There are a variety of strategies being pursued to make pharmaceutical products out of microbiome research. Broadly those are: 1: "bugs as drugs" - genetically engineered microbes that perform some function. The idea here is that having the microbe in situ performing some function will be a much better way to administer a particular compound (or set of compounds), or remove a compound, than a traditional pharmaceutical. Large pharma companies have studied phenylketonuria as a metabolic disease for which the bugs as drugs approach would be great. Find a microbe that consumes phenlyalanine at a high rate and administer it at high levels (or get it to stably engraft in the host) and you have a treatment that would be vastly better than current dietary regimes. 2: "community engineering" - this takes many forms from fecal transplant, to trying to engraft a certain small cocktail of strains, to altering what the in situ community is doing by feeding a probiotic. The idea here is that there are tens of thousands of metabolites that microbes are producing in the gut, and by balancing or tailoring the set of metabolites that are made, you can improve health. Fecal transplants have good data for clearing recurrent C. diff in phase III clinical trials - this is the best developed of the microbial therapeutic strategies currently. Everything else is phase I or before. 3: "microbial natural products" - this is the world I work in (shameless self-promotion - if you want to come work at a very early stage microbiome startup email me at will@interface.bio). The idea here is to find the particular chemicals/metabolites that microbes make that have positive influences on our physiology. Most research here is focused on immune conditions, metabolic syndrome/dietary stuff, though there is increasing interest in depression and other conditions.

At a broad scale, I would say it will be 1-2 years before fecal transplants receive approval as a therapy for recurrent C. diff infection, at least 5 years before a bug-as-drug will be available, and at least 7 years before a microbe-derived natural product is on the market as a pharmaceutical. It takes an incredible amount of work to get from these associational studies to a pharma-grade product.

In the interim, I think there will continue to be a bunch of diagnostics and probiotics companies that (IMO) are bordering on absolute nonsense. There is very little predictive value to the tests supplied by most of these companies, and the data on probiotic efficacy is bad in humans. There is good evidence of probiotic and prebiotic effectiveness in animal husbandry (e.g. fish and livestock) but the data just aren't there in humans.

Also have an IBS diagnosis.

Had a great doctor that helped me get started, after many that did a shoddy job, and this has been my experience as well.

Very much a 'seems like IBS, try low FODMAP, see what works and doesn't via experience,' which was pretty amazing/alarming how little is understood about our guts.

I'd love to know when the science is going to start catching up. Especially since I think it'll be interesting to find out if something has been added to our diets that's causing an increase in intolerance over the last decade+.

I don't have much knowledge on supplements or even diet - beyond it's intersection with the microbiome. From the microbial perspective I think traditional dietary stuff is enough - eat fibrous plants and legumes and that's all you need to do.

I think you hit it on the head - the C. diff stuff is good and will meet FDA criteria soon (the phase III data from ECOSPOR was good: https://www.clinicaltrials.gov/ct2/show/NCT03183128).

In general we only have mouse or other animal data for other indications.

There are retrospective analyses of patient cohorts receiving anti-PD1 or anti-CTLA4 therapies which have identified certain microbiome states as supportive of those therapies. I believe that these are probably real effects, though I don't think the particular microbes matter - instead I think it's the metabolites they produce and how those influence resting immune state (https://www.science.org/doi/10.1126/science.abf3363 - but you can find many more).

A paper I really like shows that a specific protein from a common gut microbe (Akkermansia muciniphila) confers resistance to diet induced weight gain, insulin insensitivity, etc. (https://www.nature.com/articles/nm.4236).

In general, I think the majority of microbiome work has been associational and demonstrative of the kind of hypothesis-free science that is prone to all sorts of statistical artifacts and misaligend incentives between truth-finding and paper publishing (garden of forking paths, file-drawer effect, etc. etc.)

Fascinating question - and not one whose answer is known.

Fiber is good for microbes merely by the virtue that humans lack the glycan-degrading enzymes that are necessary to break it down, so it reaches the colon intact where the microbes can eat it. Humans can digest starch (though it can be physically and chemically modified to be harder to digest) but not the hundreds of other types of fibers that are found in a traditional diet.

