The Microbiome

Microbiome Research Tools

Led by the ASM, and carried out in partnership with the American Chemical Society (ACS) and American Physical Society (APS), The Kavli Foundation has committed $1 million dollars to the Kavli Microbiome Ideas Challenge.

This Ideas Challenge recognizes the need for an interdisciplinary approach to microbiome research and invites the broad scientific community to submit their ideas for novel experimental tools and methods aimed at understanding microbial interactions and function from new perspectives.

Submissions for the Kavli Ideas Challenge closed December 2nd, 2016 at 11:59 PM CST. Winners will be announced in April 2017.

To read the full press release, visit:

White House Announces National Microbiome Initiative; Foundation Establishes Ideas Challenge

The White House Office of Science and Technology Policy (OSTP), in collaboration with Federal agencies and private-sector stakeholders, has announced a new National Microbiome Initiative (NMI) to foster the integrated study of microbiomes across different ecosystems. Read press release.  In support of this initiative, The Kavli Foundation has committed $1 million to a Kavli Microbiome Ideas Challenge supporting development of next generation scientific tools for investigating life on a microbial scale. The Kavli Microbiome Ideas Challenge will be led by the American Society for Microbiology, and carried out in partnership with the American Chemical Society and American Physical Society. Read press release.

The Microbiome

Our planet teems with microorganisms such as bacteria, archaea, viruses, fungi and algae that have evolved with their hosts over millions of years. The human body alone is estimated to contain as many microbes as human cells—about 40 trillion according to new estimates; and a few grams of soil may contain tens or even hundreds of thousands of microbial species. The complex communities these organisms form are called "microbiomes." Each of them—from the human gut microbiome to the soil's; and from the ocean's to the atmosphere's—is distinct, made up of organisms that are uniquely adapted to that environment. Most of these microbes perform functions that are beneficial, even essential. Of course, sometimes they are harmful. A key goal of microbiome research is to understand the interplay between helpful and harmful microorganisms and the factors that control this delicate balance. Learn more

About a Unified Microbiome Initiative

Enterococcus bacteriumThe bacterium, Enterococcus faecalis, is one of many commensal microbes that live in the human gut (Credit: USDA)

In October 2015, a diverse group of scientists in the United States and abroad called for a global effort to better understand microbiomes, or communities of microorganisms. Microbes are not just passive bystanders in a given environment but are essential to many life processes. In humans, for example, they synthesize vitamins, aid digestion and fine tune the immune system; in the soil, they make essential nutrients and destroy toxins. The group of scientists who issued the call for a "Unified Microbiome Project" proposed a large-scale, public and private initiative to advance the science of microbiomes through the development of new research tools and interdisciplinary collaborations. The long-term goal of such an effort is to be able to harness the power of microbial communities to improve human health and the health of the planet. Learn more

The Science Behind the Microbiome

New Tree of LifeThis is an expanded view of the tree of life, showing that bacteria make up two-thirds of all Earth's biodiversity, half of that from uncultivable bacteria called 'candidate phyla radiation.' The Archaea and eukaryotes, which includes humans, makes up another third. The red dots represent lineages that cannot, at present, be isolated and grown in the lab. (Credit: Jill Banfield, UC Berkeley, and Laura Hug, University of Waterloo)

Traditionally, researchers have studied individual microbial species in isolation. However, most microbes can’t be grown in a laboratory so our view of the microbial world has been limited. Fortunately, recent advances in DNA sequencing technologies and other molecular techniques have provided new ways of looking at microbial communities. This has led to an explosion of knowledge about microbiomes, as scientists use these tools to catalog the stunning diversity of species that inhabit the planet and study their genes. Their discoveries are rewriting biology: For example, the number of bacteria phyla, or groups of related lifeforms, has expanded from 35 to nearly 1,000 in recent years. (By comparison, all multicellular animals in the world comprise only a few dozen phyla.) These catalogs provide a baseline for understanding how microbiomes change over time—in health and disease—and how microbiomes respond to different factors such as diet and climate.

The future of microbiome research will be understanding the full suite of functions that microbes perform, how they influence each other and their environment, and how this power can be harnessed to improve human health and the environment. Meeting these goals will require advances in biology and nanoscience. Indeed, the nanoscale is the scale of biological function, and technologies built at that scale will be essential to image, sense and manipulate microoganisms. Learn more

The Kavli Foundation and the Microbiome

The Kavli Foundation supports fundamental research into science at the atomic scale at five Kavli Nanoscience Institutes, including the work of nanoscientists developing new tools, materials and approaches to probe the world at very small scales. Starting in December 2014, The White House Office of Science and Technology Policy and The Kavli Foundation separately convened a series of coordinated meetings on the microbiome. The meetings focused on identifying challenges and opportunities in microbiome research and on developing strategic recommendations for accelerating discovery. These meetings culminated in a roadmap for accelerating discovery in the field: the Unified Microbiome Initiative proposal. Learn more

Selected News Stories

Submit your ideas for groundbreaking experimental tools and methods for understanding microbial function.

The Kavli Microbiome Ideas Challenge will provide $1 million in grants for innovative tools to investigate how microbes live in complex communities. Three scientists - Tim Donohue, Julie Biteen and Terry Hwa - discuss why it matters.

Public-private initiative aims foster the integrated study of microbiomes across different ecosystems.

The $1-million science competition will support the development of scientific tools for investigating life on a microbial scale.

In this live webcast, three of the scientists behind The Unified Microbiome Initiative proposal—Janet Jansson, Rob Knight and Jeff Miller—discuss how to unlock the power of the microbial communities that shape our world and influence our health.