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Harnessing the power of RNA for a healthy gut microbiome

I was a scientist at Los Alamos National Lab in the US when I identified a science-based personalized diet that completely cured my early onset arthritis. I realized that the gut microbiome would play a central role in personalized nutrition and redirected all my science projects towards it. We desperately needed better technology for analysing the gut microbiome and metatranscriptomics offers the best value. It is better than 16S or metagenomic sequencing in two important aspects:

1. It identifies all living microorganisms at the strain level (no DNA-based method can do that).
2. It quantifies the expression of thousands of microbial genes that produce metabolites important for our physiology and health.

Metatranscriptomics: a functional readout of the gut microbiome

It turns out that the gut microbes produce hundreds (probably thousands) of biochemicals that our physiology depends on. They also are known to produce chemicals that are harmful to us: it’s the biochemical output rather than the composition of the gut microbiome that affects our health.

Everyone has been looking for the healthy gut microbiome using the wrong technology, i.e. DNA-based compositional analysis. Everyone has been looking for the healthy composition; it turns out it doesn’t exist, and we have the data to show that.

Using our Gut Intelligence test, we have analysed close to 30,000 human stool samples. From these, we selected the 251 healthiest people’s samples. At the strain level, the presence-absence similarity among the healthiest cohort level is as little as 3%. That means there are two of those people that have 97% different strains in their gut microbiome. Practically speaking, they have completely different gut microbiomes, yet they are both very healthy. The reason they’re both very healthy is that their unique gut microbiomes are producing a similar set of biochemicals.

Finding the healthy functional gut microbiome

The healthy gut microbiome does exist at a functional level, but it needs a functional readout to find it.

If two people have very different gut microbiome compositions, how can those people be healthy? They can be fed personalized diets, each stimulating the production of similar set of healthy biochemicals.

Now we have reduced the problem to:

  1. Understand each person’s gut microbiome composition
  2. Identify the diet they need to consume for that particular composition to produce healthy and not harmful biochemicals
  3. Confirm the healthy biochemical output using the Gut Intelligence test
Developing predictive models of personalised glycaemic index

In 2018, we carried out a large clinical study at Viome. We enrolled 600 participants and fed them specific foods for two weeks and during that time we continuously monitored their blood sugar level. We fed them a combined 25,000 meals! All study data were analysed using AI and supercomputers, and enabled us to develop a predictive model of personalised glycaemic index. Just using our Gut Intelligence test, we can predict the personalized glycaemic index for anyone with 80-90% accuracy. We cannot make any health claims, but our predictive model should enable our customers to choose their diet that minimizes blood sugar spikes after meals.

The future: empowering people to a healthy gut

We are carrying out many clinical studies on obesity, diabetes, depression, cancers, etc. Here is a project I am very excited about:

If you ask someone right now, “Will you get pancreatic cancer?”, the answer is “I have no clue”. It turns out that the gut microbiome likely may play a big role in the onset of pancreatic cancer. Using our technology, and collaborating with world-class clinicians, we want to understand how to prevent pancreatic cancer. One day, I hope our app will show gut microbiome biomarkers of pancreatic cancer, and personalized diet recommendations that prevent its onset. This will empower people to say “I’m not going to get pancreatic cancer.”

This scenario applies to most chronic diseases such as depression, anxiety, psoriasis, heart disease, diabetes, Alzheimer’s, Parkinson’s, multiple sclerosis, etc. To give another example, people don’t have a heart attack because they ate a steak the night before. They have a heart attack because of 30 years of inflammation in their body caused by poor diet choices and poor microbiome functions. That’s exactly when we want to intervene, decades before the symptoms, so that we know we will not develop the disease.


At the Microbiome R&D and Business Collaboration Forum: Europe, I described the technology behind the Viome’s Gut Intelligence test and addressed some misconceptions. I also described the predictive model of the personalized glycaemic index we have developed, and the healthy gut at the functional level and not at the compositional level.


Momo Vuyisich is the Chief Science Officer at Viome, USA. He presented a company showcase at the Microbiome R&D and Business Collaboration Forum: Europe.


Don’t miss the 7th Microbiome R&D and Business Collaboration Forum: USA. Download the agenda.

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