Human Microbiome

The human microbiome is the collection of millions of microbes that colonize the human body. The McDonnell Genome Institute is applying next generation sequencing technology to analyze the genomes of these organisms, characterize the communities they form, and measure how communities change in different health and disease states.

Human Microbiome Project details

Right now your body is teeming with microscopic organisms. In fact, they out number your own cells ten to one.

Thousands of different microbial species colonize our bodies and together contain over one hundred times more genes than in our genome. This group of microorganisms is called the microbiome and helps keep us alive.

The McDonnell Genome Institute was part of an initiative to sequence the entire genomes of 3000 individual microbes found within our human microbiome. One of the ‘Roadmap’ projects from the National Institutes of Health (NIH)’s Common Fund, this ‘Human Microbiome Project’ (HMP) began by sampling and sequencing the microbial communities at 18 different sites on the body – located in the mouth, nose, skin, vagina and gut. These initial samples came from 300 young, healthy adults who helped to provide researchers with an idea of what microbes live inside of us when we are in a normal, healthy state.

Healthy and diseased microbiomes

Much like the Human Genome Project was created to catalog the entire sequence of our own DNA, the Human Microbiome Project worked to catalog the genetic information of the microbes in and on the human body that contribute to our survival. By looking at the genetic variation of microbes at these different body sites, as well as among different individuals, scientists hope to understand more about how our microbiome keeps us healthy or may contribute to disease.

Additionally, a group of Washington University researchers worked with the McDonnell Genome Institute to sequence the microbiomes of certain diseased patients – including those with Crohn’s disease (an inflammatory condition affecting the gastrointestinal tract); children with fever of unknown origin; and an often fatal condition in premature babies called Necrotizing Enterocolitis, that causes inflammation of the intestinal tissue. The McDonnell Genome Institute also collaborated with researchers at other institutions who looked at how the microbiome is associated with sexually transmitted diseases and the male adolescent urethra, as well as a project dealing with the skin microbiome as it relates to acne.

These demonstration projects were started to help guide the direction of future clinical research by looking at the potential links between the makeup of our microbiomes and specific disease states. This research could ultimately provide doctors with new diagnostic and therapeutic approaches for a number of diseases.

Microscopic, but worthy of respect

We often forget that microbes have been on the Earth long before we ever came on the scene. Most of the microbes that we harbor do a lot for us – from helping to digest our food and absorbing nutrients we need, to churning out vitamins we can’t make ourselves and even protecting us from other harmful microbes that could make us sick. Many of these organisms are with us from birth to death and influence our growth and development. This is the impetus behind work like the Human Microbiome Project, which will help us understand more about these microscopic life forms that are so crucial to our survival.

A lot to sequence

It took many years and much technological advancement to get to the point where scientists could even undertake something like the Human Microbiome Project. But with next generation sequencing techniques, it is possible to sequence hundreds of individual microorganisms’ genomes and do it in a reasonable amount of time and at a lower cost than ever before.

But there’s a catch – unlike animals and plants, a large proportion of microbes aren’t willing to give up their DNA so readily. In fact, many of the microbes in the human body depend on other surrounding microbes and nutrients for their survival and can’t grow on their own outside of that environment.

In order to figure out what kind of microbes live in the human body, researchers took samples from one of five predetermined body sites (mouth, nose, skin, vagina and gut). Since they can’t sequence each microbe’s genome separately, they sequenced and studied the entire microbial sample at once – a field called metagenomics. The samples contained hundreds of different microbial species, each with their own unique genome. To identify the types of species present in the sample, the scientists used key genes that are known to be associated with certain microbes. They then looked up the genomes of other microbes that have already had their entire genomes sequenced. This allowed them to compare and catalog many of the important genes and species that are in a given body site sample. The more deeply they sequenced each sample, the more information they obtained about the microbial make-up of that sample.

All in the community

Studying microbes within their communities rather than individually plays a key role in understanding the human microbiome. A major goal of the Human Microbiome Project was to help researchers determine the similarities and differences among the microbiome of healthy and diseased individuals. These communities have been characterized among groups of people, and observed changing in different health and disease states.

With the development of more advanced sequencing technologies that shorten sequencing times and reduce costs, the McDonnell Genome Institute can more effectively sequence the massive amounts of genetic information present in the human microbiome and discover what types of microbes are important to our health and well-being and what types we should be targeting to prevent disease.