Human microbiome

The human microbiome is the total collection of microorganisms living on or inside the human body. These microbes reside in many anatomical sites, such as the skin, the gastrointestinal tract, the lungs, and the oral mucosa. They are also found in the salivary glands, the uterus, the ovaries, and the biliary tract. This complex community includes several different types of life, such as bacteria, archaea, fungi, protists, and viruses. While micro-animals can live on the body, they are usually excluded from this scientific definition. Understanding this microbiome is vital because it represents a massive, living ecosystem that exists alongside our own cells.

Microorganisms interact with the human host in several distinct ways. Some are commensal, which means they live in our bodies without causing any harm. Others have a mutualistic relationship, where both the microbe and the human benefit from the interaction. However, some microbes can be harmful. Even if they are not pathogens, they can produce metabolites that cause issues. For example, the body converts trimethylamine into trimethylamine N-oxide through a process called FMO3-mediated oxidation. Scientists often refer to the microbes that are expected to be present and do not cause disease as the normal microbiota or normal flora.

Researchers study the microbiome using several advanced genetic techniques. One primary method involves studying deoxyribonucleic acid, or DNA. Scientists can use targeted amplicon studies, which focus on specific known marker genes to identify different types of microbes. A more recent method is the shotgun metagenomic study, which looks at the entire collection of genes to understand the functional potential of the community. Another way to study these organisms is through ribonucleic acid (RNA), proteins, or metabolites. A major challenge in these studies is separating the microbial DNA from the host's own human DNA.

To identify specific microbes, scientists often look for marker genes. For bacteria and archaea, the most common marker is the 16S rRNA gene. For fungi, researchers look at the Internal Transcribed Spacer, or ITS. These genes have highly variable regions that allow for detailed identification. They are also surrounded by conserved regions, which act as binding sites for primers during a process called PCR. This technique is fast and cost-effective, though it can sometimes lead to errors if the primers do not bind perfectly. To manage data, researchers often cluster sequences into Operational Taxonomic Units, or OTUs, based on a 97% similarity threshold.

One of the most significant scientific efforts in this field was the Human Microbiome Project, or HMP. The goal of the HMP was to sequence the genomes of the microbiota found in the skin, mouth, nose, digestive tract, and vagina. A major milestone occurred on June 13, 2012. On that day, Francis Collins, the director of the National Institutes of Health, announced the initial results. The findings were published in major scientific journals like Nature and the Public Library of Science. By mapping the microbial makeup of healthy humans, the HMP created a vital reference database for future research.

The scale of the human microbiome is truly immense when looking at the numbers. It is estimated that there are approximately 38 trillion bacterial cells in the human body. This is a similar order of magnitude to the 30 to 40 trillion human cells we possess. The genetic diversity is even more striking. While humans have approximately 20,000 genes, the bacteria in our bodies have an estimated 2 million genes. This means the microbial genome is about 100 times larger than our own. During the HMP, researchers analyzed over 5,000 samples from 242 healthy volunteers. They examined 15 to 18 different body sites to find more than 10,000 microbial species.

Scientists are currently working to understand if there is a "core" microbiome shared by most humans. If a core group of microbes exists, researchers might be able to link specific microbial compositions to different disease states. We know that the gut microbiota is highly variable between different people and even within the same person. However, there is evidence that the underlying microbial dynamics might be universal. By studying these ecological networks, scientists hope to develop new ways to treat diseases. Controlling these microbial communities could eventually help solve many harmful health problems.