Modern city dwellers have lost about half their gut microbes | Hacker News Reader

Modern city dwellers have lost about half their gut microbes

science.org

398 pointsHooke297 comments

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.

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.

The movement to cities was more likely the result of an arms race rather than preference. Most anthropological evidence points to deterioration in quality of life (e.g. diet, height, disease, teeth, inequality) when comparing hunter-gatherers and city dwellers.

Larger populations, specialization of labor, and fortifications made city-states militarily superior to small bands of hunter-gatherers and allowed cities to dominate a surrounding region (at least until the modern horse). When a region was depleted of wild game then cities and their croplands were the most reliable source of food. Armies from city states would not infrequently raid and capture smaller groups of humans and bring them back to cities as slaves.

So cities were likely a forced choice, as smaller nomadic groups were forceably absorbed into the domains of city-states or repelled toward less hospitable lands.

People moved to cities for economic opportunities.

"People moved to cities for economic opportunities" and "people can't financially afford to leave the cities" seem like just the glass half full / glass half empty versions of the same thing.

Put it one way it's bad, put it one way its good. It's a choice with tradeoffs - I'm just pointing out that those tradeoffs aren't some uniquely new "collapse of our society" thing.

This is an interesting revelation. Thanks for framing it this way.

Riffing:

I think there’s a middle phrasing similar to “cities are the most efficient allocation of resources we have yet invented.”

Similar to the “democracy is the least bad system of government yet invented.”

There’s some corollary to survivorship bias at play here as well. Cities are an apparently natural consequence of human civilization so we know a lot about their flaws. But civilizations that didn’t migrate toward cities either failed or records of their existence was lost.

Except that those two are NOT just two ways to frame the are thing. They literally mean much different things.

The difference is that when people "move to city", it means the village where they are from offers them even poorer conditions. Less food, less work, lower pay.

"People can't afford leaving city" suggest there is active price to be paid for ability to be somewhere - transport, house elsewhere being too expensive or some such. It does not even suggets opportunity cost.

Otherwise said, first sentence means people move to city because it is better for them economically. Second does not say anything about whether it is good for you, just that moving away would cost too much. Also, some people stayed in economicaly bad places, because they could not afford to move to the better place. Transport and initial housing pay was too much.

> Whats scary is that we have more and more civilization diseases and we have no idea whats causing them beside guesses.

We do have some good mechanistic hypotheses, but most reviews fail to describe them because a lot of research is hand wavy. However, things are slowly reaching mainstream.

Let's consider type 1 diabetes (T1D), which is a common autoimmune disorder where beta cells in the pancreas get destroyed by your own immune system. T1D was rare a century ago, and we know from patient records that incidence increases rapidly whenever a society becomes industrialized. For example, take the Karelia region split between Finland and Russia. People on both sides of the border have the same genetic background. However, children on the Finish side have 10x more incidence of insulin autoantibodies [1]. Microbiomes on both sides are actually very different, with Russian children resembling ancient non-industrialized ones.

The immune system is essentially a huge distributed memory where individual cells recognize small protein or lipid fragments as self or foreign, and then collectively decide whether there is an infection in the particular microenvironment they are exploring. We know T1D typically begins because the immune system recognizes a particular insulin chunk, the amino acid sequence SHLVEALYLVCGERGFF, as foreign. In other more complex autoimmune disorders this part is less clear.

It turns out that many gut bacteria mimic that particular insulin chunk [2]. That probably gives these commensal bacteria the ability to survive and avoid immune responses, and it is a flag of the symbiotic relationship these bacteria have developed with higher organisms in the last 100 million years. Now, the bacterial ecosystem of a modern gut has a lot less diversity than it should and therefore it is very fragile. We don't know exactly what happens before T1D, but one possibility is that these bacteria grow too much in abundance and therefore initiate autoimmunity as T cells found in the pancreas of T1D patients can't distinguish between one protein chunk from these bacteria and insulin.

There are similar patterns in other autoimmune disorders like multiple sclerosis. This patent aims to edit bacterial mimics that cause autoimmunity using a CRISPR system in a pill [3].

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950857/ (Figure 1)

[2] https://www.medrxiv.org/content/10.1101/2022.05.11.22274678v... (Extended Table 1)

[3] https://patents.google.com/patent/US11224621B2/en (see e.g. Example 4)

My understanding is that, in healthy humans, gut bacteria are not presented in huge numbers to the immune system because the intestinal barrier (tight junctions) prevent most of them from migrating into the blood stream.

Are then not antibodies against gut bacteria a clear sign of a damaged gut barrier?

(FWIW there seem to be suspicions that Ankylosing Spondylitis is also caused by a certain type of bacteria being present _and_ getting into places such that antibodies against them are formed.)

This is a very good question.

There is a lot of literature that supports the role of gut bacteria inducing Tregs, and now there is also some evidence of epitope transport from the gut into the thymus.

Hence, I think these events might matter even if they are not very frequent.

But you could be right, and perhaps there's not really a relevant mutualistic relationship between host and commensals in terms of epitope crossreactivity.

Which "civilization diseases"?

Diseases of civilization usually refers to things like diabetes, obesity, heart disease, cancer. I'm not 100% sure but I think the common threads are metabolic and inflammatory.

cancer has nothing to do with civilisation. it was already recorded way before we had modern and industrial societies

> it was already recorded way before we had modern and industrial societies

This doesn't falsify the claim at all. Diabetes was first recorded 3500 years ago, and none of the other diseases on the list were literally invented by industrialization. Diseases of civilization refers (essentially) to diseases whose casualty rates dominate in societies of abundance and industrialization, by contrast to the predominance of (eg) infectious diseases in pre-industrial societies.

I do agree that it stands slightly apart from the rest of the examples, in that (eg) a contemporary hunter-gatherer still has a fair chance of getting cancer while they have a very low chance of diabetes/obesity. But it's pedantry to claim flatly that it doesn't qualify, especially given plenty of scientific usage[1][2][3] that contradicts the claim.

[1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6362881/#:~:tex.... [2] https://link.springer.com/article/10.1007/BF00933491 [3] https://www.karger.com/Article/Abstract/323926

Sounds like you're fighting confirmation bias with confirmation bias.

Your points are valid, don't get me wrong, but there is also a lot of research causally linking microbiome deficiencies with various health problems.

Also worth noting your shots seem more aimed at the journalist's style than the researcher's work. I for one, think this is super valuable and promising research

> Your points are valid, don't get me wrong, but there is also a lot of research causally linking microbiome deficiencies with various health problems.

I’m sure there is. But it isn’t in this article. So reading this to learn about it is a waste of time.

> Also worth noting your shots seem more aimed at the journalist's style than the researcher's work.

That’s a correct assessment, yes.

> I for one, think this is super valuable and promising research

A good source for that conclusion may exist, but this isn’t it.

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 like wishful thinking to suppose, as you do, that the consequences are benign.

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

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

The article should contribute something other than being a glorified bulleted list. Why bother writing anything if in the end there is no substance?

I think OP was rather bemoaning the lack of useful information and scientific rigor. Their points were good I thought.

Whilst microbiome is a fascinating topic people are quick to lend unsubstantiated pet theories new credence, harboured by the topics nasence and complexity.

Anecdotally, logical fallacy bingo is a great actual game and I recommend everyone play

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 negative implications for that ecosystem.

For whatever it's worth to you, Science magazine is a companion to the extremely prestigious Science Journal and it often tries to summarize the research in the journal. The tiniest amount of searching shows that the biologist whose work is being summarized a is one of the leading experts in this area.

> 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 microbes present.

There’s no further mention of how these computers work or what they do or what is novel about them. And that’s the most interesting part of the piece.

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.

> 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.

Maximum ages haven't really increased much, yes; but life expectancy at eg age 10 has increased a lot, too, throughout history to modern times.

Any source for this?

Parent's point is that you can draw a correlation to a beneficial factor without examination of whether causation exists just as easily.

You correctly identify that it is unlikely your lifespan is increasing because the average gut bacteria diversity is decreasing, more likely they are simple correlated.

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.

> The work got safer and injuries happen significantly less often.

For this kind of statement about lifespan i assume that we remove all accidental deaths since they are just causing noise versus the actual lifespan

Neither accidents nor sicknesss are noise. Both are and especially were fairly frequent reason of death. And whether you survive them has a lot to do with both medical and social improvements.

Lifespan is a poor metric for quality of life. You can be alive whilst being plagued by multiple illness. Healthspan is what is important (how long you can live without suffering from a major ailment) and that is where gut microbiome plays an important role.

No shit. That’s the point. I can draw a correlation between basically anything. That doesn’t make it interesting.

