Research Initiatives Around the Microbiome

Bonnie Feldman, Digital Health Analyst & Bus Development Consultant

What does a “healthy” microbiome look like? Who is part of a microbiome? How can we quantify and analyze our microbiome?


The Human Microbiome Project (HMP), a $173 million project by the NIH, was initiated to address these questions. It focuses on a comprehensive characterization of the human microbiome and the development of computational tools for the analysis of microbiome data. In 2012, NIH announced the first referenced data of a normal bacterial makeup in healthy individuals. Tissue samples from different body sites of 242 people were collected and sequenced to understand the structure and diversity of the healthy human microbiome. Scientists found that the microbiome contains 360 times more microbial genes than human genes that are involved in vital metabolic functions like digestion or the production of anti-inflammatories. Read the original article published in Nature to find out more.

The American Gut project follows another approach. Rather than carefully selecting test subjects, the founders wanted to involve the national and international public. So far, several thousand people have followed their call. If interested, you can still join the American Gut project!

Earlier this month, American Gut published preliminary results for more than 3,000 participants which described microbial composition and factors that affected the gut habitat, such as age and diet.

Individual Findings- Lone Fighters

Large studies are not necessary to contribute to the understanding of our microflora.Larry Smarr gathered information from blood and stool samples that showed early signs of the disease process, years before the first detectable symptoms of his late onset Crohn’s disease.

In another self experiment, Jeff Leach, founder of the Human Food Project and collaborator of American Gut, studies the effects of various dietary patterns on his gut microbiota.

And lots of unanswered questions

The research on the human microbiome is just getting started. Although important steps have been made towards defining the human microbiome and its role in diseases, many questions remain to be answered. Are associations with health and disease causal?How can this newly generated knowledge contribute to the development of interventions? In which diseases does the microbiome play a causal role?

Group Findings

A few years earlier, in 2012, an NIH press release announced the definition of a normal bacterial makeup in healthy individuals. This provides a much needed reference in order to study the role of the microbiome in diseases. This research article by Bäckhed et al.  elaborates on how understanding the properties of healthy microbiota could contribute to the development of interventions. The results of HMP have implications for other research fields such as epidemiology, as described by Foxman and Rosenthal.

Although science has provided important insights into the role of the microbiome in some diseases, it is still unclear whether these relationships are causal.

Next time you look at a fellow human, pretend to be Neo from The Matrix, only try to see the trillion cells and around 23,000 genes that make up his or her body. Then, take a second look and try to imagine that the microbes within his or her body outnumber the human cells by a factor of 10.

Stay with us to find out in the next post, how scientists deal with this vast amount of information that would blow even Neo’s mind.

What questions would you like to learn more about next?

First posted on Dr Bonnie 360 7/24/2014

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As principal of DrBonnie360, Bonnie Feldman, DDS, MBA brings a triple lens to her consulting, writing and speaking- that of an entrepreneurial dentist, a Wall Street analyst and a digital health analyst and consultant. Most recently, she has interviewed more than 200 digital health companies, while attending more than 50 meetings, always asking the question of how new digital tools and data help us each of us. Her research on “Big Data in Healthcare Hype and Hope” has been enjoyed by over 50,000 global professionals. Her work has been featured in O’Reilly Strata, Greatist and Forbes. She has been an invited speaker at the Stanford Medicine X, Bio-IT, Data to Drugs to Diagnostics, StrataRx, the Burrill Digital Health Conference, Games for Health, the Center for Connected Health, the Nye Collaborative Digital Health Summit, and the mHealth Summit. Her latest research has uncovered a large and growing need in the autoimmune community to apply new data and digital tools to improve treatment. She welcomes collaborative partners in this initiative.