How to test your microbiota

There are a range of testing methods out there if you’re interested in checking if you might have an infection, or if you would like to find out what your whole microbiota is right now. Here I will go through some of the most popular methods available today. There is a simple comparison table at the end of this article.

If you think you have an active infection, you should start by contacting your doctor or other healthcare professional (e.g., GP, nurse, specialist, pharmacist). They will ask about your symptoms and medical history. This may be enough for them to diagnose an infection, especially if you are a recurrent sufferer. If they are unsure, they may take a urine or vaginal sample and attempt to grow microbes from the sample (this is called culturing). There are two types of culturing that are generally done in a diagnostic lab.

As the name suggests, this is what is done as standard in most labs. This involves putting a small amount of the sample on a type of agar (nutrients that bacteria or yeasts like to grow on) that is particularly suited to the most common pathogens, e.g., E. coli for suspected UTI. This method is generally quite successful at detecting common bacteria that grow in “normal” conditions, i.e., 37°C in air. However, there are a host of infection-causing microbes that require different nutrients, temperatures, etc. These are often missed using this method.

This is similar to standard culture but tries to get past the limit of only detecting specific microbes by using a selection of different nutrients and allowing them to grow longer. This method is more likely to find the microbe that is causing the infection, especially if it cannot grow in air (these are called anaerobes)

There are simple at-home tests that you can do if you suspect you may have an infection. These tend to be cheap and quick, but are not always the most accurate, often missing infections. You may also need to visit a doctor or pharmacist to confirm the infection and to receive treatment. Test Strips are thin strips that contain various chemicals that can change colour when there are various substances present in a sample, e.g., white blood cells, nitrites or specific microbes. Some common examples are:

• dipsticks can indicate a UTI
• Candida strips detect thrush in vaginal discharge
• pH strips to check if vaginal or urine pH is normal (around 4 – 4.5 is a healthy vaginal pH, anywhere from 4.5 – 8 is normal for urine)

Microbiome Test Kits are available if you have recurrent or lingering infections that are not responding to your treatment, or if you are simply curious about your microbiota. Urine and vaginal kits are available from many different companies. You receive a kit in the post containing sampling supplies and instructions. Simply collect a sample (either a small amount of urine or a vaginal swab), fill out your details, and send the sample/s back to the company. They will use biochemical techniques, like PCR, to detect the DNA of microbes that are present. Because the organisms do not need to be alive (DNA can be retrieved from dead microbes) this is a great method to find organisms that are difficult to culture, like anaerobes.

See the diagram below for our roundup of testing methods.