Friday the 13th, 2016 was a lucky day for the field of microbiome science, human and environmental health. The National Microbiome Initiative (NMI) launched with more than $121 million being invested from U.S. Federal agencies into microbiome research. We are realizing that microbial ecology really runs our world and lives. So the NMI seeks to understand how microorganisms interact with other species and the environment to protect and restore healthy microbiomes.

The NMI is truly interdisciplinary and inclusive. What is unusual about the NMI is the intricate web of funding sources, both federal and private, the assortment of microbiomes to be studied and resources to be developed, and the diversity of people, from professional scientists to citizens doing the work. It is this web of different communities coming together for the common goal of understanding how microbiomes work that has stirred up so much excitement. It’s this cross-talk between such a diversity of people that I feel will rapidly advance the field of microbiome research in the next few years. The NMI has three main goals: 1) understand the “ground rules” for microbial interactions, 2) make new microbiome tools for analysis and sharing data, 3) educate the public, K-12, and college level students.

National Microbiome Imitative banner

Universal Microbial “Ground Rules”

To figure out the “ground rules”, the NMI will fund work on microbiomes in different places including soil, marine, plant, animal, and humans, instead of funding only a few large groups.We live in a microbial world. Microbes live in and on host plants and/or animals. Microbes are in our air, soil, and water (liquid and frozen) where they process nutrients for the ecosystem. Yet we do not fundamentally understand how these interactions work when they are healthy versus sick. Environmental changes like oil spills, fire, or agricultural run-off disturb ecosystems and microbial interactions. Sometimes these systems return quickly to their original healthy state. Sometimes they do not. Why? We see the same thing happen with people, other animals, and plants. Why are microbiomes resilient to some disturbances and not others? Comparing across very different systems and organisms may help answer these questions.

New Tools

Large projects such as the Human Microbiome Project (HMP) and Earth Microbiome Project (EMP) developed and continue to refine laboratory and computer tools for microbiome research. Standardization of lab and computer protocols is essential for comparing across microbiome systems and laboratories. Both the EMP and HMP have established such protocols. Tools such as QIIME, Site Painter, the MIxS standard for reporting information about a sample, and more allow anyone with access to the lab equipment and computer access to conduct their own work. Increasingly across the country, public libraries, maker spaces, and high school labs have this equipment. Bringing new minds with different needs, concerns, and backgrounds to the lab bench is what I am most excited about the NMI.

Strengthening Microbiome Research Collaborations

The beauty of the funding with the NMI is that it includes private partners. Partnerships between academic, government, private industry, and citizen scientists has the potential to more rapidly move new findings from bench to bedside or oceanside (in the case of oil spills). The HMP and EMP have led to new technologies that are used throughout the private and public sectors. From DNA sequencing methods to probiotics, new clinical and research applications have been developed. The human genome project is estimated to have generated ~$141 dollars of economic activity for each $1 invested. I’m certain microbiome related goods and services will be generated by this initiative. Currently, probiotics alone account for $1.3 billion dollars of sales, despite the relatively low benefit most probiotics currently on the supermarket shelves seem to provide. There is an increased interest in microbially based products, from skin to gut probiotics and infant formula to phage therapy. As with any product, there are good products out there and snake oil. It is promising that many reliable companies are partners with the NMI. In future posts, I’ll begin introducing some of those companies and the science behind them. The first interview is with Martha Carlin of The BioCollective. A marketing professional turned citizen scientist, Martha started TBC to make microbiome sampling more affordable and return a portion of any profit made from any discoveries made from your poop sample!


Sketch of a three leaf clover with each leaf corresponding to different aspects of the proposed NMI.
The U.S. National Microbiome Initiative will support microbiome research.

Small Investment, Large Returns

Honestly, from a government budget standpoint, $121 million for two years across both the National Science Foundation and National Institute of Health isn’t really that much money for something that affects us all. The human genome project, the project to sequence the first human genome, cost $2.7 in the end ($300 million UNDER budget!). $115 million was invested in only studying the human microbiome project for the first five years. Compare that to the National Institutes of Health’s expenses in 2015 of $298 on brain cancer (affecting 0.1% of the US population), $349 million dollars for lung cancer (0.3% of U.S. population), or $616 for liver disease (1.4% of U.S. population). Of course, spending money on these diseases is important! I have or have lost a family member with all of these diseases, but from a population standpoint, these diseases affect very few people. Microbes influencing not only human but also environmental health – such as cleaning up oil spills or super fund sites or recycling nitrogen for plants and animals, $121 is an investment that we all will benefit from.

For more information on the National Microbiome Initiative read the NMI proposal released by the White House or read my tweets and those of others watching the NMI unveiling live using the twitter hashtag #NMI.

What Do You Think?