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What Your Microbiome Wants for Dinner (nautil.us)
204 points by dnetesn on Dec 10, 2015 | hide | past | web | favorite | 97 comments

This article opens with, "[New science] is also showing us that advocates of trendy paleo and vegan diets are missing the big picture of how our omnivorous digestive system works." But it concludes with, "Pick a modest-sized plate and make meals using vegetables, legumes, leafy greens, beans, fruits, and unmilled whole grains as the main ingredients. Add some meat if you want and dollops of healthy fats on the side or sprinkled through the plant foods. Desserts and sweets are special, so save them for the special times." Omit the optional meat an you have a vegan diet. What about the "big picture" are vegans missing?

And omit the legumes and grains and you have paleo. Agreed, it's pointlessly contrary.

You don’t even need to omit the grains. You can just eat Dinkel or Urkorn, two very common (like, in every bakery) types of grain that existed even in the paleolithic times.

EDIT: Seriously, how is this not contributing? Please provide a comment if you think it is not contributing.

Those grains aren't good for paleo though since we didn't really eat them while evolving. Our bodies haven't been primarily digesting them for very long.

I don't think that we have very solid evidence on the diet we ate "while we were evolving" (when did that period stop?).

I think you underestimate how fast evolution happens. Lactose tolerance is a fairly recent, but widespread adaptation.

Yep, rates of evolution (in particular mutation rate and drift) are proportional to population size, and we have a larger population size than we ever have in the past.

~2 billion base pairs * ~1 in a billion error rate = 2 mutations per generation (on average)

Edit: Slight clarification and a brief (and greatly oversimplified) lesson on how this works.

Let Ne = effective population size. And I'll define "fitness effect" as the advantage conferred by a particular mutation in a particular fitness landscape. e.g., If you're an E. coli, the fitness conferred by penicillin resistance is very high if you're sitting in a pool of penicillin, but generally mildly negative otherwise because you're wasting energy.

When the fitness effect size is much larger in magnitude than 1/Ne (or 1/2Ne if you're diploid, like us), the fate of the gene is largely determined by natural selection. (But add the occasional coin toss in there b/c the real world is messy.)

When the fitness effect size is much smaller in magnitude than 1/Ne, the fate of the gene is largely determined by genetic drift. https://en.wikipedia.org/wiki/Genetic_drift (tl;dr Mostly chance mod a few other effects, like if the mutation of interest has a physical location close to another mutation with strong selection pressure)

However, there are slightly deleterious or slightly advantageous mutations, whose fitness effect size is close to 1/Ne (or 1/2Ne for diploids), and things get kinda interesting, because it's a combination of genetic drift and natural selection. For instance, if it's a slightly deleterious mutation, it will decrease Ne slightly (increasing the proportion of mutations that are considered neutral of the new value of Ne), and the previously "slightly deleterious" mutation may now be effectively neutral for the new value of Ne.

There is a lot of evidence that the "slightly" deleterious and the "slightly" advantageous mutations contribute substantially to evolutionary dynamics.

This is further complicated by the fact that the fitness (whether a mutation is deleterious or advantageous) is not constant everywhere geographically, or over time.

Speed of evolution depends on how strongly the adaptation influences reproductive success. It's possible that grain causes subtle long-term damage that mostly kills people past reproductive age, whereas lactose tolerance is of immediate benefit. If this is true then grain tolerance would evolve much slower than lactose tolerance. But note that the "subtle long term" damage argument applies to all foods, and it's uncertain if grains are significantly worse than any other.

> It's possible that grain causes subtle long-term damage that mostly kills people past reproductive age, whereas lactose tolerance is of immediate benefit.

Sure, and it's also possible the human body has already adapted to processing grains without long term damage, and it's possible that there was never any damage by consuming grains in the first place (the body is highly adaptable). All this line of argument is stating is that without any information, we have no information.

What Retric was stating is different though. There exists digestive adaptations that have happened relatively rapidly in relatively recent history, therefore merely the fact that foods were not available in more ancient history is not sufficient to argue that they "aren't good" for the body.

And, as many gluten-sensitive (but not allergic) people told in a recent thread on reddit, where the topic came up, they have next to no issue with the hand-baked bread you find in small bakeries in Europe, but the issues often only show when eating mass-produced bread.

