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Modern city dwellers have lost about half their gut microbes

science.org

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Re: Modern city dwellers have lost about half their gut microbes

#261

Post by lwouis »

mulmen wrote: post #210
jasonfarnon wrote: post #185

Earlier quoted context omitted.

Why is it “scary”? Nothing in this article established any cause for concern. I think when people see a difference in modern life versus traditional, and that difference was unexpected and unintended, that in itself is cause for concern. I don't need to believe claims about how important the gut biome is to the brain etc. But I would be surprised if the there weren't some consequence of the difference, and it seems l…

You answered the wrong question. The article reproduced a claim without substantiation. I didn’t conclude that the effects are benign. I claimed that this article does nothing to assist me in deciding if they are.

Not knowing which way the scale tips is in-itself scary, I think. It means moving into uncharted territory.

Similarly, global warning is rising temperature, and we are trying hard to model the effects, but it's really all it is: models and guesses. We would much prefer if we could go back to the climate we were familiar with for the past 20,000 years. That one we were starting to understand to some extent. Now all bets are off

Re: Modern city dwellers have lost about half their gut microbes

#262

Post by mjsweet »

altfredd wrote: post #201
mjsweet wrote: post #168

Can someone comment on the effect of chlorinated town water on gut microbes? Would treated water have an affect as opposed to consuming rain or bore water?

> effect of chlorinated town water on gut microbes Unless you are drinking a tap water (pretty extreme thing to do!), the effect is probably non-existing: https://cooking.stackexchange.com/q/67027

I live in Australia, I would say most people would drink tap water at home. We have a sink top filter that filters water, so we use that. I don’t think drinking tap water in this part of the world is abnormal, on the contrary. Out of curiosity, where are you from?

Re: Modern city dwellers have lost about half their gut microbes

#263

Post by watwut »

ekianjo wrote: post #194
mulmen wrote: post #161

This article is mostly cliche popsci trash that isn’t worth reading. Good for a game of logical fallacy bingo. The only interesting development seems to be the methodology but that only gets a passing mention. The rest is basically fearmongering. > In humans, for example, gut bacteria influence how the immune system responds to pathogens and allergens, or interact with the brain, affecting mood. Ok. But what does tha…

> Lifespan has also increased with decreased gut biome diversity. Life expectancy increase is mostly a factor of decreased death at birth or in early years. You dont see an exponential increase of 100 years old. People die at about the same age as before, give or take.

This is not true. An average adult lives longer still just not by that much. Whole bunch of deadly diseases or injuries are not deadly anymore. The work got safer and injuries happen significantly less often.

What did not changed is maximum longevity people have assuming they don't get sick or injured.

Re: Modern city dwellers have lost about half their gut microbes

#264

Post by watwut »

majormajor wrote: post #182
pojzon wrote: post #175

Earlier quoted context omitted.

Whats scary is that we have more and more civilization diseases and we have no idea whats causing them beside guesses. Worsening of the environment we live in impacts us in ways we cannot even imagine. Scary is that we cannot go back, coz its financially impossible for most.

Cities were historically unhealthy, etc, etc, as well. Yet people kept moving to them. So "most people can't afford to [leave civiliation]" is far from new. Perhaps the life everyone has been fleeing to get to cities was never what you think it is for most.

People moved to cities for economic opportunities.

Re: Modern city dwellers have lost about half their gut microbes

#265

Post by nebfield »

rvba wrote: post #247
ebolyen wrote: post #84

Earlier quoted context omitted.

Great summary! Although I would argue that 16S is still a perfectly good (and cost-effective) method, especially with DADA2. There are also neat sequencing techniques that like CCS which give you really high resolution of a target region (amplicon) without sequencing a lot of redundant/uninformative DNA.

How big are the samples analyzed by the machine? 1 gram? 1 miligram? Are they taken from random parts of the poop? (Outside, inside?) Even 1 miligram is probably a lot of DNA, but I wonder how to know if the place of sampling is important

Very small amounts are sampled, on the order of grams. I'm not sure exactly, I worked on the bioinformatics side of things. I think an Illumina MiSeq requires 50 - 500 nanograms of DNA to work well.

