Questions regarding human microbiota

[HenryLewis]

Ok, so before you guys look at me crazy, this is research for some leisure sci-fi writing...

 

Where do we get our microbiota from?

Like, obviously test tube babies have microbiota too, how do they get them?

Do people with relatively large genetic variation exhibit noticeable differences in their microbiota composition?

Do people that live in different geographic areas exhibit noticeable differences in their microbiota?

If you swapped all my microbiota with someone else's, whom is vastly different from myself (but same sex), would we live?

Edited June 8, 2015 by HenryLewis

[StringJunky]

An infant's microbiota gets kickstarted by ingesting material as it comes through its mother's birth canal.

 

What you eat roughly determines the composition of gut flora.

 

People have been given fecal transplants so, yes, you will likely live.

[Delbert]

Since I understand that our own cells are outnumbered by a factor of ten to one by foreigners, any change (like a complete swap with someone else) would doubtless have a significant effect - like we may drop dead!

 

Ten foreigners to one of us! So who or what are we, just somewhere for a load of bacteria to live?

[StringJunky]

...So who or what are we, just somewhere for a load of bacteria to live?

Yes, our full species name is: Homo streptostaphlyloenteroccocolactobifidosapien. sapien

Edited June 20, 2015 by StringJunky

[CharonY]

Since I understand that our own cells are outnumbered by a factor of ten to one by foreigners, any change (like a complete swap with someone else) would doubtless have a significant effect - like we may drop dead!

 

Ten foreigners to one of us! So who or what are we, just somewhere for a load of bacteria to live?

 

Nope, as already pointed out, fecal transplants are in medical use and our human physiology is so similar that the overall properties of microflora are not drastically different (though the composition does vary a bit). If we were that sensitive to bacterial load, any amount outside of a sterile room would kill us.

[StringJunky]

 

... If we were that sensitive to bacterial load, any amount outside of a sterile room would kill us.

...and we'd only have sex once.

 

The more I learn about our interdependence with our microbiota, the more absurd it seems that people spend a fortune and effort killing "germs". I also have a new wariness of antibiotics and how they affect my gut bacteria.

Edited June 25, 2015 by StringJunky

[Delbert]

 

Nope, as already pointed out, fecal transplants are in medical use and our human physiology is so similar that the overall properties of microflora are not drastically different (though the composition does vary a bit).

I presume you mean faecal transplants, because I'm unable to locate fecal in my dictionary. Sorry to be picky, but I don't want to misunderstand anything.

 

Up till now I was under the impression that it was a good idea to keep faecal matter away from re-ingesting, to apprehend a reproductive path for parasites, if nothing else.

 

Also, I understand we can probably obtain valuable bacteria from the birth process etc. But then what do we do? Probably flush the lot out - some possibly irreplaceable - after a visit to the doctors for an antibiotic after a minor cough or cold!

 

As for replacing the lot, there was quite an interesting prog on the radio4 (UK) the other evening whilst I was travelling home in which a researcher remarked about interaction. I recall she said that if life on Earth started again with exactly the same starting conditions as it was at the beginning, life would've taken a different path with the undoubted certainty that we wouldn't be here. I would've thought a similar - possibly chaotic - process may well take place with the bacteria within us such that our internal interactions probably results in a different outcome inside us for each one of us. And the consequence of changing the lot might be significant.

 

On a slightly different tack, I recall a report in the news a while back where someone had had a replacement organ (can't recall what it was, but it might have been a kidney), whereby he experienced a changed personality or something different about his mental state or interests or even ability to that similar to that of the donor!!!!! If that can do that what on earth would a complete bacterial change do?

 

Dismissing such a change as "If we were that sensitive to bacterial load, any amount outside of a sterile room would kill us." I think is a somewhat simplistic view.

Edited June 25, 2015 by Delbert

[StringJunky]

I presume you mean faecal transplants, because I'm unable to locate fecal in my dictionary. Sorry to be picky, but I don't want to misunderstand anything.