It’s more likely that gluten sensitivity is just caused by a cross-interaction with an additive used for bleaching or similar.

More likely glycophosphates (roundup)

Aren't lactose tolerances wildly different between populations? With e.g. Northern European ancestry people having very high lactose tolerance and East Asian ancestry people having much lower lactose tolerance?

Of course paleo is absolute BS, so why does it matter?

rather than just saying an absolute, why not give some facts as to why "you agree with those who say paleo is BS".

I'm not suggesting it isn't but your dismissive comment doesn't enlighten those who are not aware of the controversy.

Not explicitly about paleo, but with lots of anti-paleo evidence: http://www.amazon.com/How-Not-Die-Discover-Scientifically-eb...

Is there a controversy? Eating more nutrious food and fewer calories (assuming a previous diet of too many calories and poor nutrucian) typically benefits people whether it's paleo, vegan or just a regular healthier diet.

Paleo's basic premise is loosly based on the malnourishment seen when we transitioned from a diverse hunter-gatherer diet to a much less diverse agricultural diet (largely caused by iron deficiencies). Its a misunderstanding of history. We ate those foods before, but they weren't the ONLY things people ate. The result is ultimately still restricting diet to healthier foods which means it's nutricious, but still unnecessarily restrictive and without a realistic premise.

I don't get why paleo diet is not congruent. So our DNA is build upon iterations(generations), and the aliments that were eaten in the majority of those are better suited for our current generation.

Any argument?

The "vast majority" of our ancestors were single cell beings.

Right, so including how close in time were those generations happening(compared to the actual one), then that diet would be still valid?

Valid for what? You have no obligation to eat what your ancestors ate. Our ancestors certainly didn't, which is why they didn't eat like single-celled organisms. If what you are thinking were true, it would be true for them as well.

Not to mention the fact that your food has evolved as well.

I didn't say obligation. After reading here: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091895/

My question was an oversimplification.

No matter the seed you will find in the vast majority of cases they contain anti-nutrients that are toxic to mammals. Lectins, glutens, phytates, etc.

Since when is gluten "toxic", not just "leads to an allergic reaction in a minority of the population"?

There is far more in wheat than gluten. Seeds of many kinds are filled with specific chemical compounds that are toxic to mammals. Plants actively participate in chemical warfare at many levels, via the roots, leaves and seeds. https://en.wikipedia.org/wiki/Seed_predation#Seeds_and_their...

How dare you let reason get in the way of the pitchfork masses.

"Reason"? I think you spelled "assumption" wrong.

But fermentation (like in sourdough) can fix this right?

Yes, fermentation lowers not only the gluten it also reduces the toxic chemical defenses built into seeds as well in many cases. Beware though, most "sourdough" available in anything less than an artisan bakery is generally standard white dough with lactic acid added to it and some weasel words on the label to make it sound like it's naturally leavened.

The "add some meat if you want" part.

If you omit something it is not the same anymore. It is like omitting pasta from a spaghetti bolognese: you will end up with something completely different and not even remotely pleasant.

Err not really. The typical vegan diet contains large amounts of potato, heavily refined carbohydrates, and processed foods. It also lacks an emphasis on probiotic and prebiotic foods such as sauerkraut. The article also didn't say the diets were massively different, but rather that they had a different emphasis. You can eat a vegan diet and avoid all of the prebiotic and probiotic foods.

There's no typical vegan diet, just like there's no typical non-vegan diet. Vegans can eat whole foods, junk food, high-carb, low-carb, high-protein, etc. There's no macro or micro nutrient that comes exclusively from animals. (Btw, I've never seen Sauerkraut that wasn't vegan.)

I've been vegan for 10 years, have lived in 3 different countries and have met a lot of vegans, usually in situations where food was involved. My personal experience indicates that, overall, vegans eat less processed/refined foods than non-vegans and are more knowledgeable about nutrition than the average.

My experience is that they eat a lot of potato chips and biscuits. Where do you get your vitamin b12 from?

Regardless, the rest of my comment points out why the person I was replying to is wrong. Even your comment points it out. All you need to do to be a vegan is not eat animal products. This means you can avoid all of the foods that are good for your biome. That was the entire point of the quote from the article that was completely missed by the op.

In addition, not all vegetables are equal with regards to bacteria.

