DNA is everywhere

Where ever you go and whatever you do, you leave traces of DNA behind. DNA is part of the roughly 500 million skin cells you shed every single day. It is also found in the tiny droplets of saliva you release when you talk, sneeze, or cough, and it should come as no surprise that DNA is also present in your urine and stool. So although DNA is widely known for its use in forensic science, the DNA we leave everywhere can also be used to detect disease outbreaks and monitor drug use through wastewater analysis.

In our microbiome tests, we also measure how much DNA your sample contains, but most of the DNA in stool is not your own.

It is actually a mixture of DNA from different sources. Most of it belongs to bacteria, but small fractions may also come from archaea, fungi, viruses, single-celled or multicellular eukaryotes, as well as from your own human cells.

What Should You Expect From Your Relative Levels of Bacterial DNA?

Bacteria are the main component of the gut microbiome. They are small compared to human cells, but their total number in the colon alone roughly equals the total number of cells in your body. Therefore, we expect to see high relative levels of bacterial DNA.

In our healthy reference group, which your microbiome test is compared to, we are able to assign about 70% of the DNA to bacteria, while slightly less than 30% cannot be assigned with sufficient confidence.

In scientific studies, a relatively low bacterial proportion has been associated with conditions such as Crohn’s disease and depression compared with healthy reference groups.

What About DNA From Archaea?

Archaea are also microorganisms that live in the gut, but not everyone has them. In fact, a recent Korean study found that fewer than half of tested samples were positive for archaeal DNA. Among those who had archaea, their relative abundance varied widely, from 0.1% to 21.3%.

Certain conditions are associated with higher levels of archaea:

Constipation-predominant irritable bowel syndrome (IBS-C)
Chronic inflammation, which appears to favor Methanosphaera stadtmanae, this organism has been shown to triple in abundance in people with inflammatory bowel disease (IBD)
Overgrowth of archaea can also occur in the colon and throughout the body. Archaea use hydrogen produced during carbohydrate fermentation to generate methane, and studies show a strong link between excess archaea and constipation

It is worth noting that archaea could not be reliably detected until relatively recently, so the scientific literature on them is still in an early stage. They play several underexplored metabolic roles and may influence health in indirect and not yet fully understood ways. No pathogenic archaea are currently known, but much remains to be discovered.

What Can We Expect From Fungal DNA?

Fungi are another major group of microorganisms that form part of the microbiome. Like bacteria and archaea, fungi interact with human health and disease. Normally, bacteria dominate the gut microbiome, while only small amounts of fungi are present. In our healthy reference group, the average relative amount of fungal DNA is below 0.1%.

However, under certain conditions, fungi can outcompete bacteria and disrupt this balance, including:

Chronic inflammatory conditions such as IBD, especially Crohn’s disease
Autoimmune diseases such as atopic asthma
Fungal overgrowth after antibiotic treatment

How Does Your Own DNA End Up in Your Stool?

Your body is constantly renewing itself. Old cells die as new ones take their place, and just like your skin, your gut regularly sheds dead material.

This happens so frequently that every five days you essentially have a completely new layer of cells lining your intestine. When old cells die, they go through a controlled process that maintains the gut barrier and destroys most of their DNA. The small fragments that remain can be found in your stool in very low amounts - usually less than 1% of the total DNA in feces.

However, certain processes in the gut can dramatically increase the amount of human DNA in stool. These processes cause more cells to be damaged or die, or they disrupt normal cell breakdown. They include:

Injury
Inflammation
Infection
Abnormal growth
Other causes such as substance abuse

High levels of human DNA in stool are undesirable because they indicate loss of gut barrier function and are associated with an increased risk of Clostridium difficile infection. They also reduce the sensitivity of microbiome analyses by making it harder to detect low-abundance microbes.

Conclusion

The sources of DNA found in your stool - and their relative proportions - can reveal a great deal about your health and well-being.

A high proportion (>70%) of bacterial DNA is considered normal, while lower levels may indicate problems.
Depending on diet and lifestyle, some archaeal DNA may be present, but most people have none. High levels are unusual and may indicate inflammation.
In general, fungal and human DNA should be very low. High levels are linked to various conditions and should be investigated further by a healthcare professional.