 

 

 

Faecal - UK. Fecal - US

 

 

Up till now I was under the impression that it was a good idea to keep faecal matter away from re-ingesting, to apprehend a reproductive path for parasites, if nothing else.

The transplant material is screened and inserted as a suppository.

 

 

Also, I understand we can probably obtain valuable bacteria from the birth process etc. But then what do we do? Probably flush the lot out - some possibly irreplaceable - after a visit to the doctors for an antibiotic after a minor cough or cold!

Yes, and some people will be setting themselves up for chronic bowel problems if they don't takes steps to facilitate repopulation of their gut with the symbiotic bacteria.

 

 

On a slightly different tack, I recall a report in the news a while back where someone had had a replacement organ (can't recall what it was, but it might have been a kidney), whereby he experienced a changed personality or something different about his mental state or interests or even ability to that similar to that of the donor!!!!! If that can do that what on earth would a complete bacterial change do?

Cobblers

 

 

Dismissing such a change as "If we were that sensitive to bacterial load, any amount outside of a sterile room would kill us." I think is a somewhat simplistic view.

if someone was immuno-compromised and/or the sample had a disproportionate amount of pathogens then, yes, it could cause problems but most people, no. I have read of people desperate with severe IBS and they have applied faecal enemas from their own family... with success. Not to be recommended as the norm though ... under medical supervision is the way to go. This was how I first heard about it.

[Delbert]

Faecal - UK. Fecal - US

Thanks for the info.

 

 

Cobblers

Well, presumably that's following your considered, reasoned and scientific evaluation. Anyway, just a couple I've found on the jolly old interweb: http://news.bbc.co.uk/1/hi/health/8084936.stm and http://www.namahjournal.com/doc/Actual/Memory-transference-in-organ-transplant-recipients-vol-19-iss-1.html to select just two.

 

It seems to me on a non-scientific evaluation that this is another one of those quick-fix scenarios without due diligence to any time affected consequence. Doubtless it all seems to work wonderfully on a short term evaluation.

 

Drifting off a tad back to the radio4 prog I mentioned the other day (Tuesday evening) still ringing in my ears (it's doubtless on website replay), when I think she mentioned one particular interaction. This being some highly infectious disease similar to Ebola (can't recall what it was) carried by bats. And it's now likely to jump to humans because of farmers grazing their pigs to feed on acorn like nuts - similar to what I understand others do when grazing their pigs on acorns here in the UK. I recall her saying the infection is transferred via contamination - droppings etc, not necessarily from the nuts but the general fauna. In other words it is simply humans introducing pigs to an area where they wouldn't have been naturally.

Edited June 26, 2015 by Delbert

[StringJunky]

The BBC article is reporting donors beliefs. Anecdotes are not evidence.

 

Your second link deserves a double-facepalm.

 

 

Magnetic field theory

 

Cells in the heart have a unique magnetic property and respond to and interact with magnetic fields. There may be an as yet undiscovered electro-magnetic connection between the brain and heart expressed in a form of energy that contains some level of cellular memory.

 

Unprepared spirit theory

 

Psychic healers interviewed by Dr Pearsall speculated that these experiences were caused because the donor’s spirit was still attached to the earth and had not yet moved to its abode in the higher subtle worlds.

[Delbert]

Perhaps the point I'm trying to make (in my clumsy way), which perhaps is something like the program I mentioned, is the interactions between living organisms or bacteria is highly complex possibly bordering on the chaotic. To the effect that as mentioned in the radio prog, even starting with the same - nay, exactly the same - conditions and ingredients, any outcome would be different each time. And I'd suggest the machinations within our guts of countless bacteria would be subject to the same. Rendering any suggestion that gut contents would be exchangeable like (say) a new engine in a car is false. In contrast, I'd refer to it like changing or swapping the unique fauna of two jungles between each other. They probably wouldn't survive very long even with only a small difference in environment.

 

Why is it we think we are detached from nature with all its intricate and fragile interactions; with the certainty that most of them are so vastly complex that we'll never fully understand them.