Well, the author points out that meat is beneficial, but eat just a small amount with meals so it largely gets absorbed in the small intestine (and he explains why this is important).

The other valuable information is why whole grains are OK to eat (I favor them in small portions only) and processed grains are so bad for us.


My thought as well. Milk, cheese, and eggs are unfashionable at the moment, for whatever reason; but that doesn't make them less valuable or desirable.

Is animal welfare the reason for dairy goods being out of fashion? I doubt it; it's easy to come by humane milk and eggs, although humane cheese, butter, kefir, yogurt, etc. are less common. And yet, vegans are the new vegetarians -- even the Jains are going vegan -- while we also get the paleo diet with its own reasons for being anti-dairy...

There's also hostility to bread. Bread and milk are historic European staples; a part of me suspects that hostility to these (at least in white Americans) is really about hostility to the past.

The milk that many regions of the world consumed was genetically different to the most common milk that humans consume today. It has been proven that a2 milk is digested differently to a1 milk.

I switched to a2 milk and the difference to my digestive system was extremely obvious. Time will show that for many people, if they consume milk, it should be a2 milk.

If anyone else wants a quick summary of what you can find on Google Scholar for this: There is currently no strong evidence in support of the idea that A2 milk has better digestive or other health properties than A1 milk. Most of the stuff I found out there concluded that there was no significant difference, and the few that I found on the rest of the Internet were contradicted elsewhere.

This is correct and does not contradict anything I said. It is quite easy to try it for yourself and see if it does anything. Of course you will want to avoid consuming large amounts of other dairy sources while you are trying it.

In order to build confidence in the results of a personal experiment like this one, it's best to (double-)blind it as much as possible and log lots of concrete data every day (e.g. keep track of your bowel movements, sleep quality, alertness levels, blood pressure, etc). This should help limit the impact of any (conscious or subconscious) preconceptions or other psychosomatic effects.

Also, change as little else in your life as possible while you're performing the experiment to control for confounding variables.

While anecdotal evidence is useful it doesn't prove anything. Research is stronger, but more limited in scope.

That's an interesting article, for sure. It also applies to what I've been diagnosed with as well. Type 2 diabetes.

I'm applying data science to this disease. It's what I do, and can afford. Unfortunately, my doctor thinks that pushing pills is an adequate response, which I heartily doubt.

The more I understand this disease, it has to do with either: pancreas is dead (type 1), or your glucose response/insulin response is badly out of whack due to a metabolic carbohydrate problem (type 1.5/2). I was diagnosed with a fasting glucose of 161 and a1c of 7.1 . Met with doctor, and talked about it shortly. Was prescribed metformin and testing kit with 100 strips. I am currently not taking any drugs.

I keep reading that the problem is carbohydrate overload to my genetics. Can I validate or invalidate that? Indeed. I was told to test blood sugar 1x a day for 3 months. That's inadequate, as it's only an instantaneous sample. What about after I eat? What about when I go to bed and wake up? Can I deduce anything about my pancreas and its slow and fast response to glucose? Indeed.

I've started testing myself 4x every meal(1 before meal, 3 half hour increments after meal ends), and 1 when I wake up and go to bed. Turns out that yes, carbs has, in my body a direct correlation to my blood sugar. And it's pretty stark.

Now, if my hypothesis is correct, I can control my blood sugar purely with carb counting and eating to the glycometer. If after 2 weeks this does not show significant changes in my basal glucose rate, as well as weight losses, then I will go on drugs.

However, I already have 2 good side effects: I'm not craving for food any longer, and I no longer overheat. I'm not sure how to classify those effects, but not being slave to extremely annoying bodily issues does seem very beneficent.

Congrats on your approach to managing your condition. Couple of things to think about.

First, you may find a continuous glucose monitor helpful to get a more granular view of what's going on. Dexcom [1] makes the most popular one, which is also hackable [2].

Second, keep in mind that all carb avoidance isn't equal. If you up your protein a lot, you could still get postprandial glucose spikes due to gluconeogenesis from protein breakdown. A good low-carb diet for you will be a low-carb, high-fat diet.

Third, for extra bang for your buck, go for a walk after you eat. The CGM, if you get one, will verify the efficacy of that.

Fourth, look into high-intensity exercise, which will help combat your insulin resistance. All exercise is not the same. Weight training is particularly good.

