r/HumanMicrobiome

Bacteria testing based on stool is widespread, but unreliable. There is little known about the gut microbiome and how each bacterial species behaves inside it. It is just now being discovered.

Instead, a more concrete methodology would rely on established fecal tests for chymotrypsin, trypsin, and elastase (all used to break down protein) to detect any odor causing enzymes in the stool.

I have not looked into it yet, but the enzymes would be the ones related to odor such as methane-producing, sulfur-compound producing, toluene-producing, etc. The gas made in the gut should be a gas that somehow causes constipation for the host and gets across the gut into the blood.

It seems the established methods use antibodies, but a baseline would need to be measured from "normal" people to see how much of a particular enzyme they have, to see what is considered "normal." This could take decades, but its worth studying.

As for methane, which is shown to slow down the gut (causing constipation), a substance of note is bromoform, used in the cattle industry to prevent cow methane. It is toxic to humans, but I am sure a suitable dose or delivery method (perhaps directly to the colon via rectum) will come soon. Or other substances exist to prevent methane in the human gut. Ask AI for more.

Further, a SIBO test might not detect this mechanism. SIBO relies on the methane gases climbing up through the stomach. In this case, methane is contained in the colon, but the secondary effect being bodily toxins unable to leave and hence being emitted from us due to constipation preventing toxins from leaving quickly. This is compounded by most SIBO tests requiring you to fast beforehand, preventing colonic effects from being shown.

On Reddit, the standard advice for fixing your gut microbiome is to eat better: more fiber, more fermented foods, more probiotics. But it misses the root problem, and it rests on a flawed assumption that poor diet is what knocks the microbiome off balance in the first place. As soon as you stop eating like this, the bad gut comes back.

For many people, dysbiosis begins with a specific event, such as food poisoning, COVID, or a viral illness. Put it this way, People with healthy guts can eat McDonald's and junk food with no to few consequences, not because their diets are special, but because their guts are fundamentally colonized by beneficial bacteria. That colonization is what makes them resilient. That is how you can tell a gut is truly good: even when subjecting it with bad bacteria (junk food), the existing gut architecture is able to wash out.

Most of us, outside of outliers, were presumably born with a healthym, functional gut. Dysbiosis usually isn't a baseline condition; something disrupts it, and OFTEN it's a one time event like COVID, a viral illness, etc. Once that happens, more fiber or a daily probiotic often doesn't fix anything, because the effects are transient. Underneath, the gut is still dominated by the wrong bacteria. I have nothing wrong with people eating fiber and good bacteria, it promotes general health and people should do this. And it offers symptom relief for those with these problems.

BUT IT DOES NOT FIX THE GUT ITSELF!!! It's like having a sink that doesn't drain properly because there's a blockage. Toxic sludge accumulates. A functional sink can effectively drain most everything. A non functional sink piles it up. This is the equivalent of putting in draino or manually throwing the food waste in the trash can as opposed to down the drain. Puts less strain on the sink, less sludge accumulates but THE TOXIC SLUDGE WILL STILL PILE UP IN THE FUTURE BECAUSE THE BLOCKAGE HASN'T BEEN ADDRESSED!!!

Treating the root issue means shifting the gut back to eubiosis, which requires re-establishing a lasting population of beneficial bacteria. Transient probiotics can't do that, because they pass through rather than colonize. A truly healthy gut SHOULD be able to sustain bad actors (junk food, inflammatory food, bacteria) to a reasonable degree and go back to eubiosis. Because in that case, eubiosis IS homeostasis. Solutions to the gut should address THIS not telling people to eat more fiber.