[CharonY]

You are missing the point that there are constant interactions between host and the bacteria. There are constant changes occuring at any minute. You use soap, you change the properties of your hand massively. You eat something, your gut sees a massive change in nutrient levels. Yet there is a kind of an equilibrium happening (which can change). The difference between biological systems and an engine is that it is very sturdy and can react very well to distortions.
A transplant is generally used when the patients has some conditions that put their biota out of whack leading to rise of unfavorable communities that e.g. may promote further inflammatory actions. In the best case the new biota eventually settles to a new system that hopefully gets rid of most the harmful ones that initiated. So regardless of your feelings about it, it actually works and does not kill the host.

Also note that if your biota changes during your own development and what settles on you is based on what you are exposed to. If there is only one specific community that is safe for you, it would mean your chances of dying from infection just after birth would be massive. The fact is that we can accommodate a wide range of communities although there are certain groups that tend to settle stably in the various niches of our body. And it is far from total chaos, or at least, about as chaotic as other ecological studies.

 

Or look at it that way, your skin is so similar to mine that exchanging our bacteria would have little effect (they will in either case be various compositions of Staphylococcus, Propionibacterium, Streptococcus, Pseudomonas, Corynebacterium (and a few others that I forgot) as the major candidates. Unless you have a certain genetic condition of your skin for example, the composition may shift once it is exchanged but that is about it.

Edited June 26, 2015 by CharonY

[Delbert]

You are missing the point that there are constant interactions between host and the bacteria. There are constant changes occuring at any minute.

Thought I was saying exactly that!! Clearly as I said, my contribution might be clumsy. Constant interactions as you say. And as the radio4 interviewee reported interactions are so complex - possibly bordering on the chaotic - that with exactly the same starting point and conditions, in the fullness of time one ends up with a different outcome. She was referring to evolution on Earth mentioning that any other such outcome we wouldn't be here. Which with the changes we have clearly made, represents a significant difference in the biota on Earth with what it doubtlessly would've been without us.

 

As I mentioned, she outlined the relatively trivial aspect of allowing pigs to forage on a few nuts (in areas where pigs wouldn't normally be) could end up with a highly infectious disease in humans. I seem to recall she even inferred that HIV was as a consequence of something similar! And also Ebola.

 

I quite understand that in the event of someone suffering from a problem whereby a biota transplant would be viewed as beneficial to the point of lifesaving, it should be done. But that's not the question as I understand it, but rather the possible biological or bacterial consequences.

 

I think the natural world is full of disadvantageous consequences from what we've done, which at the time seemed a pretty good idea.

 

Unless I've totally misunderstood your comments, it seems we agree on just about all.

Edited June 26, 2015 by Delbert

[CharonY]

I think we start off on a point of agreement but the conclusions you draw and especially the extrapolations you make(people would die if they exchanged floras) are quite different. There are various degrees of what you may perceive as chaotic interactions and there are underlying mechanisms.

For example, every birth incorporates transplantation of the gut biota, so to say. It is by far something drastic. Every time you take antibiotics you re-arrange your flora as another example. The process of establishment of biota is under investigation and it is not a total random process.

[StringJunky]

I think we start off on a point of agreement but the conclusions you draw and especially the extrapolations you make(people would die if they exchanged floras) are quite different. There are various degrees of what you may perceive as chaotic interactions and there are underlying mechanisms.

For example, every birth incorporates transplantation of the gut biota, so to say. It is by far something drastic. Every time you take antibiotics you re-arrange your flora as another example. The process of establishment of biota is under investigation and it is not a total random process.

Each species will settle in its niche environment. won't it, so it's hardly random?

[Delbert]

I think we start off on a point of agreement but the conclusions you draw and especially the extrapolations you make(people would die if they exchanged floras) are quite different. There are various degrees of what you may perceive as chaotic interactions and there are underlying mechanisms.