Your MD's reaction is sadly typical. You're taking the right approach by taking matters into your own hands, using her as a backup.

[1] http://www.dexcom.com/dexcom-g4-platinum-share

[2] http://www.nightscout.info

Thank you.

I've looked at the Dexcom unit. I would like to run with it for 2-3 needles (20-30 days) to get accurate data on things I surmise are good, but yet cannot prove.

I've also worked on guessing the score before I test. Interestingly enough, after about 2 days with the meter, I within +-2 points. That really surprised me.

And a very good point about the exercise after I eat. I have been doing that in the evening, not always after I eat. I'm going to believe you without proof, only because my body knows I need the exercise. I've also heard that HIIT is also great (meter backed results).

If I do worsen, I do have the metformin I can fall back on. I'd rather not make that the first response if diet shows more effect.

Great to see someone taking charge of their condition and using data to do so.

Have you tried squats after eating.

Use of the largest muscles in the body may help with extra glucose sensitivity.

Seems like good advice. I think this is recommended in the four hour body too. I'm not sure why it was down voted.

I wholeheartedly agree.

When I asked my doctor about what kind of exercises to do, and whom to ask about that for safe weight loss via exercise, he said "Oh just do exercises".

I also have an existing shoulder injury, and meeting with an orthopedic surgeon. His answer was "Don't do these 2 exercises because of exacerbating the condition, but the rest are safe. And These will help."

I'm still kind of in the research phase on what I can do that will cause a good amount of change. But my research also shows that a safe amount to lose is 1lb/week.

Here's an interesting study that found that different people have different blood glucose reponses to the same foods.


>Participant A maintained a stable blood glucose level after eating a cookie but responded with elevated glucose levels after eating a banana. Conversely, participant B experienced an increase in blood glucose level after eating a cookie, but not after consuming a banana.

>In another striking example one of the participants, a middle-aged woman who was obese and pre diabetic learned that her “healthy” eating habits may have actually been unhealthy for her. The researchers found that in her case, eating tomatoes resulted in an “unhealthy” blood sugar spike, as the woman ate tomatoes frequently over the course of the week long monitoring period, this “healthy” habit may have been undermining her health.

I like your scientific approach. It would be awesome to have continuous monitoring of blood sugar, heart rate, body temperature, blood pressure, and other vital signs.

From what I have read, early type 2 diabetes can be completely controlled via diet changes as you have already started to see. The amount of insulin your body needs to make is by far the largest for carbohydrates, then somewhat less for protein, and then near zero form fat.

I liked this talked which summed up the argument for treating diabetes (type II at least) with diet and not drugs: https://www.youtube.com/watch?v=da1vvigy5tQ

Are you able to watch this BBC TV program? (I hope it's the right one: my wife suggested it.)


I'm not able to watch it. Is it this per chance?


No, completely different ;-)

Episode that impressed my wife basically showed a women stop having diabetes 2 a few weeks after being put on a no-carb (well, no sugar and no high-glycemic carbs, but meat, fruit and veg) diet.

This is awesome. What are the most informative times to test after you eat?

My fasting glucose was 99 so I'm not sure what to make of that. I ordered a glucose monitor just to learn how different foods affect me.

Did you notice any differences depending on the carbs? White rice, brown rice, sweet potatoes.

And what about accompanying seasoning? Olive oil, coconut oil, fatty meat/fish.

It may be worth looking into how different forms of exercise may affect insulin sensitivity; additionally, fasting (as well as the two combined).

I've heard a number of times that proper water fasting can heal diabetes.

P.S. Absolute fasting can be dangerous.

I've been a Type 2 diabetic officially for 18 years but impaired glucose tolerance for longer. You're on the right path, there's a lot you can do to slow down the progress of the disease.

I'm not a doctor however so take any advice with a grain of salt. (But not sugar, definitely not that.)

> I keep reading that the problem is carbohydrate overload to my genetics.

Read up on "glycemic index". This index tells you how close your food is to pure glucose e.g. table sugar has a glycemic index of 68 so it has 68% of the insulin response of pure glucose. The index correlates to the type of carbohydrate and how processed it is, although there are some surprises e.g. premium ice cream has a G.I. of 37.


