With a more detailed understanding of the microbiome, we can begin to improve it directly and strategically, rather than by blindly moving around pieces of it (which is essentially what a fecal transplant does). First of all, doctors can recommend diet and lifestyle changes that can positively affect the microbiome. These can only go so far, though, and people are not exactly excellent at following such advice. So, in addition to diet and lifestyle changes, we can provide microbiome supplements. Based on a person’s current microbiome composition and lifestyle, we can introduce just the bacteria that are necessary to improve their overall health. Many of the most commonly-needed bacteria can also be “farmed” for mass use.
There is, however, a caveat to all of this — the guts of some people just don’t “accept” certain introduced bacteria8. In other words, when beneficial bacteria are introduced, they might find the existing microbiome hostile and won’t be able to gain a foothold in it. To fix this, at least potentially, we will need to take people’s existing microbiome into account when we attempt to modify it. In order for microbiome-based medicine to work, it will need to be almost completely personalized.
This, in turn, raises another problem: we need to be able to very quickly and efficiently “measure” a patient’s microbiome before treating it. Since the microbiome is constantly changing, a lab test would be impractical. These microbiome surveys would need to be done frequently and quickly, which is not possible if you need to send samples to a lab and wait for results to be returned. Instead, we need testing equipment that is small and easy to manufacture. One of the best ways to do this would be to have a DNA sequencer that satisfies these qualities. This device could “read” DNA from “samples” and then use the information it collects to deduce what types of organisms were in those microbiome samples. The good thing about such a system is that it can be incredibly accurate. But people need to manually give microbiome samples to the sequencer, which is something that should be improved upon.
It would be nice if we could put a small device right inside a patient’s gut which would automatically measure what kind of creatures are in their microbiome. There are ethical implications with this, which we’ll get to later, but for now, let’s focus on the technology.
The most obvious mechanism by which this device could work is for it to be another, even smaller DNA sequencer. This is definitely possible, but getting DNA sequencers to a small enough size to sit unobtrusively in someone’s gut will take a bit of time. That’s not to say that it won’t happen — it most certainly will — but right now, one of the smallest DNA sequencers in existence — the MinION, developed by a company called Oxford Nanopore — is about an inch wide and four inches tall9. For a DNA sequencer, it’s ridiculously small. It achieves this small size by using a new sequencing method based on nanopores, which are, as their name suggests, microscopically tiny pores10. As a strand of DNA is fed through these holes, we can observe its behavior and use that information to assemble a picture of what that strand is like10. Despite its innovation, the sequencer is pretty big — it would clog up the small intestine, which is about an inch in diameter11. And this size doesn’t include the space that will be taken up by shielding to protect the sequencer from gastric juices. Until we invent smaller sequencers, we need other solutions.
One possibility is to have a more rudimentary DNA test that, instead of sequencing DNA, merely searches for genetic patterns found in various microorganisms. Because this method only searches for a limited set of patterns, it won’t be able to detect the full diversity of the microbiome — but this type of system can be more compact, meaning that it can be used for continuous microbiome monitoring. The data from this device can then be used to create a sort of custom probiotic tailor-made for each person, with the goal of improving their health as much as possible.
If we make a system like this, we need to make sure that the collected microbiome data is secure. This is relatively easy to do. First of all, the data shouldn’t be sent to a central database. Rather, microbiome data should be stored locally on the devices that need it. Additionally, when the data needs to be sent from one place to another, it should be sent using E2E (end-to-end) encryption, which is essentially an ultra-secure way of encoding data12. (That’s a very oversimplified explanation which glosses over a lot of interesting details. Maybe I’ll write an article on encryption someday.) However, this encryption will need to be included in the setup from the very beginning.
So far, we’ve been focusing on the bacteria in the microbiome — and perhaps justifiably, since bacteria are the dominant inhabitants. The same strategies and technologies can be extended to fungi, as well. But we’ve forgotten about one other thing: viruses.
