Microbiology: Create a global microbiome effort

Microbes have been discovered on Earth, from the boiling waters of Yellowstone’s hot springs in Wyoming to the cold, dark Antarctic lakes under 800 meters of ice. A holistic understanding of the role of Earth’s microbial community and its genome – its microbiome – in the biosphere and human health is key to addressing the many challenges facing humanity in the twenty-first century, from energy to transition.

Recognizing this, a group of prominent US scientists this week proposed the creation of an Integrated Microbiome Initiative (UMI). UMI will bring together researchers and representatives from public and private agencies and foundations to study the activities of Earth’s microbial ecosystems.

UMI is conceived as an American initiative; Originated from meetings sponsored by the White House Office of Science and Technology Policy and the Kavli Foundation of Oxnard, Calif. But the Earth’s biome is not defined by national boundaries, and efforts to uncover its secrets must be global.

We believe that to be successful, microbiome research will require a coordinated effort across the international community of biologists, chemists, geologists, mathematicians, physicists, computer scientists and clinical experts. As three scientists working in three countries – Germany, China and the United States – we call for an International Microbiome Initiative (IMI), supported by funding agencies and foundations around the world, in addition to UMI. This will ensure the sharing of standards across borders and disciplines, and harmonize the multitude of microbiome initiatives that exist.

Microbial Revolution

Science is only realizing the absolute importance of the microcosm. This is thanks to developments such as low-cost high-throughput sequencing; Advances in sample preparation that allow researchers to sequence genomes from individual cells as well as from microbial communities; Improvements in computing power and imaging technologies; and the development of bioinformatics tools to help make sense of the data.

Thus biologists are gaining insight into the identity and function of microbes that cannot be grown in the laboratory – the vast majority of Earth’s microbiome. Currently only 35 bacterial and archaeal phyla are recognized based on the classical approach to microbial taxonomy. Sequencing efforts over the years have pushed the number closer to 1,000 (Reference 2).

Newfound groups of bacteria are calling into question old assumptions about the tree of life, and revealing vast holes in our understanding of the planet’s biosphere and its evolution. The discovery in 2003 of giant viruses containing hundreds or thousands of genes broke the current definition of living organisms. (Viruses were long thought to straddle the line between living and non-living things, due to their excessive reliance on host genes.)

It is also becoming increasingly clear that microorganisms provide ecosystem services that are critical to local and global sustainability. The microbiota provides nitrogen, phosphorus and other essential nutrients in crops, trees and other plants and in the soil in which they grow.

They break down pollutants and suppress the activity of pathogenic microbes. Recognizing the untapped power of the soil and plant microbiome in increasing agricultural productivity, companies such as Monsanto are investing millions of dollars in research and development in this area.

Microorganisms in the oceans produce 50% of the oxygen we breathe, and – through photosynthesis – remove roughly the same proportion of carbon dioxide from the atmosphere. They also remove up to 90% of the methane from the world’s oceans. Over the past decade, research cruises such as Tara Oceans and the Global Ocean Sampling Expedition have sampled, sequenced and analyzed ocean microorganisms.

These have provided insight into the role of marine bacteria, archaea, viruses and eukaryotic microbes as global primary producers that provide nutrition at the base of the food chain; remineralization (conversion of organic molecules into inorganic forms); and carbon deposition on the ocean floor.

Some of the most profound insights into the vital role of microbes for human well-being have emerged from the analysis of microbes in and in our bodies – their genomes, transcriptomes, proteomes and metabolomes. (These are analyzes of genes, RNA molecules, proteins and chemical metabolites). For example, complex gut communities protect us from disease, provide nutrition and influence our development even before birth.

blocks

There are two major obstacles to advancing our understanding of the role of microbes in the biosphere. The first is the fragmentation of the life-sciences sector. Second, there is a lack of coordination between the various ongoing microbiome research efforts.

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