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 changes in the host. Except in modern humans, where it is evolving at a much faster rate since industrialization. It's a very interesting observation in my opinion and asks important questions about how the modern lifestyle is affecting the biome. For instance, what happens if a pregnant mother takes antibiotics? Will a family of bacteria get killed off in that mother's evolutionary branch?

The article is most certainly popsci and written for laymen, but I don't think it is trash at all. Not sure why you think so. It highlights some very interesting discoveries and offers you a window to dive in and learn more things on the subject if you are interested.

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 and asks important questions about how the modern lifestyle is affecting the biome. For instance, what happens if a pregnant mother takes antibiotics? Will a family of bacteria get killed off in that mother's evolutionary branch?

That’s a great question! But it isn’t in the article.

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.

OP understands neither science nor complex systems. Science is never ”ready” so by their logic nothing would ever get published, and something as integral to human ”system” as the gut microbiome being reduced to half can have dramatic nonlinear effects to health, making an alarmist approach 100% valid

> OP understands neither science nor complex systems.

This seems like an uncharitable take. I can't imagine how an alarmist approach is "100% valid" when there are not any known problems caused by this. The article is only stating that living in urban environments is correlated with a decrease (by A Lot) in gut microbes. Even if it is true that a significant decrease in gut microbes is a Bad Thing, the article does not argue that well. Indeed, it seems to intend to argue that with little or no substance.

> Consider [OP's] comment as feedback from an editor to the author.

If the comments are just criticisms about the content in the article then they seem apt. Many of the points hold up when I am critical about the article's arguments. It's possible to argue that position and also be in favor of publishing this information.

I found it interesting and useful. Much more so than this criticism which comes across as overly pedantic. It quotes various researches. It isn’t meant to be a study or paper onto itself. Anyone interested in the scientific details would lookup the publications from the people mentioned. Articles like this is to give you an overview and spark some interest among the general public.

All good points.

But it's scary because without gut bacteria we'd all be dead. We depend on them so much that I sometimes wonder if they're the host and we're the "parasite".

What you said about correlation v cause and such is spot on. And perhaps the article fails because of what you listed.

Nonetheless, losing half of something that our living depends doesn't feel like grounds for celebration. The fact that we just don't know, well that's concerning as well.

Having a community of different species is good. The way that those communities work is that they keep each other's populations in check. If we go out of balance and one dominates we can see disease states coming from not only an imbalance of metabolic products but even infection from the population that went out of control.

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.

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

What's a "former PI"?

The private investigator with whom you have severed ties.

principal investigator

“The person(s) in charge of a clinical trial or a scientific research grant. The PI prepares and carries out the clinical trial protocol (plan for the study) or research paid for by the grant. The PI also analyzes the data and reports the results of the trial or grant research. Also called principal investigator.”

"Principal investigator". Roughly a research group leader.

https://en.wikipedia.org/wiki/Principal_Investigator

The former "Principal Investigator" of the (research) project. Often the professor who is responsible for obtaining the grant and driving progress

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.

Looks like interesting research though!

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.

Most likely extracting and culturing then PCR

Edit: grabbed from the methods section. I was wrong, they didn't culture :)

>Fecal samples were collected by physicians and preserved in RNAlater (Qiagen) at −80 °C until extraction of genomic DNA (28) (details in SI Materials and Methods).

The paper uses 16S rDNA sequencing, which is a bit old fashioned now but it was a good method when the paper was published. The steps basically involve:

1. Extract all DNA from poop, normally using a kit that basically makes DNA stick to tiny plastic beads. You wash the beads in a bunch of different chemical solutions to isolate DNA from the original sample and purify it. There are a lot of different methods to do this.

2. Amplify a small section of DNA that's universally unique to bacteria and archaea which is used as a barcode. This barcode has some areas that change a lot across different species and some areas that don't change much.

3. Sequence the amplified DNA. The DNA sequencer determines the sequence of nucleotides in each DNA amplicon (an amplicon is a piece amplified piece of DNA). An example DNA sequence is ACCTGGCT

3. The DNA sequencer produces millions of DNA sequences in parallel and stores them and some metadata (e.g. quality and confidence measurements) in text files

4. When this paper was published, a friendly bioinformatician would have taken the text file and clustered the different sequences. Sequences 97% similar were binned together as a rough approximation of a species. Different taxonomic levels have different cutoffs, but it's all quite vague and there are better methods now that involve denoising sequences from quality measurements (e.g. dada2 method)

5. A count for each different bin is generated, and "representative sequences" for each bin are matched against taxonomic databases to see what species are present

6. Normal ecological analysis is done on the count data to calculate alpha and beta diversity or do other types of analysis. Once you have counts, it doesn't matter that the data are from bacteria instead of sheep or penguins

Newer methods involve sequencing every single bit of DNA in a sample, not just a specific region. This is called metagenomics and it's very hard to do and requires very big computers and big DNA sequencers.

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

> I think an Illumina MiSeq requires 50 - 500 nanograms of DNA to work well.

You can go as low as 10ng depending on the library you use (or so the vendors say), but I'm not sure it's the case for these specific applications (my experience is with other, equally difficult samples, but from a single source).

Really cool, thanks for the details. It's reminiscent of a plot point in a sci-fi I'm reading, Zendegi - the protagonist is hell-bent on cracking the problem of simulating the brain in a computer, but funding is running out. Her coworker excitedly explains that he's awarded a grant for his project: simulating the interactions of microbe species in latrines, for purposes of preventing outbreaks of disease. He wants our protagonist to jump ship on the brain stuff, says it will always be there, that she can do some real good right now, and the skills will transfer over, she won't be wasting her time learning how to simulate the microbial communities in poop.

(Alas, an eccentric billionaire with hopes of uploading himself to a supercomputer swoops in to fund the mind-mapping project...)

> 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.

Very likely. Almost all probiotics people take are transient. Meaning they just pass through and don't form long term colonies in our guts. There's a few exceptions with some soil-derived probiotics but those are also the least predictable

It seems really likely to me that our bodies have likely adapted to an environment where exposure to certain types of bacteria is very common. For example, there's been a lot of research on the potential of ammonia oxidizing bacteria (AOB) such as Nitrosomonas to reduce body odor when applied topically. There's companies trying to use this to sell you "probiotic shampoo" and other skin care products. But you know where else Nitrosomonas is commonly found? Most soils. These bacteria are also extremely easy to kill off with shampoos and even the small amounts of fluoride added to tap water

Given how deeply we depend on microbes for digestion it doesn't seem far fetched to think our skin microbiome has also adapted to a ready supply of these microbes to help us in certain ways. Besides keeping us less stinky by eating our sweat, skin microbes have also been shown to help with acne,[0] protect us from UV damage,[1] and has even been shown to have deep interaction with our gut and brain health.[2]

[0] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6534434/

[1] https://mdpi-res.com/d_attachment/microorganisms/microorgani...

[2] https://www.sciencedirect.com/science/article/pii/S075333222...

Interesting, I discovered once that soil on my socks could make them not smell. I don’t know if the specific soil mattered though, and the circumstances for my discovery were never replicated.

>Almost all probiotics people take are transient. Meaning they just pass through and don't form long term colonies in our guts.

is this also the case for frequent ingestion? say you eat probiotic yoghurt on a regular basis, are you saying the good stuff is in a constant cycle of dying and being replaced?

> Besides keeping us less stinky by eating our sweat That sounds wrong. Sweat itself doesn't smell until microbes have had a chance to act on it. You can sweat right after a hot shower and you won't smell.

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?

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.

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.

> You have to fertilize your microbes so to speak and eat these sorts of foods

[citation needed]. It seems unlikely that fermented foods are not consumed in urban areas at all. I’ve also no idea if other primates consume any fermented foods, but I’d guess probably not.

> People are becoming even lactose intolerant

Do any other primates drink milk after infancy? If not, that’s not really a valid concern in the context of the article.

No. In fact, almost all mammals stop producing lactase once they stop nursing from a mother. Humans are quite rare in that there's a significant population with the mutant "lactose tolerant adult" gene.

The study is of US cities.

I would be curious to see if you took, say, South Korean cities, what the results would be. (Seoul is one of the largest megacities in the world, and kimchi is an extremely common fermented food.)

One tricky part with fermented foods is that the salty ones appear to increase rates of colon and stomach cancer as I recall.

I read something years ago about how as the Japanese population adapted a more western diet, heaps of ailments came upon them as you’d expect, but their salt intake declined so dramatically that they stopped experiencing stroke and GI tract cancers nearly as much.

I think you’d need to pin down just how much salt was causing those issues though and then ask if the benefits of the salty fermented foods outweigh the current problem of having depleted gut microbiomes and atrocious diets.

