Wherever you go and whatever you do, you leave traces of DNA. The DNA is part of about 500 million skin cells that you shed on average every single day. It is also inside tiny droplets of saliva that you spread into the air when you speak, sneeze or cough. And, it should come as no surprise that DNA is also in your urine and faeces. So, despite the known forensic use of DNA that we leave everywhere, it can also be used to detect disease outbreaks and community drug use from wastewater surveillance.
Most of the faecal DNA, however, is not your own DNA!
In fact, it is rather a mixture of DNA from various sources. Most of it belongs to bacteria, but there could also be small fractions of DNA from archaea, fungi, viruses, single-celled or multi-celled eukaryotes, and even your very own human DNA.
What to expect from your relative levels of bacterial DNA?
Bacteria are the main constituent of the gut microbiome. They are tiny compared to human cells but their numbers in the colon alone roughly equal all the cells in your body. Hence, we expect to see high relative amounts of bacterial DNA.
In our healthy reference, we are able to assign an average of 70% DNA to bacteria, while a bit less than 30% cannot be assigned with enough certainty.
Yet, there are conditions linked to a low relative amount. Bacterial load was reported to be lower in people with conditions like Crohn's disease or depression when compared to in a healthy reference.
What about archaeal DNA?
Archaea are not found in all humans. In fact, in a recent Korean study, less than half of the tested samples were positive for archaeal DNA. In addition, the relative abundance can vary strongly with values between 0.1 to 21.3%. Our healthy Danish reference has an average of 0.08% DNA that we can attribute to archaea.
There are certain conditions that have been shown to exhibit a high abundance of archaea:
- Irritable bowel syndrome of the constipation subtype (IBS-C)
- A state of chronic inflammation seems to be favoured by Methanosphaera stadtmanae. This organism has been shown to triple in abundance in people with inflammatory bowel disease (IBD).
- A condition called intestinal methanogen overgrowth (IMO) may also be reflected by a high abundance of archaeal DNA.
It is worth noting that up until recently, archaea could not be detected reliably. Therefore, the published scientific literature is at an early stage. Archaea fill numerous underexplored metabolic roles and thus seem to influence our health in obscure, indirect ways. There are no known pathogenic archaea but there is also still a lot that we do not yet know about them.
What would we expect from fungal DNA?
We have previously written about fungi, another large group of microorganisms that is also part of your microbiome. As you know, much like the bacteria and archaea that you are already familiar with, fungi interact with human health and disease. Typically, bacteria dominate the microbiome, with only small relative amounts of fungi present. We see that our healthy reference has an average relative amount of fungal DNA below 0.1%.
But in some conditions certain fungi can outcompete bacteria which shifts this balance:
- A state of chronic inflammation such as in people with IBD and more specifically Crohn's disease [1, 2].
- Auto-immune diseases such as atopic asthma.
- Fungal overgrowth after treatment with antibiotics.
How does your own DNA get into your stool?
Your body is constantly renewing itself. Old cells die off as new cells take their place. So, much like your skin, your gut is regularly shedding dead material.
This happens so frequently that about every five days you have a completely new set of cells lining the inside of your gut. When the old cells die, they follow a protocol that maintains the barrier function of the gut and another that includes the destruction of most of their DNA. The fragments that do remain can be found in your stool in very low amounts. In most people, this is less than 1% of the total DNA found in stool. Our healthy reference, for instance, has an average of 0.002% human DNA in their stool, but up to 5% is considered normal.
However, there are processes in the gut that drastically increase the amount of DNA found in faeces because they lead to an increase in cells being damaged or dying; or because they disrupt the protocol for orderly self-destruction. These processes are:
- Abnormal Growth [1, 2]
- All other causes of pathological shedding such as drug use
Apart from being representative for several types of troubles in your gut, having high amounts of DNA in your stool is not desirable, as it is an indicator for the loss of barrier function and associated with a risk of infection by Clostridium difficile. Moreover, it decreases the sensitivity of our analyses making it harder for us to find very low abundant microbes.
What sources of DNA we find in your stool and their relative amounts, can tell you a lot about your health and wellbeing.
- Having a large portion (>70%) of bacterial DNA is considered normal, while low relative amounts could point to issues.
- Depending on your diet and lifestyle there may be some archeal DNA. The majority of people seem to lack archaea. High amounts are unusual and could be an indicator of inflammation.
- Generally, fungal and human DNA should be very low. High amounts are associated with numerous causes and should be investigated further with your GP.
Author: Christian Lieven