Microbiome interactions shape host fitness | Hacker News Reader

Microbiome interactions shape host fitness

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69 pointstosh25 comments

Its an interesting article in that it is looking at fitness (of fruit-flies, the model system used in the study), not lifespan alone.

Going in, I was expecting all of these interactions would be like the GWAS (genome wide association studies) interactions. I was expecting maybe single digit (max) percentage changes in the overall fitness / lifespan / etc.

But, if I understand the article correctly [1], different combinations of gut bacteria drove variations in lifespan by up to ~20% (which is a HUGE shift), which makes me a little skeptical.

All in all, a fascinating, if very unclear study.

They are very interesting correlations, but mapping the cause-consequence relationship is probably one of the biggest challenges in modern biological research; in this context & diseases like (many) cancers. In an ideal world, we really would like to have that degree of understanding to be able to develop effective, targeted cures (the holy grail of modern medicine?)

Finally, there's a lot of 'buzz' around microbiomes / microbiomics etc, etc. But I think one needs to be cautious in interpreting these results. This twitter thread [2], on an article / paper claiming modulation of schizophrenia by gut microbiome, is an articulate criticism(IMO) of such a claim.

In general (not the fly paper referred to in [1]), I think a significant fraction of microbiome / trait association studies, as exemplified by the schizophrenia study discussed in [2], are just throwing stuff up & seeing what sticks; and they are.. perhaps not the most rigorous of ways of doing science..

Finally, a slightly older, but still good article in NY Times that discusses some of the issues around the hype, etc. [3]

[1] https://www.pnas.org/content/115/51/E11951

[2] https://threadreaderapp.com/thread/1095012297200844800.html

[3] https://www.nytimes.com/2017/03/06/upshot/exciting-microbe-r...

[multiple edits to improve readability :~]

>But, if I understand the article correctly [1], different combinations of gut bacteria drove variations in lifespan by up to ~20% (which is a HUGE shift), which makes me a little skeptical.

just one example - [wrong makeup of] gut bacteria association with type 2 diabetes in humans (there are a bunch of studies like this https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4880177/ ). Diabetes would cause lifespan variations on the scale of those 20% easily. Beside diabetes there are other similarly well pronounced/acute/severe effects as well as less pronounced "chronic" style effects and thus 20% may easily be on the lower side.

I was trying to research the best probiotic to start taking (for humans not fruit flies) and I became totally bewildered... any recommendations or research from hacker news welcome!

One I often see cited: lactobacillus plantarum 299v

Why not yogurt/buttermilk? It was recommended to me though I dislike both and have never taken them in my life. But I suffer from chronic mouth ulcers and most doctors I consulted say it is because I avoid natural probiotics found in yogurt etc...

Yogurt covers a huge range from almost flavourless through salty all the way to sickly sweet... Surely in your case it would be worth experimenting to find one that you can tolerate?

Unfortunately television advertising often has just as much an effect on doctors as it does the regular person. Despite what they often say, most supermarket yogurt/buttermilk often loses all of its probiotic bacteria during the processing of it, to make it safe to eat. Along with that, a good majority of people are lactose intolerant and only some, but not all, lactose is broken down in the fermentation process. If you have any inflammatory symptoms, like ulcers, I wouldn't personally recommend dairy sources; but there are loads of great alternatives!

My personal supermarket favourites are sauerkraut, tempeh, kimchi, miso (I put miso paste in everything...), kombucha, and pickles. Basically any fermented food really.

I recommend trying to make some of your own if you find the time. I make dosa quite often on the weekends, which is a kind of delicious Indian pancake. Also tried my hand at making Natto, which is this strange but delicious sticky soybean thing. Had Salgam in turkey which was amazing too (it's a weird salty, spicy, fermented pickle juice).

Check out Wikipedia for a reasonably complete list: https://en.wikipedia.org/wiki/List_of_fermented_foods

Pick one with a long list of lactobacilli.

Probably the most important thing you can do for your microbiome is eat enough fibre. Eats some beans and some carrots. Cut back on the high fructose corn syrup and save antibiotics as a last resort.