So, I’m certainly not suggesting everyone avoid salty fermented foods. I eat (and make) a fair amount myself and as I alluded above, I suspect it’s better for me than eating food that is, on balance, worse for me.

There’s no perfect diet, but there are clearly worse diets. I try to avoid the latter.

Seems unlikely. A lot of the traditional West African diet is fermented and they have the lowest rates of colon cancer on Earth. Smoked foods and foods containing nitrates/nitrates are correlated with stomach and colon cancer, but not salty or fermented foods. Studies that show a correlation of salt intake with cancer are very possibly confusing intake of smoked meat or processed meat (also high in salt) with colon cancer. For example, when adjusting for processed meat, one study finds that salt is not correlated at all with colon cancer. [1]

[1] https://www.clinicalnutritionjournal.com/article/S0261-5614(...

Interesting, thanks for that. I hadn’t seen it yet. Though the rest still stands, and as mentioned in the paper, reducing sodium intake is still recommended for other health benefits. There is a wealth of other research showing that most people in North America should dramatically reduce their sodium intake.

> Reduction of processed meat intake may be an effective strategy for CRC prevention, while sodium reduction should still be recommended to achieve other health benefits.

Apart from that, I’m still seeing evidence of correlation with stomach cancer, even if not in the lower GI tract:

https://www.wcrf.org/salt-shaking-up-the-link-with-stomach-c...

Given the connection to stomach cancer and cardiovascular disease, it does seem wise to be careful about salt intake.

Regarding west African diets, are they high in salted fermented foods or just fermented foods? It seems if the food is low in salt, it’s probably just fine

There is a wealth of other research showing that most people in North America should dramatically reduce their sodium intake.

The evidence for this seems much less conclusive than most people think: https://examine.com/nutrition/awful-nutrition-myths/#summary.... The tl;dr is that most of that salt comes from crappy food, and that’s what you want to fix - it’s not the salt as such.

It really is the salt though, and examine says as much:

> Some myths contain a grain of truth. Studies have associated excess salt with hypertension (high blood pressure),[54] kidney damage,[55] and an increased risk of cognitive decline.[56][5

The thing is, a lot of people have no idea that their salt intake is way too high. You’re right that the salt tends to come from processed foods, but the salt is still a problem.

I’m not trying to suggest the processed foods are not a problem, either. It’s a compounding problem, and it’s a massive one.

To be fair, that says "a grain of truth", and that's contained within a section entitled: "Myth 6: Salt is bad for you". The summary says:

But a drastic decrease in salt intake has not shown uniform benefit in clinical trials. Most people will benefit more from a diet of mostly unprocessed foods than from micromanaging their salt intake.

As an example, salt-sensitive hypertension is a condition which some people have, but most people don't. If you don't, then salt will generally not affect your blood pressure adversely (it will go up temporarily if you eat a whole Domino's pizza, but will quickly go down again).

There are some interesting points in this podcast and related resources/sources (not a fan of all of this site’s content, though Gregor is good at compiling research):

https://nutritionfacts.org/audio/the-sodium-debate/

My take away from this and other sources is that we don’t have proper long-term, randomized, human trials to determine exactly what to say about this. At the same time, there are cases where a reduction is clearly helpful but no typical cases where an increase is beneficial.

I’m certainly not out to debate or disprove you here — I’d really like to eat more salt, but the evidence I come across doesn’t justify it. I’d rather be wrong, though.

You may be thinking of this.

https://www.newser.com/story/119965/so-do-pickles-really-cau...

Not quite. I’d seen information about fermentation-related carcinogens, but like the article says, I haven’t come across anything suggesting this is problematic unless you eat a lot of this stuff every day (like the people in China who were a part of the study mentioned in the article).

I linked to an article pointing to heavily salted, preserved foods being correlated with stomach cancer in a response to another comment. Though salted fermented foods fall into this category, so would things like jerky or salted olives for example. It isn’t clear to me what should be avoided necessarily, though it seems like decreasing sodium intake is a net positive regardless.

In any case, I think eating these foods is likely okay or even healthful so long as it doesn’t make up a large part of your diet.

Salt tolerance varies a lot with blood pressure

Eating yogurt or sauerkraut will not render you (once again) lactose tolerant.

Lactase (the enzyme that breaks down lactose) production is regulated by a human gene; how would a probiotic like yogurt alter a gene?

https://biologydictionary.net/lactase/

You could always ingest other bacteria that can digest and break down lactose and rely on probiotics to digest the lactose for you instead of having a gene.

That's what ruminents do anyways, you need a steady colony of these helpful bacteria or you lose the tolerance. While that seems troublesome, for many animals that's how metabolism works for their entire life.

Epigenetic reversal of some inhibitory histone marks at the promoter region of the enzyme? Driven by some yet-to-be-discovered signaling cascade induced by reintroduction of lactose and proliferation of lactose loving microbes?

Just spitballing, this is pure speculation, but is plausible.

I have noticed pseudosciences are becoming fashionable again.

Well, as you probably know, genes are regulated more or less according to environmental cues all the time, including being very much subject to presence and behavior of commensals/parasites/symbionts.

I don't know any specific data whatsoever about inducing lactase, but it seems perfectly plausible that microorganisms such as lactic acid bacteria could interact with the system.

This has been studied, but the results tend to argue that it's purely genetic, eg)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6669050/

> Studies that have measured changes in endogenous lactase activity after an intervention period consistently show a lack of enzyme induction, suggesting that lactose intake does not affect an individual's lactase activity. Although these studies are scarce and have relatively few subjects, data from cross-sectional studies support the theory of purely genetic regulation

That's interesting, and thank you for bringing it up.

What I was speculating about though, and what may be more relevant for the (Science) article, also includes things along the lines of a microbe manipulating the host gene expression to improve its living conditions. For instance a species that derives energy by fermenting glucose to lactate might under certain conditions have better benefit from that piece of metabolism if it can also make the host act as a sink for the product.

Again, not sure if that particular example is real or documented, but the idea has some consequences for the sort of adaptations and connections one might find.

I thought it would be that as well. But I went quite a while, probably almost two years, without ingesting milk at all. And I just had my 34th birthday two weeks ago. I figured there’s just no way I can still process milk and it turns out I absolutely can. No issues at all. Reading into it, it seems to be genetic.

https://medlineplus.gov/genetics/condition/lactose-intoleran...

You just either get the right genes or you don’t. I’m curious as to how long into my life I’ll be able to drink straight cow milk and be fine. Still got a bit of experimental time left. Hopefully, anyway.

Also both my parents can drink milk without issues.

You can't say something is "perfectly plausible" right after admitting you don't know any data supporting that hypothesis.

The negative symptoms of lactose intolerance is exactly due to microbes in the gut digesting lactose and producing metabolic byproducts such as gas. People who aren't lactose intolerant are free of such symptoms because lactose is digested with enzymes produced by the body before it reaches the gut thus depriving gut microbes of sufficient quantities of lactose to cause negative symptoms.

> People are becoming even lactose intolerant.

This isn't new, and certainly isn't some crisis of the last 100 years. Historically only a minority of the planet has ever been lactase persistent into adulthood. It's a well-understood genetic trait, not some product of gut microbes.

You can think of this being evolutionary beneficial, if some milk is bad, the whole village don't all get sick.

Also a possible reason for why people have different taste preferences.

It's probably simpler than that: it's simply not energy-efficient to keep producing an enzyme throughout its life for a sugar that's rare-to-non-existent in an organism's diet for most of that life. Because mammals don't have any means of obtaining milk once they separate from their mother, lactose intolerance for their lifetime after weaning is almost universal among mammals. Over millions of years, the slight energy efficiency win of turning off that enzyme's production post-weaning probably won out.

Humans are odd in that we harvest milk for consumption at all beyond our own mother's, which is probably why we're the only species with a notable population with the genetic mutation that allows some of us to digest it – there's no competitive advantage to that mutation in most other mammals, because where would they even obtain milk?

The specific enzyme that breaks lactose is lactase. It's built from almost 2000 amino acids. In comparison, Alpha-Amylase, the enzyme that breaks starch, is much smaller. Couldn't find an exact count but it appears in the ballpark of 200.

I think it's just that mammals don't drink milk once they are weaned.

It seems that lactose tolerance is the new thing here.

Lactose intolerance is normal, but for a few people, presumably dairy animal farmers, something happened to their genes and they became tolerant, and it was an evolutionary avantage because they had access to all that milk. But because access to farmed milk is relatively recent from an evolutionary standpoint and people can live with lactose intolerance, the trait hasn't spread to all of humanity.