Sampling and storage methods can significantly change the bacterial composition of an environmental sample (in this case, poop). The exact protocols will depend on the aims of the study. The gut microbiome is a gradient and very dynamic. Different parts of the gut will have different bacterial compositions. Some people might prefer to get a locally accurate sample from a biopsy of the intestine, but you won't manage to recruit many participants. Other studies may prefer to use faecal samples as a proxy for overall gut state, which lets you recruit more people. Some protocols may homogenise (blend) the poop before sampling, others might not. Here's a nice review:

https://europepmc.org/article/MED/28830090

Re: Modern city dwellers have lost about half their gut microbes

#266

Post by rr888 »

lbeltrame wrote: post #4

About ten years ago my former PI (second author in the below paper) did quite a job on this in Burkina Faso, analyzing the composition of the gut in children living outside cities, in cities, and a comparison with European children. Obligatory disclaimer: I was working in his laboratory at the time, but I wasn't involved in that research. https://www.pnas.org/doi/10.1073/pnas.1005963107

Its fascinating as its not clear between rural African and European urban children, who is healthier. Stereotypically Africans are probably closer to nature, less stress and fewer processed foods, where Europeans have more medicines, variety of foods and less exercise.

Re: Modern city dwellers have lost about half their gut microbes

#267

Post by watwut »

mulmen wrote: post #161

This article is mostly cliche popsci trash that isn’t worth reading. Good for a game of logical fallacy bingo. The only interesting development seems to be the methodology but that only gets a passing mention. The rest is basically fearmongering. > In humans, for example, gut bacteria influence how the immune system responds to pathogens and allergens, or interact with the brain, affecting mood. Ok. But what does tha…

I think that your comment is excessively uncharitable bordering on a lie.

The article does not make reader scared at all. It does not call for any major action. It is about what kind of research that is being done and tl;dr to what they found. And then quotes from researchers most of them about "that research is really cool".

It is popularization article with excessively low amount of anything emotional. It is interesting article too. But you somehow want to to be scary and then blame it for not being sufficiently scary while blaming it for being scary.

Re: Modern city dwellers have lost about half their gut microbes

#268

Post by watwut »

mulmen wrote: post #230
jcoq wrote: post #192

Earlier quoted context omitted.

I think you're largely missing the point of this article, which mostly summarizes a novel technique for comparing gut biome diversity, and which goes through a small amount of effort to summarize the growing (if not clearly established) scientific consensus about the importance of healthy gut biomes. I don't think it takes very much imagination to understand why the loss of diversity in an ecosystem might have negati…

> I think you're largely missing the point of this article, which mostly summarizes a novel technique for comparing gut biome diversity As I already said, it doesn’t largely do that. It mentions it in literally one paragraph that is itself mostly fluff. The most substantive line is literally “with computers”: > With computers, they were able to compile the fragments of DNA sequenced into whole genomes of the gut micr…

Most of article is tldr of various researches with links if you are interested in how they collected poop to make tests or used computers.

Re: Modern city dwellers have lost about half their gut microbes

#269

Post by watwut »

mulmen wrote: post #210
jasonfarnon wrote: post #185

Earlier quoted context omitted.

Why is it “scary”? Nothing in this article established any cause for concern. I think when people see a difference in modern life versus traditional, and that difference was unexpected and unintended, that in itself is cause for concern. I don't need to believe claims about how important the gut biome is to the brain etc. But I would be surprised if the there weren't some consequence of the difference, and it seems l…

You answered the wrong question. The article reproduced a claim without substantiation. I didn’t conclude that the effects are benign. I claimed that this article does nothing to assist me in deciding if they are.

Why should article assist you in deciding of they are? That decision is not science. That decision is politics.

Re: Modern city dwellers have lost about half their gut microbes

#270

Post by Agamus »

mulmen wrote: post #238
potamic wrote: post #235

Earlier quoted context omitted.

It is scary because the gut microbiome in humans is evolving much faster in recent times. This is coming from a study that maps evolution of gut microbiome in primates to the primate evolutionary tree. They found that families of gut bacteria can be passed down over millions of years in a species. The gut microbiome has always coevolved with the species. As the species diverges, so does the microbiome adapting to the…

Consider my comment as feedback from an editor to the author. I don’t think this is fit to print. I agree with you. This could be an interesting topic. But the article provides no substantive information. Anything that is learned will be in spite of this article, not because of it. What you describe is the potential that I maintain this article fails to live up to. > It's a very interesting observation in my opinion…

I'm not trying to be snarky, and while I largely agree with you, I feel like I'm missing something. Are you saying that the only time that it is 'fit to print' something about this topic is when we have arrived at the conclusion, and are ready to present objective facts?

Or, perhaps we shouldn't print speculation about interesting topics unless we have the answers to the questions being discussed?

Or, print should be reserved objective facts?

I agree that hyperbole like "scary" are confusing to many people. But in this case, I think the scientist is appealing to slang in an effort to communicate with non-scientists.

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