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 that have to do with diversity? Humans have not been an emotionally rational species at any point in the past. Arguably the relationship between gut biome diversity and civilization is inverse. Maybe we want fewer microbes.
Lifespan has also increased with decreased gut biome diversity.
This is why correlation alone is uninteresting. You can find it anywhere.
> Splitting the difference, people in less developed parts of the world have between 60 and 65 of those bacterial groups, an observation that ties the decrease in microbial diversity to urbanization.
Oh come on. How does a line like this get published? This is fine if you define “ties” as “moves with” but not “is connected to”. IOW correlation doesn’t imply causation.
> Kyle Meyer, a microbiologist at UC Berkeley, argues such losses are not necessarily a problem. “Maybe we don’t need them,” he points out. But Moeller is worried. “We are really doing some scary stuff to our microbiomes,” he warns.
Why is it “scary”? Nothing in this article established any cause for concern.
The guy that developed the methodology is now in search of a problem his solution fits.
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.
How does one analyze the gut biome? I imagine it involves running poop through a machine - what kind of machine? I would love to learn more about the technical process.
Interesting! In De Filippo et al., they mention that Bacteroidetes sp are absent in urban Europeans, but present in rural Africans; in the OP they mention a similar sounding Bacteroides being present in chimps but not in humans. Is there any similarity between these apart from their similar spelling?
> indicating the importance of preserving this treasure of microbial diversity from ancient rural communities worldwide
This study (and the FA) mention losing/presrving microbial diversity, but don't touch on how we got these microbes in the first place.
I was expecting it comes mostly from what we eat and the environment, including eventually the people around us (and the mother - baby link ?)
I kinda wondered if we hadn't lost these microbes because they disappeared from our surroundings, and we'd get them back if they became prominent again, making the (temporary?) loss less impacting.
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.
Wow is the mobile UX of PNAS bad — the cookie pop-up has no X button and if you click ‘continue’ — which I thought meant continue to the article — it directs you to the terms of service. If you press back, you see the same pop-up again.
Pretty much every culture around the world 100 years ago had some staple fermented food. Nowadays, a lot of people in western culture at least outright refuse yogurt or other fermented foods like saurkraut or pickled cabbage that used to be staples in these people's ancestor's diets a few generations ago. People are becoming even lactose intolerant. You have to fertilize your microbes so to speak and eat these sorts of foods. Plus once you are doing stuff like making your own yogurt, a jug of whole milk works out a lot cheaper than the chobani stuff.
> What about people in the US who are not in cities? That's the more interesting comparison to me. Why would that be left out?
At least in the US, my lay-intuition is that you wouldn't see much of a difference between average Americans between urban, suburban, and rural settings. That's perhaps worth testing, but I think the much more interesting test would be between wealth and class groups.
(Again, wild speculation: it's easy to imagine that most gut biota don't care about the difference between dollar-store knockoff sodas and brand-name sodas, but definitely do care about $14 free-range, organic eggs.)
I'm curious why that comparison is more interesting to you?
I can see great value in having both data points when trying to formulate a hypothesis about what causes the decline in gut-microbes in us city folks, but I find it hard to think of a use-case for solely a urban/rural comparison without other context.
(Update: I was thinking about this from a scientific perspective, ignoring the idea that people might be interested in what it means for them personally (facepalm) )
I'd be really curious where some of these wild microbes can be found so we can repopulate them.
Every time I brush my teeth, use dish washing liquid or really any man made substance with a lots of ingredients I also wonder if I'm accidentally killing off my skin/mouth/gut microbiomes. Not worried enough to only use water (not that tap water can be fully trusted either....)
I've always been shocked at how crappy the research into nutrition is and how there's very little consensus beyond "vegetables are good" and how shoddy a lot of the professional training is for dieticians. Nearly everybody eats nearly every day, how have we not figured this out?
> The researchers can't say whether the absence is a cause or an effect of the illness
My immediate thought was that people suffering from depression might eat more “junk food” due to the depression and that their poor diets might lay waste to their gut biomes. Of course, there may be other studies that contradict my hypothesis.
"Moeller and others also suggest identifying the missing microbes may be the first step toward bringing them back. “If we determine that these groups were providing important functions to keep humans healthy,” Maccaro says, “perhaps we can restore them with probiotics.”
Oh really? Nice submarine for Actimel, Yakult etc.
Well, it's either a pill, or moving out of the city, or a fecal transplant (assuming that the urban / rural divide is relevant, and not just a proxy for diet).
I don't live in the city, but if I were told that I would be healthier with more of these microbes that my environment doesn't support, I'd opt for the pill.