Or people who worked out they were tolerant to it, farmed it, and the high density nutrients allowed faster more reliable development of healthy children in adverse conditions. i.e. North Western Europe.

Also that smallpox resistance via cowpox exposure can’t have hurt survival rates in general

What does lactose tolerance have to do with "bad" milk?

You are correct. It's likely that the majority of humans have been lactose intolerant for human history. It's primarily people of Northern European descent that are not lactose intolerant, but lactose intolerance is very common outside of those groups

and west african; by two entirely separate mechanisms, which i’ve always found to be quite cool.

> and west african; by two entirely separate mechanisms, which i’ve always found to be quite cool.

What's the separate mechanism? I'm only aware of one set of genes coding for adult lactase production.

https://pubmed.ncbi.nlm.nih.gov/17159977/

I wonder if there's any advantage to inheriting both mechanisms.

Lactase persistence is regulated by genetic mutations, not gut microbes. The negative symptoms of lactose intolerance is exactly due to lactose being able to reach the gut and making the microbes there flourish by digesting lactose, creating large quantities of gas and other metabolic byproducts that cause flatulence, diarrhea, etc. People don't spontaneously become lactose intolerant just because they stopped eating something. Koreans eat lots of fermented vegetables, yet why are 70%-100% of Koreans estimated to be lactose intolerant? Why are you suggesting lactose intolerance is some new condition that arose as a product of modern life? Lactose intolerance is simply the default setting for the majority of humans around the world for most of history.

Yogurt/kefir occupies very large segments in most developed countries' grocery store shelves and new brands/varieties pop up every year. How has this industry not collapsed if "a lot of people outright refuse yogurt" according to you?

The development and marketing of lactose free dairy products in recent years is simply the dairy industry exploring new market segments, because substantial portions of the population do not have lactase persistence. Even societies whose culinary traditions involved heavy consumption of dairy do not have 100% lactase persistence. It's not some weird conspiracy aimed at making modern humans "weak". The lack of lactose is not significant enough to change the nutritional content of dairy products.

Holy shit, that is the most over-the-top, aggressive response to a guy being factually incorrect about yoghurt that I've ever read.

Can you point exactly which part was "over-the-top" or "aggressive"? Or is calling out that factually incorrect things are, well, factually incorrect somehow unacceptable nowadays? The world needs less pseudoscience misinfo, not more.

I re-read your post and while it's not overly aggressive it's the difference in tone and approach that get you. The original poster was like the hippie encouraging home-made yogurt and you were like the school principal saying 'this is bull, store yogurt has scientifically the same benefits'.

PS: I also learned while writing this I can't spell yogurt. Thanks spellchecker!

Sadly the topic of lactose intolerance is rife with misinfo, biases, and dogwhistles, hence my rapid-fire questions in the previous comment. Most commercial yogurt products sold in grocery stores today are heavily laden with sugar and so mildly fermented that their probiotic quanlities are nearly nullified. Commercial unflavoured kefir is slightly better, but the overall probiotic effect is still questionable since we don't have affirmative answers on how much of the microbes can survive through our stomach acid, or how much of them can establish in our guts vs. heading straight for the exit like passengers on a roller coaster.

As for the spelling of yoghurt there's no correct version honestly, they are all transliterations of the same Turkish word https://en.wikipedia.org/wiki/Yogurt#Etymology_and_spelling

The majority of nutritional science seems full of bullshit to be honest. I remember how we laughed at the Atkins diet when it first appeared as well all knew so well that the science told us fat was bad. Now Keto diet seems to be gaining a lot of acceptance, and refined sugar is the real enemy. Refined sugar being bad for you seems to be one of the few things that is agreed on. Will that change in another 20 years?

If you are worried about people's tone and approach, go over to 4chan for a bit then come back here. It should toughen you up.

I'm not worried at all. I was just commenting why others may see that comment (not mine) overly aggressive.

> The world needs less pseudoscience misinfo, not more.

Fully agreed. I appreciate the stern yet information-laden correction. It's certainly much better than hearing specious claims based on conjecture/misinformation that only seems plausible to the uninformed.

Also, IMO it did not sound "over-the-top" or "aggressive" at all. Some people are just so absurdly oversensitive that a simply direct method of speaking (or in this case, writing) is taken as hostile.

the "It's not some weird conspiracy aimed at making modern humans "weak"." bit seemed a bit much (and out of nowhere unless there was an edit in the original)

The insinuation in the very original comment that modern humans are abandoning fermented foods en masse and "even becoming" lactose intolerant (as if adulthood lactose intolerance is somehow a new condition rather than the default for pretty much all mammals in existence) was clearly in-line with the pseudoscientific conspiracist misinformation wave that modern lifestyle supported by technological advances is making humans regress somehow, rather than elevating overall levels of health and turning previous morbidity factors into manageable nuisances.

Yet they are all reasonable questions.

I'd be interested in knowing how asdff arrived at the idea that a sizable portion of lactose intolerance comes from people neglecting to fertilize their microbes with sauerkraut, pickled cabbage, or yogurt.

Honest question: I grew up on a farm in former USSR. We milked cows daily, when I was a kid. Back then, I never knew about lactose intolerance but to be fair, this wasn’t a topic discussed.

Considering I know nothing about this, and you seem like you do, are there any studies that looked at links between lactose intolerance and fresh milk produce?

Reason I say “fresh” is because we never refrigerated the milk. In the morning you get milk, cream is taken off top, by next morning you have a kefir like drink. All was consumed. There was no processing.

I know there is a study[0] that link exposure to farm animals being linked to less allergic reactions but never seen anything about milk.

[0]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7744242/

Fermented milk is lower in lactose because some of the lactose have already been broken down by microbes in the fermentation process. https://www.webmd.com/allergies/news/20030530/kefir-helps-la...

Lactose intolerance in many cases also doesn't have a clear cut threshold nor is it common to be hypersensitive where a single drop of milk causes projectile vomitting. Many people who are technically lactose intolerant (as in they don't self product lactase in adulthood) can consume some amount of dairy without any symptoms. Otherwise dairy products such as milk, yogurt, and ice cream would not have existed in most of Asia.

https://www.journalofdairyscience.org/article/S0022-0302(87)...

>"However, when lactose loads of up to 12 g are fed, symptoms can be minimal or absent." >"Tolerance to yogurt, acidophilus milk, and other microbe-containing dairy foods has been suggested and is thought to be due to either a low lactose content or in vivo autodigestion by microbial β-galactosidase."

Fresh milk is linked with some viruses that can cause autoimmune diseases like type-1 diabetes and bunch of other stuff.

Always makes my eyes roll when I hear people driving hours just to get fresh farm milk.

Thanks!

I didn’t know that type-1 diabetes was an autoimmune disease.

> Lactase persistence is regulated by genetic mutations, not gut microbes.

> Koreans eat lots of fermented vegetables, yet why are 70%-100% of Koreans estimated to be lactose intolerant?

On the other hand, there is Mongolia:

> But a closer look at cultural practices around the world has challenged that picture. In modern Mongolia, for example, traditional herders get more than a third of their calories from dairy products. They milk seven kinds of mammals, yielding diverse cheeses, yogurts, and other fermented milk products, including alcohol made from mare's milk. “If you can milk it, they do in Mongolia,” Warinner says. And yet 95% of those people are lactose intolerant.

https://www.science.org/doi/10.1126/science.362.6415.626

Even though most products are fermented for shelf life, unfermented milk is widely consumed by Mongolians to this day.

So how exactly does the diet of Mongolians prove lactase persistence is not fundamentally genetic? Lactose intolerance isn't something like celiacs where a dash of the substance causes adverse reactions. Most of Asia still sell non-lactose-free dairy in supermarkets. Look up any Youtube video of Korean street foods and you will see dairy products such as processed cheese, yogurt, mil, and ice cream are ubiquitous in Korea. That doesn't detract from the fact that the vast majority of the population are lactose intolerant in the definition that they no longer produce enzymes that can break down lactose once reaching adulthood.

Yeah and none of the foods on the list was raw unfermented milk.

> So how exactly does the diet of Mongolians prove lactase persistence is not fundamentally genetic?

It doesn't, but I think it indicates that genetic lactase persistence is not the only factor that affects lactose intolerance. Otherwise, how do you call a lactose-intolerant person that can tolerate significant amounts of lactose?

Koreans don't get a third of their calories from dairy products, though. Whereas if Mongolians get ~30% of their calories from dairy on average (which is credible), that would mean they are getting far more than that in summer, since dairy consumption is largely seasonal. We're talking prodigious amounts by the standards of any culture, not a dash. That consumption includes both significant unfermented dairy (milk, milk tea, clotted cream) and dairy products fermented in a wide variety of ways.

