What Is the Human Microbiome, Exactly?
nautil.us
nautil.us
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...
[2] I mean non-living food of course.
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.
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.
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.
> 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
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.
References please. There is plenty of research that suggests no such benefit of very high fiber, and plenty of issues.
Pulp Fiction: The Truth about Fiber
http://www.diagnosisdiet.com/food/fiber/
Ditto on the claim about a very plant rich diet being better:
https://www.diagnosisdiet.com/food/vegetables/
Little Shop of Horrors? The Risks and Benefits of Eating Plants — Georgia Ede, M.D.
One of the key issues is lack of a study that varies only the amount of fiber, and does not substitute fiber for processed carbohydrates.
You likely have a point since anything in excess can be harmful, but those references don't really support.
One thing to keep in mind is that you shouldn't switch diets drastically - you can't expect your low fiber/high sugar microbiota to be able to handle a large dose of fiber all at once. Think of your microbiota as something you need to cultivate.
By the way, there's increasing evidence that in the absence of fiber your gut bacteria resort to chewing back your own mucus, whereas if you give them some complex fiber to chew on they leave you alone (https://sci-hub.tw/10.1080/19490976.2018.1513765). This is temporary however and in the absence of fiber you can maintain barrier function if you simply make more mucus. But that requires more energy so you probably have to eat more. Everything has tradeoffs.
And other that just giving you the farts, many byproducts of fermentation like short-chain fatty acids (i.e. butyrate, propionate), are able to keep other bacteria at bay while simultaneously feeding your colon cells and keeping them in a non-inflamed state (https://sci-hub.tw/10.1038/s41579-019-0213-6 [Box 3]).
People with SCID have to live in a filtered air bubble (https://en.wikipedia.org/wiki/Severe_combined_immunodeficien...) so it's possible, but if I remember correctly there are side effects. Mars is kind of a similar lifeless bubble though.
How did you prove this? How do I prove you wrong?
If you somehow killed the existing biome it would grow back quickly.
this sort of stuff
https://www.sciencedirect.com/science/article/pii/S0091679X1...
Off hand I would expect living without our microbiomes to be similar to slow starvation while gorging on junk food.
Answer to your question depends on functions provided by gut microbes. We can say it's to digest the food and it's symbiotic relationship. But what if this is what we know only on the surface. What if these microbes produce proteins that are absolutely essential for many other functions as well. What if they signal messages that are of neural nature.
It's a pitfall to think that our brain is all we are as it hosts consciousness. I held this view for a long time, so I understand where it's coming from.
But try changing your diet. I won't make any suggestions but there are limitless option to biohack your body. You will see amazing effects on your brain too.
Btw, there's a neural setup i.e a brain in stomach and heart as well.
This is actually something we are able to measure. I don't find fault with anything else you claimed, but what are your credentials with regard to this topic? I'm not trying to gate-keep, but my undergrad was biochem and there are many well-understood fundamentals that some folks are not willing to concede, or that their 'theories' disregard.
Can you give an example?
Xylitol kills some harmful micro organisms like S. Mutans and Candida Albicans.
Xylitol will shift fecal bacteria from gram-negative (covered in a layer of slime) to gram-positive (no slime, healthier).
Xylitol will cause diarrhea but it's a good kind of diarrhea, plan accordingly.
They are selling expensive pills with probiotic entities that should be "free" with food we consumed for centuries. We went overboard on the sterilization. I just bought into a cattle herd so I could buy raw milk (which Europeans never lost access to, so we can compare notes).
The microbiome manifests itself whether one is on Earth or not, and whether one wants it to or not. Its composition, however, will vary based on the food consumed. Microorganisms are quite prevalent in the atmosphere whether they are wanted or not; that's how me making my own sauer kraut is possible.
A similar type of taming seems to be occurring at intestinal surfaces covered in mucus, where the body secretes a complex mixture of protein and sugars that simultaneously keeps the bulk of microbes at bay while actually feeding desirable bacteria.
You wouldn't die of lack of microbiome, you'd die of being unable to maintain your sterile environment and eventually being infected, unless you lived in a bubble (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477854/), and Mars is actually not too far from that. Much better to allow yourself to be colonized by harmless bacteria which will fill up all the ecological niches that the pathogens require to thrive.
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
[2] https://www.nature.com/articles/nrmicro2974
[3] https://www.sciencedirect.com/science/article/pii/S092846800...
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.
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.
:thinking:
I don't know about this guy. I got that link from quackwatch.
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 >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.