I had to use oral antibiotics about a year ago for reasons that could have been avoided. I was pretty upset about it precisely because it probably wreaked havoc on all the beneficial gut microbes that I had built up over the years.
Once a gene has started expressing, it's pretty hard to flip the switch back to the off position. Losing the microbes is a big problem.
It's just going to get worse. People seem to have this fetish for anti-bacterial everything.. soaps, coatings, etc. They take anti-biotics even for viral issues then they wonder why they start developing a new health problem they didn't have before, like a mood disorder or an autoimmune issue.
Here in Indonesia, antibiotics can be bought over the counter without a prescription. Many people self medicate for a cough or runny nose (they don't distinguish whether viral or bacterial, most likely the average worker doesn't know the difference).
Few have the luxury to take a sick day so the pressure is on.
What did the lost microbes do? If they helped digest things that aren't part of our diet then the there would be no selective pressure maintaining them, so they could be easily dropped, independent of the issues of vast over-application of antibiotics, etc.
Over application of antibiotics and anti-bacterial stuff is clearly causing problems, but that's not the only thing that is happening that impacts something as complex as the gut. Just as with genes, the microbiome is under constant selective pressure from evolution, and we will - over time - gain new microbes as we lose ones that aren't beneficial.
My first thoughts are (without access to the actual article)
* We have lost the microbiome that primates present
* have we gained other microbes?
* what did those microbes we lost do? If they break down heavy fibre (branches) we may simply not need them, so evolution would stop selecting for them
* This says cities, but it (a) only appears to look at the US, and (b) the article doesn't mention comparing to non-city dwellers in the US. Saying "cities" without also providing a non-city reference seems bogus, but also could simply be left out of the article.
* Following from the "US only" comment above - how stable is this microbiome between geographical regions in the US?, how about different countries in close geographic location (think Europe)?, or geographically separated countries with similar culture? different culture?
All of these things might be answered in the paper, but per-usual Science has given us a fairly useless summary article with a clickbait headline :-(
[Edited to bring back formatting. For a text only, anti-emoji, etc site HN is obnoxiously opposed to basic white space formatting :-/]
I'm curious how simple sanitary factors come into play. Something I've always found intriguing is that in Ancient Greece toilets would use shared butt brushes (sponge on a stick) in lieu of toilet paper. In an especially fancy place there might be a bucket of vinegar nearby to clean it off, but in general it was just a quick swirl through some water and onto the next bum.
The thing I find interesting there is that the Ancient Greeks had extremely limited medical knowledge alongside practices like this. And they also lived through less than pleasant times, yet they were often also quite long lived as a quick perusal of your Philosophacrates of choice can readily demonstrate. There's certainly a literal survivorship bias there, but the ubiquitousness of longevity is, if nothing else, interesting. Certainly many of these individuals would have still left their mark had they died at 40 or 50 instead.
It seems like it’s about statistics, more than anything. Some people can be sedentary and smoke their whole lives and eat lard non stop and still live to be 80. Doesn’t mean any of that helped them in any way.
It’s like that for them, too; regardless of their sanitary practices, some people will live to be old. On its own I don’t think it says much about their effectiveness.
Long-lived people have always existed. The difference is in the % of people that make it that far.
A theory: this decrease in gut microbiome diversity directly correlates with an increase in fatigue.
Ever since the first time I had antibiotics I've suffered from chronic fatigue, I'm pretty sure there's a strong connection here to the bacteria in my gut as it often feels like the main symptom is a reduced ability to digest food.
I wonder how much of the fast increasing prevalence of gut-related diseases like IBS can be explained by the changes in gut microbes, and how much is just about lack of exercise and changes in diet.
Whenever I go work at relative's farm my stomach seems to work way better, even though I do plenty of exercise in my home city as well. Perhaps the type of manual labor is better for stomach than gym/running, but I wouldn't rule out the impact of microbes either.
I really enjoyed reading Fiber Fueled which basically lays out how all the latest science links our overall health very closely to the health and diversity of our microbiome. It will be interesting to see if new research continues to find evidence to support this. It's also a pretty convincing scientific argument in support for plant-based diets which, conveniently, is good for the planet and animal welfare as well.
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?
Does anyone know of probiotics with a variety of bacteria? Currently they (and yoghurts) seem to be just a single type, which doesn't make a lot of sense to me. If there are unusual bacteria out there where do they come from and how can we get them?
I've done a bunch of anti-biotics in the last few years so what to get back to what I was.
"Does anyone know of probiotics with a variety of bacteria?"
Home fermenting and raw products (honey, fruit, veggies, etc) are probably a good place for variety. You may have a primary strain you're fermenting with, but there are likely other minority strains present too.
