
What Is the Human Microbiome, Exactly? - dnetesn
http://nautil.us/blog/what-is-the-human-microbiome-exactly
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vermooten
Best metaphor I can think of is coral - humans are the coral and we exist to
serve the biome, not the other way around.

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cantrevealname
> _humans and microbiota: each needs the other to survive_

Would we literally die without the microbiome? At least with respect to gut
flora, the answer is no[1]. I'd be interested to hear about some part of the
microbiome that is absolutely essential to human development or human
survival, the way skin and blood are essential. As far I've been able to
determine, a human being could live 5 years on Mars with a stockpile of
processed food[2], water, and oxygen, and _without the microbiome_ or any
organism within a hundred million kilometers. It would be very interesting if
that's proven wrong.

[1]
[http://www.sciencedirect.com/science/article/pii/S0165247805...](http://www.sciencedirect.com/science/article/pii/S0165247805000052)

[2] I mean non-living food of course.

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aldoushuxley001
I don’t think your first citation actually proves humans can live without gut
microbiota. I simply don’t see evidence that’s the case and it would be very
very difficult to demonstrate.

In most cases humans with severely disrupted gut microbiota (diminished
populations) end up in severe pain and health complications.

I sincerely doubt a human could live on mars without a gut microbiota (or
anywhere for that matter); we’re actually not just simple systems that require
only basic inputs to function.

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wdwvt1
Microbiome researcher here.

We routinely use germfree mice, rats, and pigs in our research. They are
completely devoid of bacterial and fungal cells. Their immune systems develop
abnormally and they have some behavioral oddities, but they have no reduction
in lifespan or fecundity.

Nutrient capture is really not that large a part of the gut microbiomes role;
most of the nutrient and caloric uptake occurs in the small intestine of
humans. The small intestine has many bacteria, but maybe 1e-3 fraction of the
large intestine. Interestingly, humans have a much larger small
intestine:large intestine ratio than close primates. Likely we evolved on such
a high quality diet (animal protein) that our need to extract nutrients from
plants declined and allowed shortening of the large intestine. When you get
high quality feed, you don't need a big bioreactor to ferment plants into
calorically valuable products like short-chain fatty acids.

This is not to say that humans aren't better off eating a very plant rich
diet. All the research suggests strongly that a diet very high in fiber feeds
a healthy guy microbiome which helps resist pathogen invasion and helps create
a balanced immune system.

In short: if you could rear germ free humans, I think they'd be just fine, if
perhaps immunologically odd.

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aldoushuxley001
Interesting.

I'm curious though, considering bacteria, fungal spores and viruses are always
floating in the air around us to some extent, and almost all food similarily
has bacteria, fungi and viruses in it (to some extent), how do you keep
germfree mice, rats and pigs germfree? What are you feeding them? And what
about them just being exposed to normal air?

I can't help but think of a GI tract completely devoid of bacterial and fungal
cells as being a massive power vacuum essentially. And even if germfree mice,
rate and pigs are born that way, wouldn't it be incredibly difficult to
prevent these free-floating bacteria or fungal spores from inoculating their
GI tracts? whether just through air or food?

I would love to see a study analyzing a germfree mouse, rat or pig that was
kept germfree to full life as best as possible and then do an analysis on
their microbiome to see if, in fact, they are germfree at the end of their
life too. I'm not confident they would be.

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wdwvt1
They are kept in vinyl bubbles. The only things that enter the bubbles go
through sterilization: a liquid sterilization for tubes/plasticware, etc.,
irradiation for food, autoclave sterilization for water and liquids. Germfree
animals have been around for more than 70 years - they are actually not that
hard to create in rats and mice because a fetus is sterile in utero.

> I can't help but think of a GI tract completely devoid of bacterial and
> fungal cells as being a massive power vacuum essentially

This is absolutely true for the right organisms. Surprisingly there are quite
a few common human gut microbes that cannot colonize a germfree gut. Reasons
are still not totally understood.

> I would love to see a study analyzing a germfree mouse, rat or pig that was
> kept germfree to full life as best as possible and then do an analysis on
> their microbiome to see if, in fact, they are germfree at the end of their
> life too. I'm not confident they would be.

This paper [0] from 1971 is a good review of the 40's and 50's work showing
that germfree hosts are basically normal and can be easily maintained as
sterile with proper procedure.