Are lactose intolerance symptoms widespread among Mongolians? If not, and if Mongolians are really genetically lactose intolerant, then it is worth asking whether the fermented dairy foods (as opposed to kimchi) they consume are mitigating that intolerance.

I developed lactose intolerance sometime during the 5 years I lived in Japan. I only noticed after returning to Canada when I resumed my old diet. I can still generally eat yogurt and kefir without symptoms, but I can't drink milk anymore without taking lactase tablets.

Would you be able to recommend a yogurt brand I could try out solely for the gut-related health benefits? Or if not yogurt specifically, anything that might even be better.

Highly dependent on what local brands are available. Look for unflavoured kefir or plain yogurt that isn't 0% fat.

Zero added sweetener, straight Greek yoghurt. Absolutely sublime.

To the typical North American diet it tastes incredibly foreign because the US of A is drenched in sweeteners.

But unsweetened foods just taste beautiful once you get used to them.

I spent two months in Turkey and can confirm this. The national drink is called Ayran, and it’s not only fantastic tasting and cheap but full of nutrition.

Its amazing the incredible, over the top flavor that highly processed junk food has. Commercial Corn chips and the like are so over flavoured, but you don't notice until you give them up for a while.

Even the fermented food that you mention will not be probiotic if they are commercially bought. Sauerkraut in a jar will be pasteurized. Even probiotic yogurt is supposedly pasteurized then some live culture added after. I make my own kefir and saurkraut for that reason.

Fermented foods are important. Milk-based foods, not so much. There's a reason most people are lactose intolerant - milk is to grow baby cows into large animals, and not suitable for consumption by adult humans.

> milk is to grow baby cows into large animals

Whence this transcendent purpose that limits suitability? Likewise, quinoa grains are to grow into full-sized plants, and not for consumption by humans, etc. etc.

Most people may be "lactose intolerant", but some of them find ways to survive and thrive on milk-based foods; meanwhile, some populations have developed tolerance to lactose, presumably because milk-based foods are important.

There is no need for transcendant purpose. Quinoa intolerance is pretty uncommon, whereas milk intolerance is the norm. Even without a lactose intolerance, there are several health issues with milk consumption, unlike quinoa consumption. That is because we've evolved for a orders of magnitude longer to eat plant material.

Yes, some northern European peoples have evolved to be more tolerant of milk. And some tibetans have evolved to live at very high altitudes. It's not a good argument to take a small exceptional population and apply that reasoning to the general case.

And this doesn't even get into all the problems with the dairy industry with regards to environmental damage and animal suffering.

But in this case with this country, that small exceptional worldwide population is overrepresented in our national population. It stands to reason that many people can infact consume lactose in the U.S. given this demographic history. The general case in the context of the U.S. population could very well refer to this population of people historically predisposed to tolerate lactase.

And on the other hand, I think there is this false logic at play with the meat/dairy industry as a whole. People assume these interconnected systems are in fact discrete. That we could do away with eating meat and suffer no consequences, in fact even see improvement in our ways of life. I am not so optimistic given how interconnected systems are. For instance, take the cow. Its not just used to derive meat. 99% of the cow is used. The pancreas is used to extract insulin and other factors. Same with the liver, and the pituitary gland. Serum is used for biomedical research applications. The hair is used for products, the hide is used. The fats are used for everything from toothpaste to flooring to crayons. Collagen and gelatin are extracted. I don't even need to go into the uses of the hide, I feel. The bones and blood are used for organic fertilizer, so I'd wager that many organic vegetarian products today actually rely on the cheap organic fertilizers produced by the meat industry versus synthetic sources. On top of that pasture land is often land that is not compatible for traditonal farming, owing to terrain mostly (e.g. Summit county in Colorado sports a lot of ranching versus farming, due to the rocky mountainous terrain being almost impossible to plow but trivial for a grazer to roam on).

Could you replace all of the parts of the cow with synthetic sources? Certainly. Would this lead to a net reduction in greenhouse gasses and other environmental externalities replacing each and every of these products with synthetic sources that hopefully aren't any more costly? That I doubt, and it worries me that headlines and other material in the media seem to ignore how all these externalizes will be resolved, assuming it will be an easy transition.

> several health issues with milk consumption, unlike quinoa consumption.

Are you claiming that most people who consume milk as a major part of their diet suffer health problems from it? Or that grain-based diets do not cause health issues?

> That is because we've evolved for a orders of magnitude longer to eat plant material.

Evolution has no telos. Evolutionary leaps into new niches are the norm, and hunting had formative impacts on the evolution of modern humans. We've also evolved for orders of magnitude longer walking on all fours (and walking erect causes health issues, such as stressing the back), but that has no bearing on what is healthy or suitable.

> It's not a good argument to take a small exceptional population and apply that reasoning to the general case.

I don't believe I did so. Northern European-origin populations are not small or insignificant, but I agree that for lactose-intolerant populations who have no tradition of using milk-based foods they are generally nutritionally unnecessary.

Dairy isn't nutritionally necessary for anyone. Perhaps it was in the past, but not now. You won't find evidence for that.

Not sure what you mean about telos. Evolution informs us about why we eat what we eat and how we might be affected by various foods, but it does not control us. We can choose what we want to eat.

> Dairy isn't nutritionally necessary for anyone. Perhaps it was in the past, but not now.

Assuming alternative sources of the same essential nutrients, I agree – no single food is nutritionally necessary or ever was. In the real world, meanwhile, dairy products are a key source of protein etc. for people in at least some regions where sufficient alternative sources are not widely affordable or available. Certainly, milk was crucial to the survival of many populations as recently as a century ago (not "aeons ago during some ancient famine").

> Evolution informs us about why we eat what we eat and how we might be affected by various foods

Evolution is an open-ended history of accidents, with much to say about what works for us (as opposed to what cannot).

> but it does not control us.

Indeed. Not only does it not control us, we cannot even conclude based on it that a novel environment or resource will not be advantageous. In the case of ungulate milk consumption, it turns out it was.

> Not sure what you mean about telos.

Evolutionary adaptations are in the nature of accidents, not guided by any purpose or implying any optimal "natural" state. Populations taking advantage of accidental fitness for new niches is a defining pattern in the evolution of life on earth, and consumption of milk by some human populations fits that pattern. Drawing conclusions about the suitability of drinking milk because "we didn't evolve to drink it" is fallacious (in contrast to, say, explaining most people's lack of lactase persistence by their ancestors' non-consumption of milk, which is sound, non-teleological reasoning).

There's also a reason why some people can digest milk: its a resource with nutrients and being able to intake a new source of nutrients offers a selective advantage to your offspring relative to offspring that cannot make use of these nutrients present in the environment. To say its not suitable for consumption by humans is a falsehood considering many adult humans can and do consume milk and make use of its nutrients.

You could posit this argument about anything we consume. Spinach leaves are to provide energy through photosynthesis for the spinach plant, and technically should not be suitable by consumption by adult humans so to speak if we took your logic to the limit. The fact that we have experienced gain of function mutations that allow us to digest spinach and recieve some nutrient benefit from it mean that we are able to take advantage of this resource. Milk in this sense is no different, even if not all of the human population has recieved this gain of function mutation of lactase persistance.

In biology there is no 'suitable' or not especially in the human sense of things being properly defined into discrete categories of expected outcomes, only what is physically posible through thermodynamics. If you physically can extract energy from plants, meat, milk, dirt, whatever, then its all suitable for consumption. having an enzyme to digest this sugar is no different than having teeth fit to grind down fibrous plant matter, or teeth strong and sharp enough to cut through cartilage and sinew.

You are speaking theoretically. That milk was necessary for survival by a small population of humans may have been true aeons ago during some ancient famine. This is not the case right now.

To say that humans can take nutrition from a substance is an argument that there is no criticism of the substance is a bad argument. Humans take energy from pure sugar, or taco bell. Yet to claim they are beyond criticism because they can keep people alive is absurd.

>people in U.S. cities...people in less developed parts of the world

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?

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) )

Because a bunch of us don't live in the city or urban environments and we're curious.

So the interest stems from a curiosity about your own gut-microbes? That seems fair enough, I may have been overthinking this...

I shouldn't say more overall, but the difference among people who have a similar diet and circumstances, but differ by housing culture, would be interesting to observe. I'd like to see apples to apples, if indeed the theorized reason of where gut differences come from is strictly (or mostly) urban vs. rural. Is it that country people are around more dirt, or that city people have different stressors, or maybe both are included? It'd be easier to tell if other differences are eliminated, imo. I've long preferred country life, having spent roughly half of my life in cities and the other half in the country, so maybe some personal interest is there too, to be honest. I do feel a lot healthier living in the countryside, perhaps my gut has something to do with that.