Most probiotics aren't useful because if you're going to manufacture a ton of bacteria, you have to go with the ones capable of growing that fast. That's typically just one or two strains used in the making of yogurt, though you could branch out to miso, kefir, kimchi etc.
And the oral delivery route doesn't work that well because they have to make it through the stomach, then get to the intestines, then survive there - which they won't if they aren't specific strains evolved to live inside humans.
If you want to do science (aka mail someone your poop) there are ways to measure what's currently inside you:
Now, instead of taking the probiotics, I make yogurt from whole milk (it's easy!) and open 3 probiotic capsules as the starter, letting it ferment for 24 hours to ensure all of the milk sugar is gone. This gives 2 quarts of yogurt and I eat a tablespoon every morning with breakfast. Way cheaper than the pills, plus I have a problem swallowing the capsules. Has worked great for me.
Try searching for "soil bacteria Probiotic". Amazon has several products that include lots of bacteria not commonly used in yogurt or similar products.
A quick search turned up this one that claims to have 12 strains of bacteria. It is also USP verified. I'm not an expert and have never tried it, but hopefully that info helps.
chobani claims six strains of yogurts, I used that as starter for my homemade yogurt batches since then. Otherwise I try and get my exposure in from the environment. I'm vaccinated so I don't bother with the mask unless there are hard rules. I will avoid overusing hand sanitizer. I take crowded public transit and otherwise walk around sidewalks and stores with a bunch of people vs private car and delivery of all my needs. I do computer work but I do almost all of it outdoors on a patio table, where I am exposed to pollen and spores and microbe aplenty (but probably better air quality than indoors given the plastic off gassing in the modern home). Basically I am trying to inoculate myself with a wide variety of things available in my local environment, just like people used to be before all this modern society stuff locked us sitting in rooms. It seems to work as far as I can tell anecdotally; I can't remember the last time I was sick.
If you want variety of bacteria, then the highest is probably in milk kefir, and the second highest in aged, hard cheese.
Kefir, we don't even know how many or what bacteria it hosts, but we know it's a lot. Different studies have reported wildly different communities, but all of them with upwards of a dozen species. For example:
> Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources
Aged hard cheese, unless made with raw milk, is usually inocculated with a couple of strains of lactic acid bacteria, but during aging a varied flora develops, of "adventitious bacteria" and yeasts from the environment.
To be honest though, I made kefir for a couple of years and I've been making cheese for about four now and I make the occasional yogurt now and then, but I'm still not convinced about the health claims of "probiotics". And I'm not the only one to be skeptical:
> A growing probiotics market has led to the need for stricter requirements for scientific substantiation of putative benefits conferred by microorganisms claimed to be probiotic.[7] Although numerous claimed benefits are marketed towards using consumer probiotic products, such as reducing gastrointestinal discomfort, improving immune health,[8] relieving constipation, or avoiding the common cold, such claims are not supported by scientific evidence,[7][9][10] and are prohibited as deceptive advertising in the United States by the Federal Trade Commission.[11] As of 2019, numerous applications for approval of health claims by European manufacturers of probiotic dietary supplements have been rejected by the European Food Safety Authority for insufficient evidence of beneficial mechanism or efficacy.[8][12]
Btw, you know what elese has plenty of lactic acid bacteria, therefore probiotics? Sourdough. Alhtough if you make kefir, you can use it instead of sourdough as a bread starter.
[+] [-] mulmen|3 years ago|reply
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 that have to do with diversity? Humans have not been an emotionally rational species at any point in the past. Arguably the relationship between gut biome diversity and civilization is inverse. Maybe we want fewer microbes.
Lifespan has also increased with decreased gut biome diversity.
This is why correlation alone is uninteresting. You can find it anywhere.
> Splitting the difference, people in less developed parts of the world have between 60 and 65 of those bacterial groups, an observation that ties the decrease in microbial diversity to urbanization.
Oh come on. How does a line like this get published? This is fine if you define “ties” as “moves with” but not “is connected to”. IOW correlation doesn’t imply causation.
> Kyle Meyer, a microbiologist at UC Berkeley, argues such losses are not necessarily a problem. “Maybe we don’t need them,” he points out. But Moeller is worried. “We are really doing some scary stuff to our microbiomes,” he warns.
Why is it “scary”? Nothing in this article established any cause for concern.
The guy that developed the methodology is now in search of a problem his solution fits.
