Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Berkeley Lab scientists help define the healthy human microbiome

14.06.2012
Computing, bioinformatics and microbial ecology resources play key role in mapping our microbial make-up

You're outnumbered. There are ten times as many microbial cells in you as there are your own cells.

The human microbiome—as scientists call the communities of microorganisms that inhabit your skin, mouth, gut, and other parts of your body by the trillions—plays a fundamental role in keeping you healthy. These communities are also thought to cause disease when they're perturbed. But our microbiome's exact function, good and bad, is poorly understood. That could change.

A National Institutes of Health (NIH)-organized consortium that includes scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) has for the first time mapped the normal microbial make-up of healthy humans.

The research will help scientists understand how our microbiome carries out vital tasks such as supporting our immune system and helping us digest food. It'll also shed light on our microbiome's role in diseases such as ulcerative colitis, Crohn's disease, and psoriasis, to name a few.

In several scientific reports published June 14 in Nature and in journals of the Public Library of Science, about 200 members of the Human Microbiome Project (HMP) Consortium from nearly 80 research institutions report on five years of research.

Berkeley Lab's role in mapping the human microbiome revolves around big data, both analyzing it and making it available for scientists to use worldwide.

3.5 terabases of data

HMP researchers sampled 242 healthy U.S. volunteers (129 male, 113 female), collecting tissues from 15 body sites in men and 18 body sites in women. Researchers collected up to three samples from each volunteer at sites such as the mouth, nose, skin, and lower intestine. The microbial communities in each body site can be as different as the microbes in the Amazon Rainforest versus the Sahara Desert.

Researchers then purified all human and microbial DNA in more than 5,000 samples and ran them through DNA sequencing machines. The result is about 3.5 terabases of genome sequence data. A terabase is one trillion subunits of DNA.

A comparative analysis system for studying human microbiome samples

Berkeley Lab scientists developed and maintain a comparative analysis system called the Integrated Microbial Genomes and Metagenomes for the Human Microbiome Project (IMG/M HMP). It allows scientists to study the human microbiome samples within the context of reference genomes of individual microbes. Reference genomes help scientists identify the microbes in a sample.

This system is a "data mart" of the larger IMG/M data warehouse that supports the analysis of microbial community genomes at the Department of Energy's Joint Genome Institute (JGI). IMG/M contains thousands of genomes and metagenome samples with billions of genes. A metagenome consists of the aggregate genomes of all the organisms in a microbial community.

"The IMG/M HMP data mart will help scientists advance our understanding of the human microbiome," says molecular biologist Nikos Kyrpides of Berkeley Lab's Genomics Division, who heads the Microbial Genome and Metagenome Programs at JGI. "Scientists can access HMP data with a click of a button and conduct comparative analyses of datasets."

Kyrpides is also a co-principal investigator of HMP's Data Analysis and Coordination Center (DACC), together with Victor Markowitz, who heads Berkeley Lab's Biological Data Management and Technology Center (BDMTC) in the Computational Research Division. Markowitz oversees the development and maintenance of the IMG/M system by BDMTC staff.

"Our system enables scientists worldwide to access and analyze the metagenome datasets generated by NIH's Human Microbiome Project. We plan to add to our system metagenome datasets generated by similar projects in Europe, Canada and Asia, and thus greatly enhance its comparative analysis potential," says Markowitz.

A job for high-performance computing

The computation involved in the metagenome data integration underlying IMG/M HMP was partly carried out at the Department of Energy's National Energy Research Scientific Computing Center (NERSC), which is located at Berkeley Lab. The Energy Sciences Network (ESnet), a high-speed network serving thousands of scientists worldwide that is hosted at Berkeley Lab, was instrumental in transferring the HMP datasets.

Two million computer hours were allocated on NERSC to carry out HMP data integration as well as sift through HMP data for 16S ribosomal RNA genes, which can be used to identify individual species. Focusing on this microbial signature allowed HMP researchers to subtract the human genome sequences and analyze only bacterial DNA.

The analysis helped scientists determine the diversity of microbial species within a person, including within different body sites in a person. It also revealed the extent to which microbial communities vary between people.

"The results suggest that each person has a relatively stable microbiome that is unique to them. You have your own personal microbiome," says Janet Jansson, a microbial ecologist in Berkeley Lab's Earth Sciences Division.

In addition, while scientists had previously isolated only a few hundred bacterial species from the body, HMP researchers now calculate that more than 10,000 species occupy the human ecosystem.

What's next?

"Now that we have a good idea of what makes up the healthy human microbiome, we can study what happens when it's perturbed because of disease, drugs, or diet," says Jansson,

In Jansson's lab, for example, scientists study the role of the gut microbiome in Crohn's disease, which is an inflammatory bowel disease. Changes in the composition or function of the trillions of microbes inhabiting the human intestine are associated with numerous diseases such as Crohn's. Understanding the factors underlying these changes will help researchers develop therapies to fight these diseases.

Similar research is also underway at other research centers. Scientists are using HMP data to study the nasal microbiome of children with unexplained fevers. They're also exploring how the vaginal microbiome undergoes a dramatic shift in bacterial species in preparation for birth, characterized by decreased species diversity.

Other Berkeley Lab researchers with prominent roles in the HMP include Gary Andersen, Shane Canon, and Konstantinos Liolios.

The Human Microbiome Project, launched in 2007, received $153 million from the NIH Common Fund, a trans-NIH initiative that finances high-impact, large-scale research. It is managed by the National Human Genome Research Institute, in partnership with the NIH Office of the Director, the National Institute of Allergy and Infectious Diseases, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Cancer Institute, National Institute of Dental and Craniofacial Research, and National Institute of Diabetes and Digestive and Kidney Diseases, all part of NIH.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy's Office of Science. For more, visit www.lbl.gov.

Dan Krotz | EurekAlert!
Further information:
http://www.lbl.gov

More articles from Life Sciences:

nachricht How do muscles know what time it is?
21.08.2018 | Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt

nachricht A novel synthetic antibody enables conditional “protein knockdown” in vertebrates
20.08.2018 | Technische Universität Dresden

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: It’s All in the Mix: Jülich Researchers are Developing Fast-Charging Solid-State Batteries

There are currently great hopes for solid-state batteries. They contain no liquid parts that could leak or catch fire. For this reason, they do not require cooling and are considered to be much safer, more reliable, and longer lasting than traditional lithium-ion batteries. Jülich scientists have now introduced a new concept that allows currents up to ten times greater during charging and discharging than previously described in the literature. The improvement was achieved by a “clever” choice of materials with a focus on consistently good compatibility. All components were made from phosphate compounds, which are well matched both chemically and mechanically.

The low current is considered one of the biggest hurdles in the development of solid-state batteries. It is the reason why the batteries take a relatively long...

Im Focus: Color effects from transparent 3D-printed nanostructures

New design tool automatically creates nanostructure 3D-print templates for user-given colors
Scientists present work at prestigious SIGGRAPH conference

Most of the objects we see are colored by pigments, but using pigments has disadvantages: such colors can fade, industrial pigments are often toxic, and...

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

LaserForum 2018 deals with 3D production of components

17.08.2018 | Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

 
Latest News

A materials scientist’s dream come true

21.08.2018 | Materials Sciences

Quantum bugs, meet your new swatter

20.08.2018 | Information Technology

A novel synthetic antibody enables conditional “protein knockdown” in vertebrates

20.08.2018 | Life Sciences

VideoLinks
Science & Research
Overview of more VideoLinks >>>