I think there is good research that shows that higher fiber diets are associated with lower risk of developing a range of metabolic and immune pathologies, but the particular mechanistic linkages are so subtle that it will require absolutely massive studies to identify them. In general, we know that humans used to eat a much higher fiber diet (e.g. the Hadza people eat 70-150 grams of fiber a day), and we believe that produces a much healthier microbial composition.

The paper you cited is really interesting! I haven't read it - but the overall idea that the mucus lining of the gut can be degraded by microbes who are sourcing carbon, energy, and nitrogen from it is well established.

I think there is consensus that some amount of gut barrier integrity is due to microbial signals. This occurs in two ways - 1) our epithelial cells sense microbial products (proteins, carbohydrates, etc.) and respond by tightening the junctions between them. The overall idea being that you want to keep the bacteria in the colon, but you must balance some level of nutrient flow. 2) The goblet cells which produce mucus in the gut, respond to microbial signals to increase or decrease their mucus production.

There is a lot of research going on trying to understand how certain diets cause defective mucus production and in turn how that can allow microbes to get to close to the epithelial lining (usually the mucus is ~100 microns thick) which results in inflammation.

Recent evidence of another function of microbial activity in the gut of hibernating animals. In short, it appears that they help the host supply enough nitrogen for maintaining muscle mass during hibernation: https://www.science.org/doi/10.1126/science.abh2950

I think it's really hard - we don't know what a healthy state of the microbiome is. There is likely a lot of individuality, what is healthy for me is maybe not healthy for you. This probably has to do with early life immune system development and what we were exposed to as kids.

At a high level we know that diversity of microbial species in the gut (but for instance, not in the vagina) is linked to better overall health state. Is this because of the microbes? Probably not, it's probably that the microbes are a sensor/responding to an overall healthy diet/ecosystem.

In general, there are commercial services to track your microbiome and they are interesting from a data perspective, but I am not sure you will get much health information out of them.

We know the answer to a healthy diet - there are no microbial talismans - but it's just not sexy. Eat lots of plants, less sugar, and exercise. I wish it was as easy to follow this advice as it is to write haha.

Fascinating question - also not totally known.

We know that microbes colonize the gut in a somewhat predictable way as a function of age. As a newborn your gut is largely dominated by Bifidobacteria, and this slowly transitions to a more complex community over the next several years of life. Events like early childhood antibiotics, malnutrition, other disease, etc. can alter this trajectory. Interestingly this kind of ecological succession seems to be driven by an interplay of both immune maturation (as your immune system matures it starts being more selective about who it tries to let in) and by chemical processes. The gut becomes more anaerobic as the number of bacteria increase (and transition away from the Bifido dominated state) and that has a strong selective effect on the microbes that will grow well.

For specific commensal bacteria we know some of the mechanisms of colonization - there are particular genetic programs that bacteria turn on when they sense they are in the gut to enhance their ability to be retained and not washed out. These programs include physical attachment, motility, and chemical signalling to try to dampen the local immune response.

Pathogens are extremely good at getting in to the gut despite our best attempts at keeping them out. Salmonella typhimurium is notoriously adept at colonizing the host - the infectious dose you need is maybe 10 microbes taken orally in a susceptible host (compare that to 10 billion microbes/capsule in a probiotic).

For these specific bugs I don't know that much. I am excited to read more.

Far from being an expert on the subject, but I read a paper that said that eating raw vegetables would usually increase the degree on inflammation, but cooked vegetables had the opposite effect.

Absolutely - the chemicals that microbes make in the gut pass into your blood stream and from there access the entire body. There are mechanisms the body uses to ensure these chemicals are detoxified (phase I and phase II metabolism in the liver) and that they are excreted if they reach too high a concentration.

More locally, the enteroendocrine cells (https://en.wikipedia.org/wiki/Enteroendocrine_cell) that line the gut translate much of the internal nutrient state of the gut up to the brain to tell you things about if you should eat, etc.

There is a lot of research on how we could alter satiety by finding the right language that these cells use. There are approved drugs on the market that mimic the activity of these cells (incretin mimetics) to reduce appetite/weight control.