Well, I don't think I said it was chaotic, but rather the radio4 prog. And not only that I said 'bordering on chaotic'. But after all, what else would one call or refer to a system where an outcome would be totally different each time from identical starting conditions? Because a different outcome is what I recall the interviewee said.

 

 

For example, every birth incorporates transplantation of the gut biota, so to say. It is by far something drastic. Every time you take antibiotics you re-arrange your flora as another example. The process of establishment of biota is under investigation and it is not a total random process.

Think I said I agree with the birth business. As for antibiotics re-arranging, perhaps that's one way of expressing it. I would say that killing some - if not all - gut bacteria is another way of expressing it.

 

Anyway, going back organ transplants possibly having a mind altering effect, Toxoplasma Gondii has just wandered through my mind. Seem to recall that there's a suggestion that some 25% of the human population are infected - without knowing it! It apparently affects the mind or personality with the result that we may be inclined to take slightly more risky actions in life. Also, I understand a high number of road traffic victims have been found to be infected - I further understand it is apparently one of the things they test victims for. Now, if the transplant donor was thus infected would the recipient then possess a different approach to risk? In other words his or her mind has been altered. And doubtless there are other such infections.

[CharonY]

Well Toxoplasma are parasites spread by cats (and also they are not bacteria). But the point is that as many other pathogens they infect host cells. This is what the normal flora is not able to do (provided the host does not have some severe condition, which would disrupt the flora). The same argument can be made for viruses (e.g. infected blood samples) etc.

 

But again, it would be a topic separate from the normal microflora.

[Robittybob1]

Well, I don't think I said it was chaotic, but rather the radio4 prog. And not only that I said 'bordering on chaotic'. But after all, what else would one call or refer to a system where an outcome would be totally different each time from identical starting conditions? Because a different outcome is what I recall the interviewee said.

 

Think I said I agree with the birth business. As for antibiotics re-arranging, perhaps that's one way of expressing it. I would say that killing some - if not all - gut bacteria is another way of expressing it.

 

Anyway, going back organ transplants possibly having a mind altering effect, Toxoplasma Gondii has just wandered through my mind. Seem to recall that there's a suggestion that some 25% of the human population are infected - without knowing it! It apparently affects the mind or personality with the result that we may be inclined to take slightly more risky actions in life. Also, I understand a high number of road traffic victims have been found to be infected - I further understand it is apparently one of the things they test victims for. Now, if the transplant donor was thus infected would the recipient then possess a different approach to risk? In other words his or her mind has been altered. And doubtless there are other such infections.

I seem to recall this as well. Is this covered in the OP? Can we discuss T. gondii?

[StringJunky]

I seem to recall this as well. Is this covered in the OP? Can we discuss T. gondii?

Micro-organism-induced behavioural/mood patterns are not just specific to pathogenic types like T. gondii, symbiotic gut microbiota in general are considered to have an ongoing important effect on our mental states... the field still has lots to learn but the microbiome is an important part of our existence. It is not an exaggeration to say that we are a walking ecosystem. "Gut-brain axis" is the term you want to search for if it is of further interest.

 

 

The gut–brain axis refers to the biochemical signaling taking place between the gastrointestinal tract and the nervous system, often involving intestinal microbiota,^[1] which have been shown to play an important role in healthy brain function.^[2][3]

 

The gut microbiota communicates with the Central nervous system (CNS) through different pathways (neural, immune and endocrine) and influences the brain, more specifically its function and its behaviour. Several studies shows that the gut microbiota is involved in the regulation of anxiety, pain, cognition and mood. These studies used germ-free animals compared to normal animals, which were later exposed to pathogenic bacterial infections, probiotic bacteria and antibiotic drugs. The gut-brain axis is an emerging concept that could be helpful for developing new therapeutic strategies for complex CNS disorders by modifying the gut microbiota.^[4]

 

https://en.wikipedia.org/wiki/Gut%E2%80%93brain_axis

..Like, obviously test tube babies have microbiota too, how do they get them?