[0] Gordon and Pesti, The Gnotobiotic Animal as a Tool in the Study of Host
Microbial Relationships, Bacteriological Reviews, 1971

~~~
aldoushuxley001
Fascinating, thanks for the reply. I always love hearing the protocols for
requirements like this, makes a lot of sense tho, re: the sterilization
techniques (irradiation for food, autoclave for liquids, etc.).

I'm surprised the germ-free animal models had such surprisingly normal
lifespans. Thanks for the link too.

Part of me is still skeptical of the degree to which the germfree animal
models are in fact germ free at the end of their lives (I'll have to do some
more digging through the literature).

Seems like these germfree animal models should yield some great insights into
the microbiome tho.

Just curious, what sort of projects are you working on? It's a fascinating
field.

Slash, what are your opinions of all these microbiome mapping tests (e.g.
Viome, etc.). I mean, our microbiomes seem to change fairly frequently such
that a singular snapshot at these relatively infrequent intervals seems
inadequate for most uses.

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atombender
Hippocrates is said to have claimed that "all disease starts in the gut".
There's been some very interesting research coming out the last few years that
seem to tie autoimmune diseases such as psoriasis [1] [2] to the gut.

It's been known for a while that some gut disorders, including Crohn's, can
manifest as skin lesions of various kinds, and bowel bypass patients can also
develop skin symptoms. It's also known for a while that autoimmune patients
have less bacterial diversity in their gut, and an increased abundance of
certain types of bacteria, especially in the small intestine. Research has
found that in such patients, gut bacteria can migrate from the gut to the
bloodstream and then to the skin. Psoriasis patients, for example, have a much
higher gut permeability than non-psoriatics (not to be confused with the
pseudoscientific Internet hysteria around "leaky gut"!) and have deficient
bile acids.

Treatment would involve resetting the gut somewhat by eradicating the known
pathogens. Astonishingly, a Hungarian study in 2003 [3], which used an
experimental treatment with bile acid supplementation, was able to completely
clear psoriasis in 78% of its subjects (even more in a second, more acute
group), which is unheard of, and about 58% were still clear 2 years later. I
don't know why that study hasn't revolutionized things; it's only been cited
11 times according to Scopus.com.

[1]
[https://www.ncbi.nlm.nih.gov/pubmed/29908580](https://www.ncbi.nlm.nih.gov/pubmed/29908580)

[2]
[https://www.nature.com/articles/nrmicro2974](https://www.nature.com/articles/nrmicro2974)

[3]
[https://www.sciencedirect.com/science/article/pii/S092846800...](https://www.sciencedirect.com/science/article/pii/S0928468003000427)

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Jacob_G
You can reverse intestinal permeability though diet. However, there is no
money in it and neither is it a complicated treatment. Thus, the papers about
it won't get published in prestigious journals.

~~~
Madmallard
[citation needed]

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tsomctl
Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain for Life
by Perlmutter

I have a theory that fad diets like keto, paleo, primal blueprint, low fodmap,
whole 30 (of which there are numerous people claiming they have major
improvements) really work because they influence the gut biome.

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throw345hn
I cant speak for other diets but I follow low fodmap diet as I suffer from
IBS. I always assumed that I was prescribed that diet to influence the gut
bacteria. I mean the bacteria ferment on high fodmap foods and bloat and
distend your stomach.

Talking about low fodmap specifically I wouldnt call it fad as it has been and
is being researched and has shown to be effective to help with IBS, maybe not
so much for other conditions.

Personally I have found it helpful in reducing the symptoms that I have.

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astazangasta
>Perhaps the most popular is the gut microbiome, which impacts human digestive
health (this is the science behind your daily probiotic yogurt).

I don't believe there is any science behind the notion that yogurt is healthy
for your gut as a probioitic. The bacteria in yogurt is lactobacillus, which
is present in gut flora but a minor resident at best.

[https://en.m.wikipedia.org/wiki/Gut_flora](https://en.m.wikipedia.org/wiki/Gut_flora)
>About 99% of the large intestine and feces flora are made up of obligate
anaerobes such as Bacteroides and Bifidobacterium.

These are not present in yogurt and no amount of yogurt eating will help
introduce them to your gut.

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forgotmypw3
The best source of microbiome culture is fermenting or rotting food, which is
already growing bacteria that eats the food that you're eating.

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astazangasta
The selective constraint on gut bacteria is not merely to eat food, it is to
facilitate the health of the gut. That is, a symbiote has different
evolutionary goals than a bug that is just out for a meal. Don't go looking in
rotten food for this stuff; the most likely place to find it is in another
person's gut.

