Gut Flora: The Natural Reservoirs Question
page at BioGaia®:
first strain of Lactobacillus reuteri (L. reuteri) for human use,
L. reuteri DSM 17938, was isolated in 1990 from the breast milk of
a Peruvian mother living in the Andes. The commercial name is L. reuteri
Protectis. Other human strains from BioGaia are L. reuteri
ATCC PTA 5289 and ATCC PTA 6475. L. reuteri
ATCC PTA 5289 used in oral health products was isolated from the oral
cavity of a Japanese woman with remarkably good dental status and
L. reuteri ATCC PTA 6475 was isolated from breast milk
Well, OK, but where did those women get those bacteria?
BioGaia is a bit vague on that:
our commercial strains are of human origin…”
Put another way, just what is the natural reservoir for these
species and strains? (And
this is all a completely separate issue from why some of those accession
numbers are “PTA”: patented.)
Why This Matters
There are still critical unknowns in optimizing
If the natural reservoir for any crucial forms of human gut microbes is solely the human gut,
there’s some risk they could go extinct, and perhaps before we even know what they
Dr. Davis has recently mentioned that L.reuteri may already be extinct in
major swaths of most modern settler human populations.
Microbe extinction had heretofore been seen primarily as a benefit.
The natural reservoir for the virii variola major and
variola minor (smallpox), for example, was strictly the
human population. It was made extinct there by vaccination and infection
control, and now (with any luck) exists only in P4 lab freezers and
computer gene models.
Persistent or Subscription Model?
For any specific beneficial bacterium, virus (including bacteriophage), eukaryotic parasite,
fungus (yeast), protozoan or unknown-unknown, does it take up residence
permanently, or does it need to be topped-off from time to time?
And in any case, what do they need to eat?
Even if “permanent”, can certain extreme events (infections,
anti-microbials, radical diet shifts, ingested toxins) cause a temporary extinction?
And without assured re-exposure and re-colonization, temporary may
Microbe Sources, Trends and Implications
||Where the human population is the only reservoir, the flora are
presumably passed maternally by various means, and by oral contact
with other family or group members.
Hazard: Once lost, it’s gone, unless
we can identify it and source it from some other community.
Even arresting this process seems to be some years off.
||Ancestral exposure would include
casually-cleaned root crops, and
darn near everything swallowed due to lax hygiene.
Some populations might even have deliberately consumed at least
some soil types, for mineral content, etc.
Hazard: These practices are now largely absent (but so are some major pathogen risks).
Children are less feral than ever.
If the natural reservoir for some key microbe was in the soil,
it isn’t now on your plate.
Question: how important is being on ancestral ground?
Question: what have modern farming practices done to the soil microbiome anyway?
||Ancestral exposure would include unfiltered, untreated and un-boiled
stream, lake, pond and pool water.
Hazard: These sources now go unused (along with major pathogen risks, some recent).
What is used instead is microbe-deficient, micronutrient-deficient, and
often loaded with microbiome hazards (water treatment chemicals).
The use of chloramine in particular may still be on the rise.
If the natural reservoir for some key microbe was in the water,
it isn’t now in your glass.
Question: what role geographically ancestral sourcing?
||Ancestral exposure would include game offal, whole insects, plant foods
with native external and internal microbes, animal droppings and insect droppings.
Hazard: Moderns clean food, often to the point of sterilization,
and don’t consume offal. If the natural reservoir for some key
microbe was the microbiome of some other species, we’re missing it now.
Question: are these sources being studied?
||Itching and diseases (many serious) might not have been the only thing
humans got from bites. The surviving hunter-gatherer guts are known to
include of what moderns would consider adverse parasites, but are they all, really?
||Any bugs on the breeze get onto the skin, and into orifice microbiomes.
Hazard: the modern urban environment is not the ancient one.
Question: is this just something to sneeze at?
||There may be sources not so far considered.
In some ape species, gut flora might be reliant on coprophagia.
Was it a feature of ancient human populations?
FMT would likely never be considered by fastidious moderns, were it not
for the fact that it often works in spectacular fashion, when all else has failed.
How important is it that people remain in contact with their ancestral natural reservoirs
of gut flora? Were it critical, we might expect to see some historical evidence of
collapses of migratory populations, whose guts were mortally maladapted to their new
locales. Archaeologists looking for ghost colonies might want to keep this possible
scenario in mind. We certainly see effects
for frank diseases, where the pre-Columbian western peoples are thought to
have gifted the European explorers with syphilis, and got smallpox in return.
Anything that is airborne, and can survive a few weeks that way, is likely common
planet-wide; similarly for things sea-borne, or able to be carried by migratory
animals, particularly birds. But it may be that some things are local, to which
local genotypes were adapted, and their descendants need to be mindful of
Some canaries in the microbiome mine might include nuclear submarine crews, and
space station astronauts. These populations are cut off from terrestrial
microbe sources for 3-6 months. Based on ONR
and NASA study proposals, there seems to be growing awareness of problems
related to this.
Colonization of other bodies in the solar system (Moon, Mars) requires that
this get resolved, particularly Mars, where the perchlorates in the native
soil are apt to be entirely hostile to any attempt to replicate Earth
Limited Time Offer
So what do we need, and where does (did) it come from?
Perhaps the top source of reference data are the surviving
hunter-gatherer populations, and they are getting some study.
We need to learn what we can, as rapidly as possible, before what they
have to tell us is obliterated by an invasion of "healthcare" and modern food-like
substances with their disastrous macronutrient balance, grain toxins,
fake fat toxins, preservatives, emulsifiers and other gut antagonists.
I’m expecting the Undoctored program to be an aggressively cautious early exploiter
of emergent information.
Bob Niland [disclosures]