The Microbiome Defined and Understood Using A.I.

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Some terminology just doesn’t sound that exciting. Take the term microbiome. If you didn’t know what the word “microbiome” meant, you wouldn’t be chastised for thinking that it’s just some boring medical terminology that when explained to you, you’d be none the wiser for knowing. As we found out, that couldn’t be further from the truth.

We’ve come across the word “microbiome” a few times, but only when we saw the below chart from CB Insights did we really want to start exploring the world of the “microbiome”:

cb-insights-microbiome-startupsSo there are 24 different startups “targeting” the microbiome? There’s clearly some opportunity here and we want to start out by fully understanding what the microbiome is and why it matters to all these startups. First, let’s take the textbook definition of “microbiome” from Google:

microbiome-definitionThis is where we started thinking to ourselves about all the bacteria that lives in your gut. Surely that’s what the microbiome refers to right? Not exactly. The gut is just one part of the whole human microbiome. As it turns out, we’re actually just giant walking parasite cages. Here’s something interesting. Did you know that this thing is living on your face right now?

The harmless mite Demodex folliculorum, seen here in an electron microscope image, lives in the follicles of eyelashes
The harmless mite Demodex folliculorum, seen here in an electron microscope image, lives in the follicles of eyelashes

That’s right. When you’re sleeping, that thing crawls out from it’s hiding place in your pores to frolic around, have sex, and lay eggs. Think that you’ll just wash it away with a good facial cleanser? Think again. You see that picture inset above? That’s a family of those things living in a human eyelash hair follicle. The fact that you have mites like that living on your face right now should make you start to think a bit. If that hideous creature is “harmlessly” lurking around your eyelashes, then what possible other things could be “harmlessly” living on your body?

As it turns out, the above creature doesn’t even fall under the scope of human “microbiota”. It turns out that the microbiome (i.e. the collection of microorganisms that inhabit your body) is so big that half of the cells in the human body actually belong to parasites. These findings are surely fascinating but what’s the big deal? We’ve always known that the body was a complex system with all kinds of bacteria and fungus inhabiting it. Why is this suddenly such a big deal?

As it turns out, the fact that we can now sequence a genome for less than $1,000 means that we can now start to explore the genetic composition of microbial communities. This is actually called “metagenomics” and it’s really just genomics on a massive scale. Here’s a quip from Wikipedia on the topic of metagenomics:

The data generated by metagenomics experiments are both enormous and inherently noisy, containing fragmented data representing as many as 10,000 species.[24] The human gut microbiome gene catalog identified 3.3 million genes assembled from 567.7 gigabases of sequence data.[26] Collecting, curating, and extracting useful biological information from datasets of this size represent significant computational challenges for researchers.[20][27][28]

So now we’re starting to see that “metagenomics” or the “genomic analysis of the microbiome” is generating huge collections of delicious big data. To say that these massive big data sets represent “significant computational challenges” is an understatement. Where do you even begin when you have DNA data that represents as many as 10,000 species? You use artificial intelligence (AI) of course.

In our previous article on the Top-5 Artificial Intelligence Companies in Healthcare, our first company listed was iCarbonX led by the genius Chinese genome researcher, Wang Jun. With their $200 million in funding, iCarbonX hopes to build a “digital you” that is fully explained using artificial intelligence. We already know how complex your genome is just by itself. Now imagine understanding how your specific genome interacts with the 3.3 million genes that live in your gut. Can you even begin to imagine the permutations and combinations you would have to explore to make sense of it all?

Wang Jun is making progress in using AI to understand the microbiome, for example in this piece of research he published over the summer titled Metagenome-wide association studies: fine-mining the microbiome. In that piece of research, he talks about investigating the associations between the human microbiome and several complex diseases. But he’s not the only one studying the microbiome with the goal of understanding it holistically.

In 2008, the United States National Institutes of Health (NIH) committed $115 million to a 5-year project with the goal of identifying and characterizing the microorganisms that make up the human microbiome. The project resulted in over 190 peer-reviewed publications, the inception of a reference database, and one very surprising revelation.


As it turns out, the genetic contribution of the microbiome to the human superorganism could be up to 100X greater than the genetic contribution from your own human genome. That daunting piece of information is probably why companies like iCarbonX believe that if they can understand the microbiome, they can understand just what makes us tick. Maybe then we’ll feel better about the fact that ugly looking worms with claws are crawling all over our faces at night.


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