[+] [-] lbeltrame|3 years ago|reply
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
[+] [-] aluminussoma|3 years ago|reply
[+] [-] jonny_eh|3 years ago|reply
[+] [-] pcrh|3 years ago|reply
[+] [-] makeitdouble|3 years ago|reply
This study (and the FA) mention losing/presrving microbial diversity, but don't touch on how we got these microbes in the first place.
I was expecting it comes mostly from what we eat and the environment, including eventually the people around us (and the mother - baby link ?)
I kinda wondered if we hadn't lost these microbes because they disappeared from our surroundings, and we'd get them back if they became prominent again, making the (temporary?) loss less impacting.
[+] [-] rr888|3 years ago|reply
[+] [-] setgree|3 years ago|reply
Looks like interesting research though!
[+] [-] unknown|3 years ago|reply
[deleted]
[+] [-] asdff|3 years ago|reply
[+] [-] goatcode|3 years ago|reply
What about people in the US who are not in cities? That's the more interesting comparison to me. Why would that be left out?
[+] [-] woodruffw|3 years ago|reply
At least in the US, my lay-intuition is that you wouldn't see much of a difference between average Americans between urban, suburban, and rural settings. That's perhaps worth testing, but I think the much more interesting test would be between wealth and class groups.
(Again, wild speculation: it's easy to imagine that most gut biota don't care about the difference between dollar-store knockoff sodas and brand-name sodas, but definitely do care about $14 free-range, organic eggs.)
[+] [-] jascii|3 years ago|reply
(Update: I was thinking about this from a scientific perspective, ignoring the idea that people might be interested in what it means for them personally (facepalm) )
[+] [-] db1234|3 years ago|reply
[+] [-] afarviral|3 years ago|reply
Every time I brush my teeth, use dish washing liquid or really any man made substance with a lots of ingredients I also wonder if I'm accidentally killing off my skin/mouth/gut microbiomes. Not worried enough to only use water (not that tap water can be fully trusted either....)
[+] [-] Bilal_io|3 years ago|reply
[+] [-] digitcatphd|3 years ago|reply
[+] [-] starwind|3 years ago|reply
[+] [-] dennis_jeeves1|3 years ago|reply
[+] [-] subsubzero|3 years ago|reply
https://www.science.org/content/article/evidence-mounts-gut-...
[+] [-] TranquilMarmot|3 years ago|reply
[+] [-] baronswindle|3 years ago|reply
My immediate thought was that people suffering from depression might eat more “junk food” due to the depression and that their poor diets might lay waste to their gut biomes. Of course, there may be other studies that contradict my hypothesis.
[+] [-] haklport|3 years ago|reply
Oh really? Nice submarine for Actimel, Yakult etc.
[+] [-] antiterra|3 years ago|reply
I think, for the time being, people are much more likely to accept a probiotic.
[+] [-] wtetzner|3 years ago|reply
[+] [-] zdragnar|3 years ago|reply
I don't live in the city, but if I were told that I would be healthier with more of these microbes that my environment doesn't support, I'd opt for the pill.
[+] [-] kaycebasques|3 years ago|reply
[+] [-] Sunspark|3 years ago|reply
It's just going to get worse. People seem to have this fetish for anti-bacterial everything.. soaps, coatings, etc. They take anti-biotics even for viral issues then they wonder why they start developing a new health problem they didn't have before, like a mood disorder or an autoimmune issue.
[+] [-] thelittleone|3 years ago|reply
Few have the luxury to take a sick day so the pressure is on.
[+] [-] olliej|3 years ago|reply
Over application of antibiotics and anti-bacterial stuff is clearly causing problems, but that's not the only thing that is happening that impacts something as complex as the gut. Just as with genes, the microbiome is under constant selective pressure from evolution, and we will - over time - gain new microbes as we lose ones that aren't beneficial.
[+] [-] jschveibinz|3 years ago|reply
https://www.hopkinsmicrobiome.com/faq
[+] [-] olliej|3 years ago|reply
* We have lost the microbiome that primates present
* have we gained other microbes?
* what did those microbes we lost do? If they break down heavy fibre (branches) we may simply not need them, so evolution would stop selecting for them
* This says cities, but it (a) only appears to look at the US, and (b) the article doesn't mention comparing to non-city dwellers in the US. Saying "cities" without also providing a non-city reference seems bogus, but also could simply be left out of the article.
* Following from the "US only" comment above - how stable is this microbiome between geographical regions in the US?, how about different countries in close geographic location (think Europe)?, or geographically separated countries with similar culture? different culture?
