by Eryn Blass
figures by Michael Gerhardt

Microbes are everywhere – in our environment, on our skin, and even within our bodies. Microbes, short for microorganisms, are living things so tiny that they can only be seen with a microscope. Microbes consist of bacteria, archaea, fungi, protozoans, and viruses (Figure 1). The communities that they form are called microbiomes. The mere thought of these microscopic creatures on our bodies makes people cringe. Yes, there are many bad microbes that make us sick and well warrant that bad reputation, but there are also some that have a beneficial role that we wouldn’t be able to live without.

Figure 1: The different types of microbes have distinct characteristics that distinguish them from one another. The differences in the microbes lie in the presence of central storage space for their DNA (nucleus), if and what type of wall surrounds their cell (cell wall), and whether they are a living thing and can reproduce themselves.
Figure 1: The different types of microbes have distinct characteristics that distinguish them from one another. The differences in the microbes lie in the presence of central storage space for their DNA (nucleus), if and what type of wall surrounds their cell (cell wall), and whether they are a living thing and can reproduce themselves.

There is still a lot we have to learn about our microscopic friends. Their importance in our daily lives motivated the White House Office of Science and Technology Policy (OSTP) to announce the National Microbiome Initiative (NMI) in May 2016 to learn more about how microbiomes influence our lives and world around us. This initiative will bring forth new projects and collaborative ventures amongst public and private sectors to foster better understanding in how diverse microbiomes influence our health, climate, food, and environment. These studies will inform us as to what comprises a healthy microbiome, and potentially how we can manipulate them to improve health, food production, and our environment.

What we’ve already learned

Microbiomes exist nearly everywhere on the planet. Human bodies house many microbial communities, both on us and inside us. There is a rich microbiome that lives within our gut, which helps us digest food and absorb nutrients. The National Institutes of Health (NIH) established the Human Microbiome Project in 2008 to deeper probe the human microbiome. Amongst many things, this project worked on identifying microbes at different parts of the human body to elucidate our microbial flora, and better understand how they can intertwine with human disease. Our diets, environments, and the medication we take can influence our microbiomes. Preliminary studies have observed differences in the microbiome in diseases such as obesity, diabetes, among others. Although these prior observations have been made, it is not known whether a change in the microbiota leads to disease or whether the microbiota changes as a result of the disease – thus more research is needed. Therefore delving deeper beyond observation and investigating how these microbiomes are changing in disease states will help determine how they may play a role and how we can intervene in these microbial communities to ameliorate disease.

Looking beyond the human body, other scientists have been evaluating the environmental microbiome. There are many bacteria and fungi that live in soil where they help provide many nutrients to plants and other organisms that have important agricultural and ecological implications. The 10-year Joint Microbial Sequencing Program project established by the National Science Foundation (NSF) and the Department of Agriculture (USDA) sequenced ecological and agricultural microbiomes. The Agricultural Research Service section of the USDA additionally investigated the role of the plant and soil microbiomes in crop production and soil conditions. The ocean microbiome has also been under investigation and has great diversity. In fact, marine microbes comprise roughly half of the world’s primary producers since they are able to harness various sources of energy for incorporation into the food chain.

Among all this effort, there are still many unknowns and questions in the microbiome field that need to be addressed. What does a healthy microbiome look like? What does an imbalanced microbiome look like, and how does this affect us? How can we move the basic descriptive work on the microbiome into applications to benefit human health, agriculture, or industry? Can we develop better tools? Can we standardize data collection and develop databases to better share data?

What we hope to learn

With these open questions, many scientists felt the need for an organized microbiome effort. Late last year two groups of scientists penned letters, published in Science and Nature, calling for a collective and systemized initiative to study the diverse array of microbiomes. Here is where the newly proposed National Microbiome Initiative (NMI) comes in: the main goals of this initiative are to support interdisciplinary research, to develop new technologies for investigation and application of microbiome-based discoveries, and to garner a collective group of people to work on these numerous projects. Federal government agencies propose to invest $121 million over the next two years, while numerous non-profit agencies, academic institutions, and companies are pledging over $400 million. Collectively, over 100 groups will participate in this effort.

The NMI will work to support interdisciplinary research in order to foster collaboration across different disciplines. Many groups in both the public and private sectors will work towards developing new research centers, funding opportunities, and support collaboration. One focus will be the human microbiome, such as understanding the role of the microbiome in malnutrition, in neurological diseases, and their influence in the development of type I diabetes, to name a few. Some will investigate environmental microbiomes, including those of oceans, plants, and even tropical forests. The role of soil microbes in crop production in Africa will also be under study with the hope to ameliorate malnutrition. Other groups will work on the question of how to best use microbes in industrial work processes such as water treatment, petroleum and others. The USDA will also evaluate the microbiomes’ influence on food production in livestock, fish, and the agricultural environment.

Fostering collaboration amongst different groups is critical. To take microbiome research to the next level of depth, many groups will work on developing new technologies. This includes developing techniques to study the microbiome at the nanoscale, performing sequencing and genomic profiling, and creating a public portal for sharing microbiome data. Others will develop tools. For example the biotech company C3 Jian will work on developing antimicrobial peptides that target specific microbes. This technology could be applied for chronic diseases if it could be a result of a microbiome imbalance, or even replace the use of antibiotics.

The final critical factor for generating data: man power. Many groups will help expand work on the microbiome by funding new faculty who will focus on their area of research. Others will help develop educational courses, research experiences, or interdisciplinary doctoral training programs. Seminars and workshops will help foster collaboration between different scientific disciplines.

The microbe future

We know quite a lot about different microbes, where we could find them, and how some of them might make us sick. Much work has been devoted to describing the microbiome of many different ecological niches and diseases. Although we still need to uncover more about the diversity of microbes around us, new studies will be increasingly focusing on how the play roles in disease states and how we can manipulate these microscopic communities to better our health and the world.

Eryn Blass is a Ph.D. candidate in Virology at Harvard University.

For more information:

Read more about the research groups involved in the NMI read here.
To learn more about the different microbes check out this link.
To read a SITN article on how bacteria can generate biofuels check out this link.

Cover image. E. coli from CDC public health image collection (taken by NIAID).

One thought on “The National Microbiome Initiative: fueling the discovery of the microscopic world around us

  1. As someone who has been reading about the role of probiotics/ the microbiome for years, it is incredibly exciting to hear that the government is acting as a catalyst to blowing this field wide open. I applaud Jose Carlos Gutierrez-Ramos for taking a leadership role at Synlogix and at the White House. Exciting times.

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