Without microorganisms, we would not and could not exist
More than three billion years ago, cyanobacteria provided Earth’s atmosphere with enough oxygen to allow us humans to thrive. Ever since, these and other microorganisms have been shaping our lives. They provide fertile soils, break down pollutants, supply us with energy and digest the food in our guts. But despite these and many other crucial roles, we know only little about most microorganisms, their interactions and their functions.
„This must change“, says Nicole Dubilier of the Max Planck Institute for Marine Microbiology in Bremen, Germany, „particularly in view of the tremendous challenges we face in the 21st century. We need to gain a comprehensive understanding of our planet's microorganisms, and this can only be achieved through a global research initiative.”
Creating and sharing genomic data effectively
Dubilier refers to a call in this week’s Science magazine for a US-based Unified Microbiome Initiative (UMI). For Dubilier and her co-authors Margaret McFall-Ngai of the Pacific Biosciences Research Center in Hawaii and Liping Zhao of Shanghai Jiao Tong University in China, this initiative falls short of the mark. In a comment published this week in Nature, they call for an International Microbiome Initiative (IMI) that reaches beyond US borders. Like an umbrella organisation it would embrace and unite national research efforts.
These calls for microbiome initiatives are fuelled by the revolutionary findings that recent DNA-sequencing technology has revealed. The information gained in the last decade has skyrocketed due to the low costs of high-throughput sequencing, advances in sample preparation, progress in computational power and the development of sophisticated bioinformatic tools that make sense of sequence data.
This quantum leap in our ability to analyse our planet's microbial communities has led to the discovery of life forms and communities we had no idea existed until recently. For example, analyses of the human microbiome, that is all the microorganisms on and in the human body, have revealed that we are colonized by as many as 10 000 bacterial species that influence every part of life from our digestion to our emotions.
One of the main problems of genomic research is that many studies cannot be compared because of differences in the way samples were taken and the data was analysed. For example, depending on the software packages that are used to analyse the sequence data, the number of bacterial species within the exact same dataset can vary by several orders of magnitude. Only a joint effort such as the proposed IMI can develop comprehensive standards that all future studies can abide by. “This would allow us to pool all the numerous individual studies into a universal dataset, which could be accessed by scientists across the globe”, Dubilier explains.
International and interdisciplinary
To make an IMI successful, science must overcome more than just national borders. “We must also learn to think beyond our own disciplines and communicate with scientists from other research fields”, write Dubilier and her co-authors. “We need mathematicians and informaticians to help us tease apart meaningful information from the mountains of sequence data. Chemists, physicists and engineers are needed to help develop new methods and instruments that will allow us to understand how microbes interact with each other and their environment.”
Generating more and more sequence data is not enough. „We are now realizing how essential – and time consuming – it is to go beyond just cataloguing microorganisms" says Dubilier. „But only then we will be able to gain a deeper understanding of the role that microorganisms play in providing essential ecological, social and economical services to humankind.”
Understand and use sustainably
An initiative such as the IMI could pave the way for a comprehensive understanding of our planet’s microbiome. This understanding will be critical for solving many of today’s challenges such as environmental degradation, climate change, population growth, or the need for alternative energy sources. Moreover, an IMI would be able to ensure that data and knowledge is made available to countries that may not have the funds to invest in their own global-scale projects.
It is critical that the IMI is launched quickly, Dubilier and her colleagues write. Before national initiatives such as the current US call are well underway, IMI’s common guidelines and targets should be discussed and agreed upon to form a common framework for national initiatives. „Otherwise we run the risk of repeating past mistakes”, says Dubilier. “Furthermore, an international initiative would be able to bring together the best experts from around the world and across all disciplines and provide them with the opportunity to work together on common goals.”
The scientists call on public agencies as well as private foundations to support and help finance the IMI. „So much can be gained by an international, interdisciplinary and concerted effort to create an IMI, while nothing is lost to national initiatives. On the contrary, more uncoordinated national microbiome programmes will almost certainly waste research efforts and taxpayers’ money. Let’s transcend national silos and gain universal insights that will benefit all humankind“, write Dubilier and her colleagues.
The microbial biome is the community of microorganisms in a given environment. The environment can be the human gut, humans as a whole, a sample of soil, the world’s oceans, or the entire planet Earth.
One initiative, four goals:
Dubilier and her colleagues suggest four goals of the IMI:
Guidelines: Set standards for methods, data analysis, data sharing and intellectual property rights and ensure their implementation.
Priorities: Develop a common research agenda that will allow comparative analyses at local to global scales.
Tools: Identify new cross-disciplinary methods for microbiome studies.
Forums: Establish platforms for the discussion and exchange of research within and between nations, develop training programmes for future scientists and outreach projects.
The need for common standards in genomic research is well recognised. The Genomic Standards Consortium (GSC), for example, which is also supported by the Max Planck Institute for Marine Microbiology, calls for common standards in the description of genomes and the exchange and integration of genomic data.
Original publication in Nature:
Nicole Dubilier, Margaret McFall-Mgai and Liping Zhao (2015): Create a global microbiome effort. Nature 529 (631-634).
Publication in Science:
A. P. Alivisatos, M. J. Blaser, E. L. Brodie, M. Chun, J. L. Dangl, T. J. Donohue, P. C. Dorrestein, J. A Gilbert, J. L. Green, J. K. Jansson, R. Knight, M. E. Maxon, M. J. McFall-Ngai, J. F. Miller, K. S. Pollard, E. G. Ruby, S. A. Taha, Unified Microbiome Initiative Consortium (2015): A unified initiative to harness Earth’s microbiomes. Science 350 (503-504).
Prof. Dr. Nicole Dubilier
Tel.: +49 421 2028 932
Dr. Fanni Aspetsberger
Tel.: +49 421 2028 645
Dr. Manfred Schlösser
Tel.: +49 421 2028 704
In this week’s edition of „Nature“, Nicole Dubilier from the Max Planck Institute in Bremen, Germany, joins forces with colleagues from Hawaii and China to call for a combined and global exploration of the Earth’s microbes.
Dr. Fanni Aspetsberger | Max-Planck-Institut für marine Mikrobiologie
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