The next step in microbiome research

As a healthcare professional, you may have begun to delve into applying gut microbiome research. How many times since then have you thought, "What do these bacteria actually do?" "Are they contributing to my client's health?" "Do they really play a functional role?" The answer to these questions is crucial to correct interpretation.

Bacterial activity and function: the next step in microbiome research

With C-FISH, Computerized Fluorescence In Situ Hybridization, you can not only measure the numbers of microorganisms but also map activity of the bacteria. So you get more information about what the microbiome is "doing.

You probably don't realize it, but the method by which (gut microbiome) research is done determines the information you get out of it. Previously, the bacteria in the stool were examined by culturing them. This method used to be very widely used and gave the first insights about the bacteria in stool. The culture method can be used to examine the bacteria that are easy to culture. Nowadays, we know that many of the bacteria that live in our intestines are not good to culture at all: thus, the method has become a limitation.

Fortunately, new innovative methods have been developed that allow us to properly study the gut microbiome and the research field has gained momentum. Polymerase Chain Reaction (PCR), Next-Generation Sequencing (NGS) and Fluorescence in situ Hybridisation (FISH) are valuable tools for research on the gut microbiome, but we must also recognize that with each method we are "looking through a different lens.

Researchers at NL-Lab, in a scientific review article reviewed the various research methods. Key findings during this search are listed below:

PCR is highly sensitive, but dependent on the quality of DNA extraction. This method is especially suitable for targeted analyses and less so for broad, unbiased profiling.
NGS is powerful but expensive and requires extensive data analysis, where the quality of DNA extraction is essential.
FISH provides unique in situ information such as activity. Modern FISH techniques (such as C-FISH) with robotic preparations and automated image analysis offer high sensitivity, scalability and efficiency.

An example

You have a client with symptoms of fatigue and persistent abdominal pain. You decide to perform a standard gut microbiome examination. The result shows that the gut microbiome is balanced and rich in Faecalibacterium prausnitzii. This is good news because this bacterium is associated with positive health effects such as a healthy gut wall and low inflammatory levels. The study provides no further clues to the client's symptoms and you begin to doubt the function of the gut microbiome.

From DNA to activity: C-FISH
C-FISH brings a different perspective. Instead of DNA detection, C-FISH focuses on ribosomal RNA (rRNA) detection. This method allows you to get information about the activity of bacteria in addition to information about the bacteria present. So with these glasses on, you see more sharply and find out that the bacteria present are not functional enough. You can now employ personal lifestyle, nutrition and/or supplementation advice with the goal of (re)activating the gut microbiome.
Imagine that from now on you can not only say, "You have lowered numbers of Bacteroides in your gut microbiome" but also, "The bacteria essential for your energy production are inactive. We can activate this with specific interventions." This level of detail can make the difference between a treatment that works and one that doesn't.

What does this mean for you?
As a healthcare professional, C-FISH allows you to go beyond what is possible with other methods. You can see not only what is there, but also what is happening. This opens the door to treatments that directly target improving the function of the gut microbiome. For patients, this means more effective therapies and better outcomes. C-FISH provides you with the tools to help your patients on an even more personalized level.