Even from a scientific perspective, it would be more interesting to see the effect of each variable independently (cities vs rural, US vs somewhere else) rather than bundling them together.

Personal interest does not necessarily equal marginal utility.

> 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.)

> but definitely do care about $14 free-range, organic eggs

Can you elaborate on why you think this is the case? Intuitively to me, most folks’ diets are going to be mostly cooked eggs which would reduce any effect on bacteria in the gut.

Sorry, I meant that as a proxy for “families that have the purchasing power to buy premium goods.” My intuition is that there’s a weak inverse relationship between food processing and food price, with less processing corresponding to healthier gut biota. But you’re right that the $14 eggs themselves probably don’t matter.

"Processing" is meaningless and largely a naturalistic fallacy; your biome definitely cares about what you eat, but not if it's been sliced up first, which is a kind of processing.

I don’t disagree. You can substitute “processed” for the “ultra processed” category in the NOVA scheme[1]. I don’t think there’s anything wrong with chopping up your apples before eating them.

[1]: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389637/

>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.

It wouldn't surprise me, but that would call into question the entire notion that the article is attempting to create -- that urban (and therefore non-urban) is the key factor in the differences it mentions in gut flora.

Could this explain trends like increasing food allergies in countries where more and more people are becoming urban dwellers?

It's not impossible, and it might even be plausible... But it's a really, really difficult question.

People outside of science: don't make the mistake of thinking that scientists haven't thought about this before! haha

What is that supposed to mean?

That it's certainly a valid thought with the information we have, and is being thought about, but requires further investigation to make an affirmative statement.

^ This is the best explanation of what I meant.

Guessing that this means there are a lot of confounding variables other than gut biome (environment, diet, genetics, etc) that are very difficult to isolate to prove causation, as opposed to correlation.

Gut biome being one of the most promising area of research, whose earth-shattering potential is about on par with the sheer complexity of the problem.

If you thought ML was difficult, try modeling a human being's digestive tube from mouth to anus down to the cell: welcome to a category of problems where climate and gravity are the "simple" ones.

On the other side of that space though, potentially the promise to increase by orders of magnitude our mastery of human condition both biologically and experientially.

We are a symbiote.

Bingo, we are just bunch of bacteria walking around. Some organism become symbiotic over time like mitochondria, so it go incorporated into our cells to make energy. The whole concept that we as human-being is one organism needs to be revisited.

This is already understood, it's not like scientists aren't aware.

The simplified concept of humans being one organism will continue to be taught nonetheless, because it's extremely useful, and not even wrong in most contexts in which it's applied.

There's nothing special about this, you can say the same thing about any simple model in biology: that the brain is an organ inside the head is a simplification, any diagram of a homeostatic system or metabolic pathway that fits on a single page is a simplification, the "central dogma" of DNA -> RNA -> protein is a simplification...

All of these things are well-known. They continue to be used as models, because, well... they're useful models. And there's nothing wrong with that!

Even more generally, reductionism works but with known limitations which warrant a more holistic approach, and we can't work our way out of most real-world problems without this multi-layered approach. Welcome to empiricism in complex systems.

I'm willing to go out on a limb and suggest that the workings of the human brain are still far more complex than that of our digestive system. If the amount of effort that has been put into trying to emulate the former with software had been put instead into trying to emulate the latter, I reckon we'd pretty much have it cracked by now (as in, you could feed some tool info corresponding to all the inputs into our digestive system and it would be able to spit out exactly what outputs would be produced in the average human). But unlike AI/ML, not enough people, ahem, give a shit...

The brain and digestive system are very closely linked.

I think to make an "AI" on par with simulating the brain, you would need to simulate the gut first. And probably vice versa!

Not sure I agree, but accept it's not my area of expertise. We don't necessarily want to simulate the human brain the way it does actually function biologically, rather simulate the its most useful behaviors, which are hard to see as being intrinsically linked to the workings of the gut.

There's an imperfect truth to the comment you're replying to.

You're right that it's unnecessary to emulate the brain down to its finest implementation details, down to the molecule or even down to the cell.

However, I contend that it's essentially impossible to create a "relatable AI" (an AI that behaves and thinks like humans do) without proper consideration of embodiment. A large part of why the brain works the way it does, at a macro level, emerges from the vehicle it's in, and broadly speaking both its afferents/inputs and efferents/outputs.

There's a guy (Jasper Lawrence, who had a horrible allergy problem) had heard of a study where they were testing to see if allergies was related to parasites. He was rejected from the study, so, long story short, he ended up flying to northern Africa and walking around barefoot to get hookworm. He now monitors and manages his hookworm infection with low doses of anti-parasite medication, and he sells soil infected with hookworms so that you, too, can get infected by hookworm and reduce/eliminate your allergies. Oh, and his allergies are gone.

I read about it here: https://www.ksl.com/article/20838871/man-infects-self-with-h...

But there are lots of stories and some studies on the subject as well. The original hypothesis was proposed in 1989 by David P Strachan. According to the theory, many modern diseases have gotten out of hand and are rapidly growing in industrialized western countries because of chlorinated drinking water, vaccines, antibiotics and the sterile environment of early childhood. Moreover, it is theorized that since we have become so good at preventing infections, we have upset the internal balance and ecology in our bodies. One missing element of hyper-clean and sterile environments is that our inflammatory responses do not function as they should. Parasites and bacteria play a symbiotic role in preserving our health.

I know a person who contracted a transient parasite infection, possibly hookworm, while doing research in Africa and walking around barefoot. In the decade+ since, they’ve suffered terribly from debilitating and incurable auto-immune diseases brought on by the initial parasite infection.

So, YMMV.

I agree that caution is in order. The question above just reminded me of the story so I thought I'd pass it along because it was from 2012.

He originally posted his story on kuro5hin[1]. It's an interesting read. He was interested in the worm because, for its survival, it has evolved a mechanism to disable the host's immune system in a particular way that eliminates allergies. At the time he wrote that nobody knows how the worm does it. Now that we can do similar things with monoclonal antibodies, I wonder if the mechanism is similar.

[1] http://web.archive.org/web/20151205143301/http://www.kuro5hi...

Please, for the love of all that is good and holy, do not give yourself hookworms.

I get they are bad, but you seem to speak from experience, either yours or others. Out of curiosity, why not? What can happen?

The history of hookworms in the US is the history of millions of intellectually and physically stunted children and adults[1].

[1]: https://www.pbs.org/wgbh/nova/article/how-a-worm-gave-the-so...

There is a great Radiolab show about both the South and modern research into hookworms.

If you have 2-10 hookworms and eat a modern diet (higher in iron), you're probably going to be fine.

If you have 30-50, you're going to have abdominal discomfort and some side effects.

If you have insane allergies or autoimmune disease, the risk/reward seems pretty incredible.

Worst case scenario if you're an adult with hookworms is you take some antibiotics and they go away.

This https://twitter.com/jimmybernot/status/1354443837897388033 is one person's story about participating in those studies.

I can only imagine how desperate he must have been. Truly debilitating levels of allergy.

"he sells soil infected with hookworms so that you, too, can get infected by hookworm"

Well, when Fry ate the truck-stop egg-salad sandwich in a Futurama episode the worms he ingested really helped him, so sign me up!

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....)

Explore the use of Miswak for your teeth.

I think the consensus is nobody really knows and nutritional science is largely trendy pseudoscience…

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?

Everyone wants to be the one eating - no one wants to be the foodless researcher.

Also mortgages to pay, and mouths of feed of this little brats they pop out are all valid reasons....

It's both difficult and largely unethical to do intervention studies on people, and we don't know how to measure individual differences between people very well.

For instance, studying gut biomes of people is mainly done by looking at their poop but that doesn't help you know what kind of bacteria are where in their intestines, and it's not like you can take them apart.

I think there's a pretty simple explanation for this. How many calories should you consume per day?

It's a trick question because it has no answer. It's going to vary dramatically depending upon environmental, physical/physiological, and genetic characteristics. And that is probably the most simple question to answer, because when you get into the specifics of nutritional content, the same is true except it's orders of magnitudes more complex with far less understood.

And many things come down to pretty precise measurement because it's all systems in equilibrium. 100 calories to your diet would ostensibly have a negligible impact because it's not much relative to your entire intake, but if you were just at the equilibrium where your consume - burn = 0, then that 100 calories is suddenly going to start seeing you gain weight dramatically faster than before.

I don't think that's necessarily the case.

There is much more that we know than just "Vegetables are good" and we know why they're good. Nutrient dense, packed with fiber to slow digestion, includes necessarily vitamins and minerals to not only absorb the nutrients of your food but to also provide you with the micronutrients you need.

