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What is the microbiome?
A microbiome is the community of microorganisms - bacteria, archaea (prokaryotes), fungi, protists (microbial eukaryotes) and viruses - and their genes that live on or in a particular environment. When we are talking about the human microbiome, this is referring to the trillions of microbes living on or in the human body, and bacteria are the most abundant of these. There are estimated to be 38-39 trillion microbes in the human body; this is more than the ~30 trillion human cells. While there is a distinct microbiome associated with many areas of the human body, the gut, oral and skin microbiomes have some of the highest numbers of microbes and are the most well-studied. There are also areas of the body that typically have no microbes (or are sterile), like our internal organs, tissues, and our circulatory system. Most areas of the body that have some contact with the outside world will have an associated microbiome.
Why are we interested in it?
While the microbiome can be associated with infections and diseases, it is also really important for key functions in our body like digestion and immunity. It is often a disruption to the healthy microbiome - which might look different in different people! - that is responsible for diseases, or is associated with making them worse. It is also more frequently being associated with other things like mental health or neurodevelopmental disorders like ADHD and autism.
How do we look at the microbiome?
The majority of microbes in our body cannot survive outside it without specialised growth media, so we primarily study it by extracting DNA from samples like poop or saliva and then sequencing the DNA.
What is DNA?
DNA is the heriditary material inside all living organisms. It contains the chemical bases A(denine), C(ytosins), T(hymine), and G(uanine) and almost every cell inside a person's body has the same DNA. The order (or sequence) of these bases determines the information available for building and maintaining an organism.
When we are looking at microbes, we can sequence either specific genes within the microbes or all of the DNA within a sample. When we sequence specific genes (usually referred to as marker gene or amplicon sequencing), these act like a barcode, identifying which taxa are there and how abundant they are. In microbiome research, we are most often targeting a gene called the 16S ribosomal RNA gene - this is shared by all bacteria and archaea, and the sequence has diverged roughly in line with microbial species differentiating from one another. We are able to compare the DNA sequence with databases of known microbes to identify the taxa within a sample. When we look at all of the DNA within a sample (referred to as shotgun metagenomic sequencing), this is more complicated computationally; when we sequence DNA we end up with many short fragments of DNA, and we either need to try to reconstruct the genomes of the organisms that they came from, or we can compare all of these fragments with databases of known organisms. The databases that we use for comparison are much larger, because they contain entire genomes rather than a single gene, and so we require much more powerful computers for this. However, this also means that we have information about all of the genes that are contained within our community so we can reconstruct information about what functions they are capable of carrying out as well as simply who is there.
Authors
Authors: Robyn Wright