The real test-tube babies, gestated ex-utero that are currently science-fiction, will not have a microbiome so their introduction will need to be tailored and introduced artificially, as and when the procedure becomes feasible. A biotech company is currently in Phase II trials for creating patient-specific bacterial colony profiles to correct bowel problems and other gut biota imbalances.

 

 

...Behind its lead prospect, Seres is working a preclinical C. diff. treatment called SER-262 and a handful of early-stage candidates for inflammatory bowel diseases and bacterial infections.

 

Key to the biotech's work is its proprietary development engine, dubbed Ebiotics, through which the company compares the gut compositions of healthy people with those suffering from a targeted disease. Using proprietary algorithms, Seres then determines what in the former gut is missing from the latter, growing the spores needed to match the two and packaging them in a tablet.

 

http://www.fiercebiotech.com/story/seres-guts-out-134m-ipo-fuel-microbiome-rd/2015-06-26

Edited June 27, 2015 by StringJunky

[Robittybob1]

Micro-organism-induced behavioural/mood patterns are not just specific to pathogenic types like T. gondii, symbiotic gut microbiota in general are considered to have an ongoing important effect on our mental states... the field still has lots to learn but the microbiome is an important part of our existence. It is not an exaggeration to say that we are a walking ecosystem. "Gut-brain axis" is the term you want to search for if it is of further interest.....

 

That was surprising and I will look into the "Gut-brain axis" further, thanks.

[CharonY]

I seem to recall this as well. Is this covered in the OP? Can we discuss T. gondii?

 

Well, now it is moving from the microbiota to infectious diseases. If that is of interest to you maybe start a new topic? While common it is as much a normal part of the human microbiota as, say Plasmodium palcifarum (causative agent of malaria).

[Delbert]

Well Toxoplasma are parasites spread by cats (and also they are not bacteria).

In cats during the reproductive part of its lifecycle, I believe. At other times it is on the ground or thereabouts waiting to be picket up by rodents and the like. And the mind altering factor then comes into play, which makes the rodent undertake risky manoeuvres so the parasite can get back into a cat or similar, i.e. the rodent 'places itself on offer' to use the vernacular. Apparently we might have a similar penchant for risky activity, should we be infected.

 

A passing comment might be that perhaps there's no such thing as a 'good mouser', when referring to a pet cat. It may simply be all the mice in the vicinity are infected with T. Gondii!!

 

As for drifting off subject, perhaps, but I mentioned the infection business as a possible consequence of biota transplants to those who apparently take the view that it's no big deal. So I wouldn't have thought it to be too far off subject.

[overtone]

1) Fecal transplants often have to reach the small intestine, not just the large one - a milkshake, not an enema.

2) There are many suggestive correlations between gut biota and such disorders as obesity, diabetes, etc. (At least one person receiving a fecal transplant from an obese person became obese themselves/ the mechanism behind the increase in obesity in people ingesting artificial sweeteners seems to be gut biota mediation/ obesity seems to be transplantable between lab rodents, in both directions, via gut biota transplants/ etc).

[Delbert]

1) Fecal transplants often have to reach the small intestine, not just the large one - a milkshake, not an enema.

Yes perhaps a milkshake would be more advantageous, the direction of transit is back out!

 

2) There are many suggestive correlations between gut biota and such disorders as obesity, diabetes, etc.

My view is that gut biota might play a significant part in our general health and state of mind. Anecdotal I know, but a friend of mine that suffers from diabetes was questioned by a nurse about how often he performs a number 2. He said every three days! The nurse firmly said: that's not right. He replied: but that's normal for me! Perhaps there's a connection there with his diabetes.

 

(At least one person receiving a fecal transplant from an obese person became obese themselves/ the mechanism behind the increase in obesity in people ingesting artificial sweeteners seems to be gut biota mediation/ obesity seems to be transplantable between lab rodents, in both directions, via gut biota transplants/ etc).

That's interesting.

[Robittybob1]

 

... At least one person receiving a fecal transplant from an obese person became obese themselves ...

Was that a causal relationship?