I wonder how many diseases are becoming more prevalent because we eat manufactured food on a long term basis. Additives have been approved on the ground that they are not harmful to our body, yet we know very little in which ways they may influence our gut microbes (e.g. [1]).

A higher proportion of North Americans tend to find certain kinds of food/snacks from other cultures gross, yet the perfectly sterilized/packaged/high-sugar food options here are probably much more harmful.

https://www.sciencedaily.com/releases/2018/10/181001101932.h...

Not only is this a period of great extinction, this is also a period of great sterilization where we are trying to kill everything that eats anything that we produce... as if we are not one of those things and somehow separate from it all. In the end this war will either be won in which case we will probably have a number of other health issues to deal with or lost in which we recognize that there is no difference between us and the environment and that we are both part of a whole that we can shape immensely.

For a visceral encounter with extremes on this theme, read Kim Stanley Robinson's novel "Aurora".

Having lost my own father to Parkinson's Disease (PD), my mother-in-law to a different progressive neurological disease and now watching my father-in-law walk through PD as well, your comment caught my attention. So I wondered if clinicians are doing fecal transplants to restore function in PD patients? A bit of searching and scanning found the following review

Gut microbiota: Implications in Parkinson's disease Parashar, Arun et al. Parkinsonism & Related Disorders, Volume 38, 1 - 7 [1]

Key passage

"This autonomic input from the gut is connected to the limbic system of the brain, which includes the hippocampus, the amygdala, and the limbic cortex. Limbic cortex is of importance since it regulates motor functions, which are impaired in PD. The connection between the limbic system and ANS is a critical factor underlying between gut health and brain & behavior [77]. Recently, it was found that fecal transplant from PD patients exacerbated motor impairment with reduction in Lachnospiraceae and Ruminococceae in recipient mice model of PD. Interestingly, same genera were significantly reduced in fecal samples from PD patients [27] link below [2].

Several case reports of patients with PD, multiple sclerosis, myoclonus dystonia, Alzheimer's disease, chronic fatigue syndrome, and autism have shown that FMT and/or antibiotic regimen was helpful in treating GIT symptoms like constipation, ulcerative colitis, and bowel disorders. Further, the therapy was helpful in relieving several non-GIT symptoms too"

[1]https://www.prd-journal.com/article/S1353-8020(17)30036-6/fu...

[2] https://onlinelibrary.wiley.com/doi/abs/10.1002/mds.26307

I think there are Nobel prizes for more work here. We know so little about how bacteria affects our bodies and the true roles that they place, despite there being billions and billions of them.

I’m pretty sure if we aren’t careful the same replication crisis that happened in social science will happen here, the interaction of the gut bacteria is so complex it will be very difficult to get consistent results.

I wonder how far away we are from simulating the human gut, so we can introduce a variable, hit 'run', and take a snapshot every x hours.

I'm guessing we're 0.0000001% of the way there, given how complex all the interactions must be.

I work in a lab where some of the researchers are working on the much simpler fly gut. Even in the simpler fly It’s very difficult to get anything approaching causality because they’re are so many variables in gut bacteria populations. It’s a huge ecosystem unto itself.

Flies can eat literal garbage so I am also curious how their guts do not have arbitrary digestive problems (let's just say there's not much quality control on the input). Also whether they develop infections.

I looked around a teeny bit and there's some stuff but what you describe doesn't show up right away.

This is a chemical (?) simulator that's been around since 1993 I believe: https://www.wur.nl/en/product/Simulator-of-Human-Intestinal-...

I also found this numeric simulator: https://learn.genetics.utah.edu/content/microbiome/simulator... but I can't view the content right now.

I think we're still far away from that, but we're trying to get there. Some successful work has been done based on AGORA models [1], where the simulations seem to roughly match the reality of simplified systems. For example, for a five-member community of bacteria, answering questions like "what happens if we remove bacteria B from the community?", but not too much beyond that yet.

[1] https://www.nature.com/articles/nbt.3703

They already do this to design fighter jets, rockets and space suits.

Those are much, much simpler systems. Your average human microbiome has 30+ trillion cells in it, too say nothing of the intestinal cells. That's not getting into the underlying complexity of the cells themselves.

The only way I see this being done is by running computer simulations. Knowing how complex our gut is, I'd say this can easily take another 100 years or so to get to the point where we can understand it in full.

Huh? Just survey people’s microbiomes, run cultures and use the drugs in the feedstock.

A number of human microbes aren't culturable yet.

I guess you do an in vivo post hoc analysis then.

In vivo bacterial population data isn't all that accessible yet either. Faecal bacterial samples have turned out to be poor representatives of the gut microbiome, so in vivo sampling requires endoscopy.

Fwiw, there are multiple biomes to sample too, with different types of bacteria lining the intestinal walls and other kinds populating the crypts, for instance.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837114/