: WANTS THERAPIES, probiotics, and/or information to help with disease or improve health. TBC Members want to know what the problem is and what a solution might be. Microbiome ecosystem level therapies are needed. Current therapies focus on individual species or small communities of microbes, but do not look at the overall microbial ecosystem.
   • Researcher issue: Would love to do experiments, but lacks the expertise to culture the microbes or access to the microbes of interest. A small portion of what is in your gut has been isolated and cultured.  This is a vast unexplored frontier.
   • TBC solution: Work with researchers and other parties to provide samples that are collected and preserved so that as many organisms as possible can be isolated and cultured later. TBC will work to isolate and culture strains to make them available to researchers or companies for therapeutics development. TBC will use its hypothesis-generating framework to work with therapeutics companies to further test and develop therapies. WGS results may help with culturing previously “unculturable” microbes [3].

6. Testing and retesting the microbes

   • TBC Member issue: Don’t know that their samples are helpful.
   • Researcher issue: Difficulty contacting potential subjects for additional samples. Only one research lab working with a given subject.
   • TBC solution: Partition stool up into 30-50 small samples. These subsamples can be purchased by multiple researchers around the world, or a lab can get additional sub-samples if an interesting result is found. TBC has permission to follow up with a person to get additional samples if necessary.

7. The beneficiaries

   • TBC Member issue: With other companies, the TBC Member’s poop sample is given to the company for analysis. The TBC Member gets a list of bacteria present and a comparison to similar people’s samples in the database. Future work done on the sample and data are the company’s property.
   • Researcher issue: Couldn’t develop the product without ideas and the research done by scientists, but also need the samples.
   • TBC solution: Built on a revenue sharing model. The TBC Member’s stool “deposit” is an investment. They are allowing their microbes to be analyzed, stored, and used for research. When a researcher buys the stool sample, the TBC Member gets a share of the sample sales revenue after TBC’s initial costs are recovered. In the future, TBC’s revenue sharing with TBC members will expand into revenue from hypothesis generation, data and culturing of microbes.

REFERENCES

1. Hoarau G, Mukherjee PK, Gower-Rousseau C, Hager C, Chandra J, Retuerto MA, Neut C, Vermeire S, Clemente J, Colombel JF et al: Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease. mBio 2016, 7(5).
2. Filyk HA, Osborne LC: The Multibiome: The Intestinal Ecosystem’s Influence on Immune Homeostasis, Health, and Disease. EBioMedicine.
3. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA, Stares MD, Goulding D, Lawley TD: Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 2016, 533(7604):543-546.

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