Edit 2023/09/06: Many comments so far raise the fact that we can't tell whether there is causation or correlation between an illness and the corresponding microbiome of the patient. My point isn't to solve that problem, correlation on its own is of interest for facilitating diagnostics: If a patient suffering from an un-diagnosed illness
X exhibits the a similar biome to that of a patient suffering from a known illness
C, then the probability that
X = C is higher than if we didn't have that correlation.
The microbiome has been a hot topic for the past decade. This talk gives a good overview of this by highlighting how the rise of "modern" chronic diseases is due to a large part to the imbalances in the microbiome following the rise of antibiotics. The old paradigm of single-pathogen to single-remedy is in need of being replaced by a new paradigm where the root causes of the illnesses lie in entire ecosystems rather single pathogens. This incidentally means that AI and big data are likely the way forward in medical diagnostics.
There is at least a dozen companies (e.g., 1, 2, 3) and research groups (e.g., 1, 2, 3) that are making headway in the field. I understand that a lot of this is still at the research stage and that regulatory hurdles only slow things down. However, from what I gather, most of the actionable outcomes from all this work are:
- merely descriptive (rather than prescriptive, i.e., they're basically the equivalent of 23andMe, but for the microbiome),
- tailored probiotics or dietary recommendations that claim to "modulate" the microbiome,
- therapeutics of Clostridioides difficile. (The few companies that did get FDA approval and financial traction in microbiome analysis ironically all ended up looking a C. difficile.)
I'm probably missing something, but these seem like meager advances compared to the data mining potential of the microbiome. While not dismissing the regulatory and data-sharing challenges, I find it surprising that a systematic data mining of the microbiome hasn't yielded more diagnostic insight in all the aforementioned diseases for which it is known to be relevant.
At the risk of sounding naive, why is microbiome sampling (which is relatively unintrusive) not used systematically by hospitals to profile various illnesses? Such data would be a gold mine of insight as opposed to the vary basic tests commonly done (e.g., blood tests or imaging). (Even fecal sampling, to my knowledge, is very rarely used.)