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Bedside to bench: Defining the normal human microbiome required many talents

Dr. James Versalovic, professor of pathology & immunology, pediatrics, molecular and human genetics, molecular virology and microbiology and director of the Texas Children's Microbiome Center, talks about the project.

We are not alone. The bacteria, fungi and other microorganisms that inhabit various parts of our body outnumber our cells 10 to 1. However, defining these organisms and understanding how they contribute to our existence requires a host of different experts – physicians, scientists and physician-scientists who can gather and analyze data in quantities unimaginable just 10 years ago.

The Human Microbiome Project, funded through the National Institutes of Health Common Fund, in which Baylor College of Medicine, the Baylor Human Genome Sequencing Center and the Alkek Center for Metagenomics and Microbiome Research at BCM played major roles, took a giant step toward realizing that goal with the publication of two reports in the journal Nature and a host of companion papers in the PLoS open-access journals. The papers present a framework for carrying out similar studies in ways that would make the data comparable and they also present the most complete picture to date of the human microbiome in the Western world.

"This is like discovering a forgotten organ," said Dr. James Versalovic, professor of pathology & immunology, pediatrics, molecular and human genetics, molecular virology and microbiology and director of the Texas Children's Microbiome Center. Versalovic coordinated the body sampling efforts in Houston and St. Louis.

"It's as though we had the heart there and are just getting around to figuring it out. The human microbiome is an organ and we have just started to understand its importance and function, even though it has always been a part of humanity."

Major findings

The reports in Nature focus on information from the first 242 healthy, normal subjects who took part in the studies (a total of 300 were recruited). The data about their microbiomes provide important insights into the interplay of human and microbial cells in human beings.

"It's a roadmap," said Dr. Wendy Keitel, professor of molecular virology and microbiology and medicine – infectious diseases at BCM. She was the principal investigator of the sampling part of the BCM microbiome projects. "It's the beginning of exploring new worlds because of the distinct clustering of communities at body sites."

The major findings include:

  • Marked differences among even these healthy adults in the bacteria that inhabit their guts, skin and vagina – diversity that is yet to be explained.
  • The fact that the microbes on skin and in intestine, mouth and vagina are different and these communities of bacteria do not seem to mix.
  • Other than two common disease-causing microbes (Staphylococcus aureus and Escherichia coli), the surprising absence of known pathogens from the microbiota of these healthy individuals.
  • This suggests that people acquire illness-causing bacteria from other sources.
  • That the bacteria of the microbiome contribute genes that are important in carrying out functions essential to human life, although different bacteria may carry out the same functions in different people.
  • For example, there are bacteria in the gut that help digest food, but they may not be the same bacteria in each individual.

A common microbiome?

Dr. Joseph Petrosino, director of the Alkek Center for Metagenomics and Microbiome Studies and co-principal investigator, talks about the project and how it, along with generous contributions, led to the Alkek Center for Metagenomics & Microbiome Studies.

"Is there a core or common microbiome found in everyone?" asked Dr. Joseph Petrosino, director of the Alkek Center for Metagenomics and Microbiome Studies at BCM and co-principal investigator of the BCM team on this project.

"I think the accumulating data, greatly impacted by the Human Microbiome Project, indicate that rather than a core microbiome, we as humans have a continuous distribution of organisms that colonize the various niches of the human body. The presence and relative abundance of each microbe is related to how host genetics impact the microbiome and vice versa."

"This study clearly demonstrates that despite how much our microbiome varies from person to person in terms of the organisms that are present, we are very much similar when it comes to the functions of the genes encoded by these organisms," he said. For example, the gastrointestinal tract microbiome of one person may contain 90 percent of a particular organism while that of someone else may have only 10 percent of that same strain.

Building mock bacterial communities

Dr. Sarah Highlander, associate professor of molecular virology & microbiology, a co-principal investigator of the project, discusses developing mock communities of bacterial DNAs for testing some of the sequencing and computer analysis methods.

Dr. Sarah Highlander, associate professor of molecular virology and microbiology at BCM and a co-principal investigator of the project, developed mock communities of bacterial DNAs as a method for testing some of the sequencing and computer analysis methods used to characterize the human samples.