IMO, the easiest way to eat more vegetables is to buy them frozen. Frozen vegetables are cheaper than fresh, sold pre-chopped, and often nutritionally better because freezing stops the decay of vitamins. You can buy them without planning ahead and not worry about them rotting. Assuming you have access to a freezer, the only disadvantage is the softer texture. I eat more vegetables than most people I know, but I spend less time preparing them. I think the inconvenience of fresh vegetables discourages a lot of people from eating them, but frozen vegetables can solve the problem.

I am lactose intolerant so taking probiotics helps me. I would look at reviews and try some, for 2 months, for example. Anyway, lifestyle, food is important, i had several health issues because of stress from school etc. Diet word can sound boring but there are many ways how to prepare tasty food without some ingredients and make it more suitable for you.

Do not rely on various forum threads, you could read bad diagnosed people or diseases you should not care about.

I'd have thought that trying to eat a varied and balanced diet most of the time would be more beneficial to your gut microbiome than constantly artificially topping it up. The fact that people need to keep taking these things daily is evidence that they're not creating any kind of sustainable culture in there.

I believe that's the benefit. They're symbiotes of a healthy environment. They enter, do something good, then leave. The one's that enter and wish to stay are the ones we don't want in us.

Basically, don't listen to anybody. Nutrition science reporting is among the worst on the planet, nutrition science itself seems only slightly better, and you can guess how bad nutrition bro-science is.

This is a very good point, but I will probably start taking one anyway...

Make your own Sauerkrout. Easy, cheap and delicious with any meal.

From my understanding, most probiotics are transient and pass through the system quickly. The microbiome optimizing community are now focused on prebiotics fibres like inulin and other resistant starches which feed your beneficial bacteria. And then there's always the nuclear option: FMT from a super donor.

Kefir (made at home - not the store bought one). Worked wonders for me.

VSL#3 is one that has a lot of clinical research (search Google Scholar or PubMed). The catch is that the company producing VSL#3 no longer uses the formula that historically was used in the vast array of clinical research conducted. Whether some of the changes matter is up for debate. However, the original formulation is now sold under brand name Visbiome.

https://www.visbiome.com/blogs/news/maryland-federal-jury-un...

Anecdote: some time ago I used a little bit of 3% peroxide for a while for a sore tooth, recommended by my dentist. I did not swallow the solution (well, probably a little bit by accident). Surprisingly, during that time, not only did my tooth get better, but also my stool improved quite a bit. And now I find this: [1]. I'm not sure what to make of it, but there might be something to it.

[1] https://sciencetrends.com/restoring-gut-health-the-benefits-...

First off, there is no "best" probiotic. The very best thing for your guts is an extremely diverse set of commensal bacteria that have adapted to cooperate with the human body, preferably inherited from your family down many generations. Hardly anyone has that any more, thanks to generations of antibiotics and diet lacking a variety of fiber.

Probiotics are like a mercenary army that you can bring in when some pathogens are causing havoc or the equilibrium is very disturbed. They generally don't stick around permanently but they help outcompete the nasty microbes. Unfortunately, they also compete with the good microbes in many cases (the "standing army").

We really don't have a good process to restore the species that get lost through antibiotics and bad diet other than good diet for a long period of time (a wide and balanced variety of whole plant fiber) hoping the good bacteria will establish themselves again, or a fecal transplant which has all the risks of a blood transfusion if the donor isn't screened thoroughly.

We try to solve things with pills, and certainly that is a very useful delivery mechanism for active medications. But there are a lot of fermented foods out there that have become unfamiliar in the Standard American Diet.

The current science is still unclear about which bacteria combo is important, in which proportions, in which part of the GI system. BUT we do know gut flora is important.

So my approach is to consume (in moderation but regularly) a variety of fermented foods that come from traditional cuisines. Yogurt with a wide variety of active cultures, Miso, Cheese from unpasteurised milk, Kimchi, etc.

Also raw vegetables will likely have traces of microbes from the soil they were grown in, though I have no idea what role those play, if any.

NOW foods does a good one.

As a child, one gains some immunity factors from ...the dirt.

Eating dirt is probably not a preferable option for most adults but we can certainly eat things that are grown in it!

The variety of life is huge. What will you grow in your garden? more than your count equals. You are a city of life in yourself. Live long, enjoy.

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