Expert Insight: The gut microbiome: Your questions answered

Watch this on-demand webinar for an introduction to the gut microbiome and the development of an improved diagnostic pipeline

13 Jan 2022

Dr Philipp Lemal, Deputy laboratory manager, Ortho-Analytic
Dr Philipp Lemal, Deputy laboratory manager, Ortho-Analytic

The gut microbiome is the collective genome of the intestinal flora and represents the totality of microorganisms present in the gut. Scientific studies show a correlation between the composition of the microbiome and various diseases, e.g., obesity or depression. 

In this free SelectScience® webinar, now available on demand, Dr. Philipp Lemal, deputy laboratory manager, Ortho-Analytic, and Dr. Beatrice Marg-Haufe, senior market manager, Tecan, provide insight into how the automation of DNA extraction from stool samples is the first step to reducing analysis costs and increasing throughput, thus facilitating the accessibility of microbiome analysis to the general public. 


Read on for highlights from the Q&A discussion or register now to watch the webinar on demand

Could you explain a little bit more about the impact of diet on the microbiome and its diversity?

PL: A lot of research is done on this, and to wrap it up, the best diet is a Mediterranean diet as it is rich in fiber and creates a diverse microbiome. On the other hand, recent studies have shown that a diet high in fat and sugar leads to changes in the gut microbiota, and that may explain a coincident increase in conditions such as type 2 diabetes and obesity. So, it is really beneficial if you preserve the gut microbiota with vegetables, nuts, fish — all these Mediterranean diet components.

What are the therapeutic options that are given after a microbiome analysis?

PL: The options can be classified into three categories; depletion, replacement/restoration, and modulation. Modulation can be achieved through dietary interventions to either starve harmful bacteria, or to promote the growth of beneficial ones. Depletion is usually done with antibiotics. For instance, inflammatory bowel disease is sometimes managed through the use of antibiotics. 

Highly dysbiotic environments might require more extreme approaches. Here, fecal microbiota transplants come into play. These aim to replace the local gut flora with an exogenous microbiota, and that has been explored in the treatment of ulcerative colitis in children and young adults. However, further studies are needed to optimize the parameters for this. For example, the dosing, the delivery, route, or the formulation. In the future, this might not be an exogenous microbiome from healthy persons anymore but might be replaced by enzyme bacterial communities.

Did automation help you increase your throughput for processing stool samples?

PL: Yes, it did. When we extracted the DNA manually, it took us maybe half a day for 20 samples. It was a lot of pipetting, and nobody likes that. The possibilities to confuse some samples or to confuse the different steps were quite high, especially while doing the extractions back to back a few days in a row.

So the manual extraction was very prone to errors. Now that we have automized it, we can run further downstream applications, and also the DNA extraction, maybe within one to two days for a 96-well plate.

Is your lab limited to routine diagnostics? Or do you also provide services for wider gut microbiome research studies?

PL: Our main business is routine diagnostics, providing our customers with the best possible solutions, and state-of-the-art analysis. However, we are scientists after all, and not limited to routine diagnostics, so we are excited when we can be part of clinical trials and studies.

For example, we have already determined the microbiome for studies at the University of Alberta in Canada, and the University of Kyoto in Japan. We would be very happy to have the chance to assist in more studies, and just have our fingers on the pulse of gut microbiome research.

How many grams or milligrams will be collected with CALEX tubes? 

PL: We only collect 10 milligrams of stool with the CALEX tubes, and this is enough to extract sufficient amounts of DNA for further downstream applications, so for PCR and NGS. Furthermore, our studies show that these 10 milligram stools are really representative of the patient's microbiome and that we don't need more specimen. This is very beneficial.

I heard stories that during the summertime, when it's nice and warm outside, the samples would ferment, and it's happened before that some of the tubes exploded. The worst-case scenario is that it explodes when the lab technician is handling it, and trust me, that's happened before. With CALEX tubes this is not an issue anymore. Our lab technicians are quite happy about that. Also, from a patient's perspective, it's nicer to just dip in three times with this pin, than rather collecting a large portion of your feces.

Where do you see the greatest potential for microbiome research in the future?

PL: Microbiome research shows promising results in various fields. What we know so far about the gut microbiome might still just be the tip of the iceberg, and many limitations, inconclusive findings, and controversies exist within this field. In the past three years, research has shifted its focus from certain types of gastrointestinal bacteria to the gastrointestinal microbial community and its diversity.

Studies are now focusing more on the gastrointestinal microbiome, its influence on inflammation and immunology, and applications as biomarkers. So, I believe that within the next few years, we will see several microbiome-based therapies emerge for a variety of diseases.

It's likely that as we move forward, when drugs get licensed, the FDA may require their impact on the gut microbiota. So, if a drug damages this virtual organ, then it may not be licensed anymore.

Overall, I think that microbiome research will lead to novel therapeutic possibilities for various diseases, and that it will bring us towards personalized medicine. However, a lot of research is needed to get to this point, and we really need comparable study designs. I believe that our novel pre-analytical approach shown here can be one first step towards this.

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