IMG/M Spearheads Analysis into Human Microbial Communities

Within the body of a healthy adult, microbial cells are estimated to outnumber human cells by a factor of ten to one. These tiny organisms cover every surface and cavity of the human body, forming complex communities that help digest food, break down toxins and fight off diseases.

Now scientists will be able to gain valuable insights into how these microbial communities affect human health – with a grant from the National Institute of Health (NIH) and the Integrated Microbial Genomics with Microbiome Samples (IMGM) data management system developed by the Berkeley Lab’s Biological Management and Technology Center (BMTC), in conjunction with the Joint Genome Institute‘s (JGI) Genome Biology Program.

“IMG/M provides a powerful comparative analysis environment that will allow scientists to examine the collective genome, or DNA, of microbial communities, also known as metagenome, more efficiently,” says Nikos Kyrpides of the Genome Biology Program at the Department of Energy’s JGI in Walnut Creek, Calif.

“We live in a microbial world, there are millions of organisms in one drop of water and even more in soil. Life on our planet cannot be sustained without the microbes and the success of metagenomics will not only help us better understand human health, but may also help us address a variety of environmental challenges.”

Initially released in 2006, IMG/M was developed through a close collaboration of software engineers, computer scientists and biologists. Since then, the system has played a central role in helping scientists understanding metagenomes in a variety of environments. In one project, researchers used the system to learn how microbes in Seattle’s Lake Washington enable the oxidation of methane, methanol and methylated amines, which are compounds contributing to the greenhouse effect and the global carbon cycle.

The new grant will expand IMG/M’s capabilities to support the analysis of human metagenomic data as part of an endeavor to create a Data Analysis Coordination Center (DACC) for the Human Microbiome Project. The DACC will be a central repository for all human metagenomic data.

To understand how microbes affect human health and how they cause various diseases, researchers involved in the Human Microbiome Project will collect metagenome samples from different parts of the human body, on individuals with a variety of health conditions. They will them use IMG/M to analyze the metagenome datasets generated from these samples.

“In the sound of the word microbe, the average person thinks of a disease or a disaster. However, the vast majority of microbes are our friends,” said Kyrpides. “In fact entire microbial communities work in harmony with us to carry out essential functions, such as digestion in the human gut. When these communities are disturbed, people may get sick or catch infections.. Microbes have won every major battle on our planet except that of the good impressions.”

According to Kyrpides, the field of metagenomics is relatively new. Until a few years ago scientists studied individual microbes by growing them in laboratories, extracting their DNA, and then examining the sequence of their genes in order to understand the organism’s genetic makeup. While this approach was somewhat successful, he notes that it had substantial limitations because most microbes cannot be grown in laboratories. When scientists extract DNA from an entire microbiome sample containing potentially hundreds of different microbial species, they don’t know which individual organism the genes come from or the function these genes carry out in the context of the community.

“The IMG/M system is an invaluable tool in the quest of finding how communities function,” says Kyrpides. “The system allows us to analyze metagenomic datasets in the rich context of all available individual microbial genomes, and provides scientists with tools to compare and identify the functional capabilities of microbial communities.”

The principal investigator on the NIH grant is Dr. Owen White, of the Institute for Genome Sciences at the University of Maryland’s School of Medicine, Baltimore, Md. In addition to Kyrpides and Markowitz, other investigators include Dr. Gary Andersen of Berkeley Lab’s Earth Sciences Division, and Robin Knight of the Department of Chemistry and Biochemistry at the University of Colorado, Boulder, Colo.