Approaches in Biomedical Research: The Microbiome, Part 1

We are excited to present our second educational series on explaining our approaches in biomedical research. This series will focus on the microbiota (commonly called the microbiome), which is the community of microbes, including bacteria, fungi, and viruses, that lives everywhere on the inside and outside of humans.

Why do these organisms matter to us? The bacterial community in our gut is extremely important to our health, as these bacteria help us break down our food, make chemicals that affect our moods, and train our immune system to tell the difference between good bacteria and the bad, disease-causing ones that should be destroyed. The composition of the gut microbiota is somewhat different in each person, but there are certain species of bacteria that are seen in most people and known to be good for our health, and others that we know can be bad for our health if they grow to outnumber the good bacteria (figure 1). When the amounts of good and bad bacteria are thrown off-balance, this is known as dysbiosis, and has been linked to many diseases.

figure1Figure 1. There are certain bacterial species that are common to everyone, but there is natural variation in the amounts of these bacteria present in the gut between different people. Some species that are bad for our health, like Clostridium, can grow in number and offset the natural balance, leading to dysbiosis.

In ME/CFS, based on published reports, it appears there is an overall disequilibrium in the types of bacteria present in the gut, which is suggestive of dysbiosis. Certain types of bacteria can make the immune system more alert, which can lead to it being overactive. If we can figure out what the different types and amounts of bacteria are that are seen in the guts of ME/CFS patients compared to what is seen in healthy people, then we can begin to understand how these bacteria are affecting the immune system of ME/CFS patients. This knowledge in turn can lead to a better understanding of the disease and the potential for novel treatments targeting either the microbiome or the immune system.

Scientists think that the number of bacterial cells in the human body outnumber our own cells, with about 39 trillion bacterial cells to about 30 trillion human cells. With more bacteria than human cells in the body, how do you figure out who is who in the microbiome? To solve this problem, we use a technology called whole genome sequencing to look at all of the different types of bacteria in the human body by determining their individual DNA sequences, which can be used to identify them.

So how does whole genome sequencing work exactly?

Patients provide a stool sample, which will have all of the bacteria in it that are in the patient’s gut. We can break open the bacterial cells in the stool to get the bacterial DNA that’s inside the cells. The whole genome of each of these bacteria is pretty long, so it is broken up into shorter pieces, or fragments, so that it will be easier for the sequencer to handle. After the sequencing is done, a computer separates all of the sequences from each other, so that there are many individual sequences, each representing one of the fragments that was sequenced.

figure2Figure 2. The Illumina HiSeq 2500 is the sequencer used by the researchers at JAX who study the gut microbiome in ME/CFS.

The computer then does an alignment of the fragment sequences, which is where it compares them to each other to connect the fragments and restore the full sequences of each of the bacterial genomes. There are extensive databases of bacterial DNA sequences available, so once we have the full genome sequence of each of the bacteria, we can compare these sequences to the database to figure out what species of bacteria each of the sequences belong to. We can then compare the types and amounts of bacteria found in the ME/CFS patients to what is found in healthy people and see what kind of dysbiosis occurs in the patients. If interesting species of bacteria are found in a patient’s stool sample, the bacteria from this sample will be used for more experiments to see how these interesting types of bacteria affect the immune system.

Stay tuned for the second part in this series, where we will discuss the experiments following whole genome sequencing, where we look at the interesting types of bacteria to see how they affect the immune system.

Microbiota, Wikipedia
Introduction to Whole Genome Sequencing, Illumina
Whole Genome Sequencing, Wikipedia
Revised Estimates for the Number of Human and Bacteria Cells in the Body, PLOS

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