All of these things might be answered in the paper, but per-usual Science has given us a fairly useless summary article with a clickbait headline :-(
[Edited to bring back formatting. For a text only, anti-emoji, etc site HN is obnoxiously opposed to basic white space formatting :-/]
[+] [-] somenameforme|3 years ago|reply
The thing I find interesting there is that the Ancient Greeks had extremely limited medical knowledge alongside practices like this. And they also lived through less than pleasant times, yet they were often also quite long lived as a quick perusal of your Philosophacrates of choice can readily demonstrate. There's certainly a literal survivorship bias there, but the ubiquitousness of longevity is, if nothing else, interesting. Certainly many of these individuals would have still left their mark had they died at 40 or 50 instead.
[+] [-] moreira|3 years ago|reply
It’s like that for them, too; regardless of their sanitary practices, some people will live to be old. On its own I don’t think it says much about their effectiveness.
Long-lived people have always existed. The difference is in the % of people that make it that far.
[+] [-] insaider|3 years ago|reply
Ever since the first time I had antibiotics I've suffered from chronic fatigue, I'm pretty sure there's a strong connection here to the bacteria in my gut as it often feels like the main symptom is a reduced ability to digest food.
[+] [-] kewrkewm53|3 years ago|reply
Whenever I go work at relative's farm my stomach seems to work way better, even though I do plenty of exercise in my home city as well. Perhaps the type of manual labor is better for stomach than gym/running, but I wouldn't rule out the impact of microbes either.
[+] [-] benknight87|3 years ago|reply
[+] [-] mjsweet|3 years ago|reply
[+] [-] david_l_lin|3 years ago|reply
[+] [-] rr888|3 years ago|reply
I've done a bunch of anti-biotics in the last few years so what to get back to what I was.
[+] [-] giantg2|3 years ago|reply
Home fermenting and raw products (honey, fruit, veggies, etc) are probably a good place for variety. You may have a primary strain you're fermenting with, but there are likely other minority strains present too.
[+] [-] astrange|3 years ago|reply
And the oral delivery route doesn't work that well because they have to make it through the stomach, then get to the intestines, then survive there - which they won't if they aren't specific strains evolved to live inside humans.
If you want to do science (aka mail someone your poop) there are ways to measure what's currently inside you:
https://www.viome.com
[+] [-] prirun|3 years ago|reply
https://www.amazon.com/Probiotics-Formulated-Probiotic-Suppl...
Now, instead of taking the probiotics, I make yogurt from whole milk (it's easy!) and open 3 probiotic capsules as the starter, letting it ferment for 24 hours to ensure all of the milk sugar is gone. This gives 2 quarts of yogurt and I eat a tablespoon every morning with breakfast. Way cheaper than the pills, plus I have a problem swallowing the capsules. Has worked great for me.
[+] [-] amanaplanacanal|3 years ago|reply
[+] [-] Splendor|3 years ago|reply
https://www.costco.com/trunature-advanced-digestive-probioti...
[+] [-] trollied|3 years ago|reply
[+] [-] rmetzler|3 years ago|reply
[+] [-] asdff|3 years ago|reply
[+] [-] cheese_goddess|3 years ago|reply
Kefir, we don't even know how many or what bacteria it hosts, but we know it's a lot. Different studies have reported wildly different communities, but all of them with upwards of a dozen species. For example:
> Sequencing-Based Analysis of the Bacterial and Fungal Composition of Kefir Grains and Milks from Multiple Sources
https://journals.plos.org/plosone/article?id=10.1371/journal...
Aged hard cheese, unless made with raw milk, is usually inocculated with a couple of strains of lactic acid bacteria, but during aging a varied flora develops, of "adventitious bacteria" and yeasts from the environment.
To be honest though, I made kefir for a couple of years and I've been making cheese for about four now and I make the occasional yogurt now and then, but I'm still not convinced about the health claims of "probiotics". And I'm not the only one to be skeptical:
> A growing probiotics market has led to the need for stricter requirements for scientific substantiation of putative benefits conferred by microorganisms claimed to be probiotic.[7] Although numerous claimed benefits are marketed towards using consumer probiotic products, such as reducing gastrointestinal discomfort, improving immune health,[8] relieving constipation, or avoiding the common cold, such claims are not supported by scientific evidence,[7][9][10] and are prohibited as deceptive advertising in the United States by the Federal Trade Commission.[11] As of 2019, numerous applications for approval of health claims by European manufacturers of probiotic dietary supplements have been rejected by the European Food Safety Authority for insufficient evidence of beneficial mechanism or efficacy.[8][12]
https://en.wikipedia.org/wiki/Probiotic
Btw, you know what elese has plenty of lactic acid bacteria, therefore probiotics? Sourdough. Alhtough if you make kefir, you can use it instead of sourdough as a bread starter.