Her mock communities served as mini-surrogates for the human studies and helped fine-tune the bioinformatics used in the process to reduce the risk of overestimation of microbial diversity in the samples. She was also involved in the generation of 190 of the 800 bacterial reference genome sequences that formed a database to map sequences obtained from the human samples.

"This project has pushed the field forward in a huge way," she said. "I think that one thing that will come from this is a new appreciation of human nutrition and how we can best ‘feed' our microbiome. I think it will influence what is on our dinner plates in the coming years."

Petrosino, also assistant professor of molecular virology and microbiology at BCM, and others in the project, applauded the healthy subjects who took part in the project. 

"People genuinely wanted to do this," he said. "It is a field in which everyone has an interest. We are told to wash our hands as children. Some of us drink ginseng, eat lots of yogurt or take probiotics. This project helps address how much these and other activities impact our health and what can be done to improve it for the next generation."

Assembling the data reported in the journals involved more than 200 members of the Human Microbiome Project Consortium from 80 research institutes who worked on the project for more than five years. The microbiome project received $153 million from the National Institutes of Health Common Fund, a trans-NIH initiative that finances high impact, large-scale research. While BCM was one of four sequencing centers and many institutions that took part, its role began with the identification of 150 of the 300 healthy, normal people as subjects. (The Nature papers describe the sampling and genetic sequencing of 242 of those subjects.) This was accomplished by a team led by Keitel, whose expertise in recruiting volunteers for vaccine studies proved crucial. Only one other site – the Washington University School of Medicine in St. Louis, Mo. – recruited subjects.

Researchers sampled 15 body sites from the 129 men and 18 body sites (the same 15 as men with three additional vaginal samples) from the 113 women whose data were reported in this first glimpse of the Human Microbiome Study project. (Three hundred were enrolled in total.) Sampling from sites such as the mouth, nose, skin (two behind each ear and each inner elbow), and lower intestine (stool) took place once for all volunteers, twice for most volunteers and three times for some. To acquire the information, the scientists purified the human and microbial DNA from each of the more than 5,000 samples collected and then sequenced that DNA. Then they used bioinformatics to sort through the 3.5 terabytes of genomic information to identify the genetic information that came only from the bacteria. The information from the bacterially encoded 16S ribosomal RNA gene allowed them to identify the bacterial species found in each sample.

Insight into complex human biology

Dr. Kjersti Aagaard, associate professor of obstetrics and gynecology, is the first author of a report in PLoS One on the vaginal microbiome in pregnancy.

From a sequencing standpoint, the task was phenomenal.

"The volume of human sequencing we are doing now captures a fraction of the diversity in an individual if we include the co-resident population of the microbiome," said Dr. Richard Gibbs, director of the Baylor Human Genome Sequencing Center and a co-principal investigator of the project.

"We also did whole genome sequencing for some of the samples to get a better idea of what the bacteria in them do," said Dr. Kim Worley, associate professor in the Baylor Human Genome Sequencing Center. "When you have a population of different kinds of bugs, you have to figure out what's important. Is it that there are different species or is it that some species in the mix has a gene that provides this one function and another species has a gene that has another function?"

"I think our insights into the complexities of ‘human' biology will be unparalleled after this effort," said Dr. Kjersti Aagaard, associate professor of obstetrics and gynecology, who took all the vaginal samples at BCM and is first author of a report in PLoS One on the vaginal microbiome in pregnancy (see accompanying news release).

"Understanding the processes that govern the structure and dynamics of human microbial communities is essential for gaining a complete understanding of human development and physiology. We still have a long way to go in understanding what these biologic networks and pathways entail. However, the scientific tools that will have to be developed to answer these first questions on what constitutes a "healthy" human microbiome will be the same tools that help us understand where human disease and a perturbed microbiome meet. We are gleaning key insights into what makes a bacteria a friend or foe, and how we can tip the balance between health and disease with more bacterial friend than foe."

"Why is this important beyond saying that what we've found is fascinating?" asked Versalovic. "This is who we are. Microbes are part of being human and a fundamental aspect of humanity."

As with other large-scale collaborative efforts, NIH ensured that the research community could freely access Human Microbiome Project data through public databases, such as the National Center for Biotechnology Information, part of the National Library of Medicine, and at the HMP Data Analysis and Coordinating Center.

The Human Microbiome Project is managed by 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.

See more information about HMP.