That's of course just one example you made. But the problem is where people go to find the right information. Don't watch instagrammers and don't look at the latest "super foods" where the benefits might only be marginal, albeit hardly palatable.

Having studied nutrition and human movement in first year University, my recommendation is for people to actually buy a first year Uni textbook on nutrition and understand what is in your food, what energy systems are, what macro (carbs, fats, proteins), micro (vitamins, minerals) are and how they impact your body. Then you can go and make more informed decisions about what you eat without someone necessarily telling you. You'll know that sugar isn't bad for you, but copious amounts of simple carbs like Mars bars are especially if you're not exercising.

Top level Athletes and body builders are the way they are because of how they train and but largely how and what they eat. If we didn't know that much about nutrition we wouldn't have many world class athletes. As the saying goes, you can't outrun a bad diet and that's true.

If you could afford a sports dietitian, I guarantee they'll know what you should be eating in combination with exercise to be healthy.

A big problem with the Nutrition industry is that its easy to make big positive leaps in what you eat, without it being a bowl of kale and beetroot. The challenge is people's ability to be able to plan and cook properly between their busy lives where nutritionally simple foods are more readily available. Additionally, in today's world of many of us sitting in offices all day, you cannot live a healthy life purely based on what you eat, you need to move your body and exercise as well.

> don't think that's necessarily the case.

>There is much more that we know than just "Vegetables are good" and we know why they're good. Nutrient dense, packed with fiber to slow digestion, includes necessarily vitamins and minerals to not only absorb the nutrients of your food but to also provide you with the micronutrients you need.

A lot to unpack here. Did deeper, do we really need those micronutrients which make "Vegetables are good". To me, to the extent I dug up, the answer is no.

Micronutrients as vitamins and minerals from fruits and veg? Yes absolutely, they’re essential.

The difference here is that we don’t need a lot of them, not like macronutrients so the majority of us are likely getting our vitamin and mineral intake okay. However deficiencies in certain vitamins can cause problems down the line, it just depends on how deficient you are. Some people also struggle to absorb particular vitamins and minerals and they only realise through symptoms which you might not expect to be because of a deficiency.

The reason vegetables are so good is because they’re usually dense in these nutrients and due to the fibre they possess complement the other foods you eat in terms of nutrient absorption and digestion.

>Micronutrients as vitamins and minerals from fruits and veg? Yes absolutely, they’re essential.

And, why are they essential? ( no, I'm not trying to be funny, or feigning ignorance). You can make your answer really short, if you do answer.

No all good I do appreciate the questioning. Makes us think.

Without going back to my textbooks a good example is iron deficiency, if you are Iron deficient your body cannot effectively transport oxygen in the blood. As it is part of hemoglobin which carries oxygen around the body. Without it you will develop Anemia. Women experience Iron deficiency symptoms much more than men due to menstruation.

Furthermore, Calcium which is essential for bone health, its absorption is aided by iron as well.

Vitamin D, a common deficiency in people that work night shift jobs or underground in the mining industry. Usually need to take supplements.

I do wish I could link some studies to further illustrate "the why" but I don't have enough time. But overall, we don't need much of these at all and we certainly don't NEED to hit our recommended daily intake everyday. The tricky part is if you're quite deficient in one vitamin, it can impact your adsorption of other nutrients as well which can cause larger impacts.

One of the challenges with the food and nutrition industry is the marketing around "if you take vitamins and minerals they will change your life". For the majority of us they won't, but they might if you're deficient. They aren't something you can take that will make you wake up tomorrow magically a better and happier person. Which is how they're marketed, like all things sensationalised.

Agreed, a lot of it shoddy 'science'.

Lacking these gut microbes has been posited to lead to depression and effect mood by a few researchers:

https://www.science.org/content/article/evidence-mounts-gut-...

The future of antidepressants is fecal transplants for healthy gut bacteria (not even kidding)

> 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.

Unfortunately, the most effective treatment I know of to change gut biome is bacteriotherapy via a method many people find off-putting and violating.

I think, for the time being, people are much more likely to accept a probiotic.

I take it you mean fecal transplants, aka inserting somebody else's feces up your rectum?

transpoosion

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.

Doing nothing is also an option! I'm not aware of an indigestion epidemic among city dwellers.

Being told to do something is not sufficient, especially when multi-billion dollar industries are behind it.

More research is needed.

However there is an obseity epidemic and a depression epidemic, and its plausible they are related. Which doesn't mean they are, but seems like something worth looking into.

The study compares humans (who happen to live in cities) to primates (who definitely don't live in cities). It doesn't compare between human populations.

The content I replied to implied that the article was a submarine advertisement for pills.

If there is a problem in need of a solution, and it isn't diet related, I'd much prefer the pill over there other options.

Kinda feels like identifying the missing microbes should instead help us track down what we’re doing that’s causing them to die off.

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.

I had a couple courses of IV antibiotics to fight a severe tooth infection. All the oral surgeons who came in to check on me recommended picking up a few bottles of probiotic drinks on my way home.

And some cheddar cheese. https://en.wikipedia.org/wiki/Lacticaseibacillus_casei is theorized to be a sort of a halo probiotic - it doesn't do the work, but it makes you GI tract more hospitable to the bacteria that do.

There are cheddar cheeses though that barely rank the name. Quality over quantity here. Buy the small block of fancy cheddar, not whatever name the food megacorporations are using locally.

Have you had any lasting effects?

I've been prescribed a "fairly serious" antibiotic for a skin condition that has been plaguing me for several years (I've gotten like 5 different diagnosis and tons of different Rx). I'm otherwise incredibly healthy, so this antibiotic scares the shit out of me and I have yet to start taking it.

No lasting effects but it was only a year ago so who knows - my completely amateur take is you've got to balance the payoff with the risk - in your case the payoff of getting rid of a skin condition that's been plaguing me for years seems like a fair trade for the risk of the antibiotics if I were in your shoes... it's not like you didn't try to let your body resolve it on its own (since you've had it for years)

Have you tried cleaning your washing machine regularly ? People often think of washing their pillow cases and sheets once a week, but if the washing machine isn't well maintained, the bacteria don't get properly killed and you spend all nights and day with them, and no amount of skin-cleaning and hydrating products will be able to work.

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.

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.

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.

This should be an election issue, that Indonesia should not be selling antibiotics without a prescription. Stupid people take them just a little then stop, and as a result are continually training tuberclosis and other bacteria to become antibiotic resistant.

Then when they can't treat things anymore, surprised Indonesian faces all around. What if the West doesn't have anything new for them? Time to die.

Before antibiotics, was not a fun time and we're heading back there soon.

Microbiome research at John’s Hopkins:

https://www.hopkinsmicrobiome.com/faq

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.

That's exactly what I was hitting on. Ancient Greeks living to quite old age were not statistical outliers, but the norm! The only way to explain this with contemporary understanding is to suggest it's just an extremely large survivorship bias, but that seems to difficult to swallow because many of those we know of from Ancient Greece we would likely still know of even had they died decades earlier as well.

This [1] study looked at the mean age of Greeks "of renown" from the 5th and 4th century and found the average life expectancy was 71.3 years! There's certainly a class bias, but when we're speaking of times of antiquity all the money it world couldn't buy you what didn't exist. So all that bias would represent is, at best, more or less secure access to food, drink, and other basic necessities.

[1] - https://pubmed.ncbi.nlm.nih.gov/18359748/

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?

> 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

> Unless you are drinking a tap water (pretty extreme thing to do!)

Around your parts you do not drink tap water?

My understanding is that the amount of chlorine added to the tap water differs between regions. I read it can be a lot in the US.

Here in Germany there is a limit by law of 0.3mg per liter and most districts use between 0.03mg and 0.05mg per liter.

We drink tap water daily. There is no noticeable chlorine smell but I heard from friends their cat seems to not like it and drinks rainwater only.

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?

I wonder if the same is happening to mouth microbes, which could explain the epidemic of oral disease in developed countries.

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.

I started taking these a month ago. They’ve worked wonders for my IBS: Healthspan Super20 Pro 60 https://www.amazon.co.uk/dp/B085632HRB

What have you noticed? (I have IBS-C)

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.

https://www.costco.com/trunature-advanced-digestive-probioti...

I've had good luck with these, taken one in the morning and one at night.

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.

