The microbiome: unanswered questions

(This may be of interest to @snowathlete , @Viking, @Vegas, @halcyon and others)

Things about the microbiome that I haven't worked out, and am trying to:

> 1: According to Blaser, the gut microbiome is formed between birth and approximately six years after which even if it is disturbed it will try to bounce back to this original configuration.

How exactly do the species inculcate in the gut during this period?

> 2: Is there really no way, bar fecal transplant, of repopulating the vast majority of the microbiome's residents that are not currently available as probiotics and fermented foods?

> 3: Complete a definitive list of non dietary interventions that have been proven or speculated to benefit the microbiome in some way. So far I have: adhering to a normal circadian rhythm; high protein diet; exercise; reduced stress.

> 4: What is the relationship between dysbiosis and leaky gut?

> 5: The major question: how exactly does antibiotic use effect the microbiome negatively? Does it merely create dysbiosis or are certain species eradicated entirely? If so, per question two, is there any way to get them back?

> 6: Soil based organisms. Any advantage over mainstream probiotics? Any non supplemental way of getting them safely?


2. I need to do more research on this, but I do think there must be general exposure in the environment. Else, how do babies get it in the first place? There are some people working on faecal transplant pills that you may have seen in the press.

Another question that we only have part info for is, what medications and supplements impact the get flora and how?

4. There are people exploring this, and I think some papers published already, but leaky gut is complex and has lots of different theories as to its cause. I want to know the answer to this too.

6. I haven't looked into this much yet, but SBO might be useful simply because they are different to the other probiotics available, which are very limited. But real soil is probably much more diverse and I suspect also contains bacteria that would colonize the gut, the same ones that we might want but lack. Whereas the SBO on the market, so far as I know, do not colonize the gut (with one exception belonging to the Bacillus genus). I haven't looked but there must be some papers on the bacteria in different soils. Failing that, I have thought it would be interesting to do a uBiome test on soil from my garden to see what the heck is exactly in it, but I'm not sure it's worth $89, or whatever it is now.
Thanks, snowathlete. I've heard and read lots about FTs, but it seems like a crude and last ditch solution as it's currently available to us, and there (logically) doesn't seem to be a guarantee that it will improve your condition if it's not directly gut related like C.Diff -- just an off chance that it might transplant some commensals that you don't have, but there also seems to be a strong chance that your donor's gut flora will be in just as bad a condition as yours, or worse (I think there have been reports of people actually acquiring new AI conditions, or having existing ones exacerbated rather than helped).

When they've finally finished working out what's good and bad in the microbiome and gotten to the stage where a commercial FT pill is available (sanitized and sans the food residue, of course), I'll be first in line to try it, but with the pace medical research moves I'm not banking on that happening for another 10 years at least (is that pessimistic?)

Thanks for the info on the soil. It seems like a double edged sword in that what you're saying is probably true, but there's also undoubtedly pathogens that are obviously filtered out of the commercially available varieties.

Like everything in this, doesn't seem as if there are any easy answers to anything!
Wow lots of questions.

In addition to the innoculation while passing through the birth canal, breastfeeding is critical for establishing the microbiome. The mammary ductal network and breast tissue is loaded with bacteria that based upon my understanding, has tooriginate from the gut. This is very new science. It has only been recent in human history that infants were born via c-section and formula fed. Your mothers GI health likely plays a very large part in the shaping of the immune system. Inflammatory disease processes are significantly more likely to occur in those who were not breastfed and/or born via c-section, but obviously this is only one of many factors.

Short-term antibiotic usage can have varying effects typically both positive and negative, but I think the ability to conduct such a risk/reward analysis and determine the net gains is precluded by the complexity of the equation. Based upon what I have seen, including a lot of metabolic data, I believe long-term antibiotic usage is always negative. Also understand that a healthy microbiome is populated by dozens of organisms that produce the same compounds used in many antibiotics. I am not sure about complete species/strain eradication, but the diversity of functional abilities of other commensals likely fills in the gap.

Best way to fix the GIT appears to be through promoting the expansion of commensal microbes via prebiotic supplementation. Forms of Mannan, Xylan, Starch that are resistant to upper GIT fermentation/digestion seems like a good start.

SBO's convey certain benefits and more importantly they do not contribute any apparent negative metabolic consequence. Most anaerobes demonstrated to be able to induce an anti-inflammatory response are soil inhabitants. B. Subtillis, commensal clostridial organisms. They play a role in the nitrogen cycle.

Blog entry information

Last update

More entries in User Blogs

  • Day 46
    Night 45 I am definitely sleeping better now than I was, but I am...
  • Day 45
    Today I woke up with a much better throat, wasn't really sore anymore...
  • Day 44
    I am more or less convinced now that post covid jab (2nd jab) I have a...
  • Day 43 - Dose 3
    Have been having chest tightness, increased anxiety and feeling off the...
  • Day 43
    A slightly different entry today. I think I am trending in the right...

More entries from dan062