You don't need to order more starter once you have your yogurt. You can use a spoonful of your last batch to start the next batch. I go 30 minutes at 180-190*f with the milk, then i let it cool to 110*f, then I add my scoop of yogurt, then I will hold that at 110*f in a separate container in a 110* waterbath (just a big pot of 110* water holding my yogurt tupperware containers that I periodically splash more hot water into) for like 8-12 hours or so (I sometimes forget about it on the stove...). Then I put it in the fridge for two days and after its good to go. If you want it to be more like greek yogurt you can strain it with coffee filter paper and use the whey liquid for various things.

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.

Is that beneficial if it's a busy area? There's some pollution that I want to simply avoid, primarily car exhaust and fine particles like tire dust.

You would be surprised. According to the EPA:

"In the last several years, a growing body of scientific evidence has indicated that the air within homes and other buildings can be more seriously polluted than the outdoor air in even the largest and most industrialized cities. Other research indicates that people spend approximately 90 percent of their time indoors. Thus, for many people, the risks to health may be greater due to exposure to air pollution indoors than outdoors."

https://www.epa.gov/indoor-air-quality-iaq/inside-story-guid...

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

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.

"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.

Try searching for "soil bacteria Probiotic". Amazon has several products that include lots of bacteria not commonly used in yogurt or similar products.

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:

https://www.viome.com

Just start gardening. There is a lot of good bacteria in the soil.

> “perhaps we can restore them with probiotics.”

Really? AFAIK probiotics, as well as antibiotics, can only affect the gut microbiome temporarily - it will restore to the baseline (defined in early childhood) if left alone and given some time. Isn't it so?

> AFAIK probiotics, as well as antibiotics, can only affect the gut microbiome temporarily - it will restore to the baseline (defined in early childhood) if left alone and given some time. Isn't it so?

Seems to be more complicated, and differ for different types of bacteria in the gut microbiome.

https://www.embl.org/news/science/gut-microbiome-changes-ove...

Requisite xkcd: https://xkcd.com/1471/

I've heard fecal transplants are the latest shit in healthcare...

Therefore the city dweller must be somewhat insane.

Because the gut biome is a key component in our central nervous system. It's basically the seat of emotion.

Anybody notice any funny behavior out of the cities lately?

> ...a researcher reported last week at a microbiology meeting in Washington, D.C.

Am I missing it or is this all we are given as a source for the claim in the headline? Not even a name?

Interesting. Perhaps someone could do a geographical survey of people with IBD (Colitis / Chrons / etc).

I'm waiting for the "designer fecal supplements". i.e fecal transplants.

I found them in the seat of an Uber during spring break

It's the diet.

City dwellers tend to eat a lot more unhealthy foods. They also eat a lot less vegetables, fruit and nuts than their rural country(wo)men.

You want more microbes in your gut? Eat more plant-based food.

Having lived both in the city and fairly rural, I can say that access to a healthy and varied diet is much much easier in the city. Both when it came to restaurants and buying and cooking food.

Small town / suburban areas can be the best with large supermarkets or dedicated markets, as long as you have a car.

That said bushland in Australia has natives that you can’t buy in the supermarket. So there is that.

But the average person probably doesn’t forage.

Maybe a varied diet is what’s causing the problem.

The study doesn't show this: it compares humans (who happen to live in cities) to primates (who definitely don't live in cities). It doesn't compare between human populations.

Ironically, cities (particularly affluent ones, but in general) probably have better access to fresh and healthy produce than do medium or low-income rural areas. Some of that is supply and demand (the economics of moving bulk produce favor large population clusters), and some of it is pricing (affluent consumers prefer cities and suburbs on average). You can see these trends in the USDA's Food Atlas[1], which shows lots of rural areas with poor access to produce.

[1]: https://www.ers.usda.gov/data-products/food-access-research-...

> near non-sequitur thesis not discussed in article stated definitively

> flimsy evidence which isn't true [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365871/]

Certified HackerNews moment!

"Cities are unnatural therefore they contain less natural foods" is the West Coast/boomer environmentalism mindset, so this is actually a California moment.

> City dwellers tend to eat a lot more unhealthy foods. They also eat a lot less vegetables, fruit and nuts than their rural country(wo)men.

Can't find it for meat in general, but it seems that rural areas eat significantly more beef than suburban or urban dwellers.

https://www.ers.usda.gov/webdocs/outlooks/37388/29633_ldpm13....

Based on the way my body responds and reviewing lab results after trying different diets, I am of the opinion that it has more to do with processed foods versus minimally/unprocessed foods. I don’t think whether it is plant or meat/dairy based really matters that much nutritionally. Enriched flour, is plant based but by no means do I believe that to be healthy. Same goes for sausage and bacon, too processed. N of 1 but since I stopped consuming processed food and stopped worrying about cholesterol while restricting calories, eating plenty of fruit & veggies, and exercising, I have actually lowered my ldl cholesterol by 40 points. Triglycerides were fine. Dr was thrilled, didn’t have the heart to tell her I didn’t follow her advice.

year ago in WSJ https://archive.today/rCjpO

How does probiotic helps here?

Only the bad ones, I hope

That's why I live in the country and gorge myself on literal feces.

It's the iron fortified flour and then the people are like OMG I have celiac and what not. There's a reason breast milk and milk in general contains lactoferrin; guess what, they also remove it from most milk that is in supermarkets.

can you please expand on this?

The burden of proof for a coeliac disease diagnosis is quite high: a biopsy from an endoscopy that shows classic signs of damaged villi (from autoimmune mechanisms), or a blood test with extremely high tTG levels and a family history of the disease.

https://www.bsg.org.uk/covid-19-advice/covid-19-specific-non...

I'd put microbiome research high up on my list of things which will turn out to be junk science in a few years. A lot of the actual numbers in this are pretty tenuous. Primates have 80 species of bacteria and city dwellers have 50? Wow, stop the presses.

A few years ago the fashionable thing was colonic irrigation (see https://journals.lww.com/ajg/fulltext/2009/11000/clinical_ef...). Now it just seems the pendulum has swung the other way and we need more crap in our colons, not less.

We're looking for reasons why we feel sick all the time but the reality is beyond basic things like being too fat and too sedentary, we are healthier than ever, and many many people had wretched miserable lives of chronic pain before modernity. The expectation of health is a modern conceit and this research is just a reflection of the constant anxiety that there is something wrong with us all - a cultural hypochondria.

Given that the ratio of bacterial to human cells in a typical human is about 1:1, I'd wager you're wrong on that. This sounds rather like a "shallow dismissal" that buts up against the gudelines here, as well.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4991899/

https://news.ycombinator.com/newsguidelines.html

I'll take that bet.

I think we're going to find the opposite in a few years.

> We're looking for reasons why we feel sick all the time but the reality is beyond basic things like being too fat and too sedentary, we are healthier than ever, and many many people had wretched miserable lives of chronic pain before modernity. The expectation of health is a modern conceit and this research is just a reflection of the constant anxiety that there is something wrong with us all - a cultural hypochondria.

Truly, "eat less trash; eat more veggies; eat less total; and move around at least an hour a day" is such good advice for most of us in "the West" that following it somewhat well would provide 100x more benefit than the next-closest thing. Plastic additives? Gut microbes? Fructose versus sucrose? Balance of omega fatty acids? Specific exercise routines? Forget all that unless you're already eating really well and staying active daily, which very few of us are.

When I read articles about these kinds of things and start to get the urge to act on them, I try to remind myself that I should go do a few squats or walk around the block a couple times instead.

Aside from things like infectious diseases, we're not healthier than ever. We have better medicine than ever, but disease states that were once rarities have become commonplace in our modern world: https://en.wikipedia.org/wiki/Lifestyle_disease

By the way, these are diseases which cannot all be blamed on "being too fat and too sedentary", as even skinny people can develop type 2 diabetes. Unheard of centuries ago.

This is true, but lifestyle diseases are somewhat easier to avoid than infectious diseases (plus all the various other things that could easily kill you in your first decade or so in bygone eras). I'd almost say lifestyle diseases seem to be, to a large degree, a choice - maybe not directly, but as a society we accept that if we want to enjoy all the privileges of modern technology and food availability etc., then we pay for it with heart disease or diabetes or certain cancers etc.

> I'd almost say lifestyle diseases seem to be, to a large degree, a choice - maybe not directly, but as a society we accept that if we want to enjoy all the privileges of modern technology and food availability etc., then we pay for it with heart disease or diabetes or certain cancers etc.

It's a choice for many, but I think it's not a fully informed one. If I'd known in my teens and early twenties what I know now, there is a zero percent chance I would have eaten and lived the way that I did. These things don't seem to hit people until the point that their personal health is affected, and sometimes not even then.

Seems to me the same way we treat environmental damage, though in that case most of the suffering will fall on our kids and grandkids. But even the choices young adults are making today aren't really compatible with having a decent planet to live on in 60 years or so, barring some technological miracles.

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