You don't have to commit the entire index to memory. Usually you can come up with several heuristics e.g. tropical fruit tends to have higher G.I. than temperate fruit.

Obviously you should test this with your own blood sugar readings as individual response to a carbohydrate challenge can be quite different.

The other components to a meal also affect blood sugar. For example, acid, protein and fat tend to slow down digestion and thus blood sugar spiking. If you must take pasta for example, take it with a tomato-based sauce (acidic) rather than cream-based. YMMV.

> Unfortunately, my doctor thinks that pushing pills is an adequate response, which I heartily doubt.

It's important, although somewhat depressing, to see this disease as a progression. A progression that you have to slow down as much as possible, but still a progression.

Know that in the future, you may have to resort to the first line of pills, and then possibly stronger ones. Try to slow down the progression as much as possible, and research the pills to see their efficacy and benefit.

Metformin is usually the first line of defence and it has a long history and little side effect. It generally fools your body into thinking it's in starvation mode, which means you can lose weight, both fat and muscle. It actually lowers insulin resistance rather than increasing insulin. Generally in amounts >1g it gives you loose bowels, so when you have to use it keep on low doses as long as possible.

When metformin doesn't work as well, generally you'll get prescribed sulfonylureas. Since they increase insulin secretion, they tend to exacerbate your insulin resistance. There is some inconclusive research that they burn out the pancreatic beta cells. Better to avoid these as long as possible, but if your glucose control is bad you may not have a choice.

I'm currently on an incretin enhancer (gliptin) + metformin.

Also look up supplements on examine.com. It's hard to tell the effectiveness of supplements, the only one that had a distinct effect on me was berberine.

The other thing you can do is exercise. Lots of it. Strength training for more muscle and more insulin receptors. Aerobic exercise to burn/absorb more glucose and lose weight. There's even recent evidence that high-intensity interval training improves diabetic markers more than sustained, low-intensity exercise.

Mind sharing your readings ?

Sure. You'll need LibreOffice. there's not many readings thus yet.

However, given some of my previous symptoms (thirst, extreme hunger, overheating) along with family history, a basic test was done. a1c=7.1 and initial fasting glucose = 161mg/dL

I'm approaching this aggressively, as I'm not sure exactly how many medical symptoms were caused/still caused by this, including mental fog during programming.


Are you overweight? I am, and recently tested a1c @ 6.1. That's not Type-2, but it's dangerzone.

I'm dieting now, I'm going to re-test each time I drop 5kg to see if it helps.

see: http://www.gizmag.com/one-gram-pancreas-fat-reverse-type-2-d...

I am. The weights are also in the data. Initially at the doctor's, I was 320. And that was 2 weeks ago.

Now I'm at 314.

And also, watch out about the a1c. They are not reliable readings to use in diagnosis. Studies from last year show a very skewed weighted average from the last 3 months that generate the a1c. Also, if you have any sort of hemoglobin-modifying illness (sickle cell, others), a1c is completely inaccurate.

140mg/dL is scientifically known to kill nerve cells. Every minute above this kills stuff. The ideal healthy human's response is between 85-100mg/dL. A resting rate away from this shows dysfunction.

However, an OGTT shows if you have problems. You take a reading prior to drinking 75g glucose. One big drink. Then you test every 30 minutes until you're back to normal, which is usually 2-2.5 hours. A doc won't say it, but every minute over 140 causes cell death, and most likely lower.

For example, this is what 12 carbs did to me:

     18:20 12/09/2015	test		143
     18:35 12/09/2015	eat	15m	
     19:15 12/09/2015	test		182
     19:30 12/09/2015	test		172
     19:45 12/09/2015	test		168
     20:00 12/09/2015	test		150
     20:15 12/09/2015	test		144
     20:30 12/09/2015	test		123

Interesting, I always assume some variance.

Following the advice of my wife (a pharmacist!), I've been on a restricted calorie diet (1300kcal) for 10 days and it seems to have worked. My resting a1c is 4.3.

I can recommend trying it - although it's not easy. The first 5 days are horrible. I only managed it because I had a stomach virus (so wasn't eating).

Pills are expensive and it's crazy to be stuck on them if you can control your glucose with diet.

One topic that was not mentioned in the article that I have found fascinating is that your gut microbiome can actually affect your cravings. (1) Your microbiome accomplishes this through a host of mechanisms including changing the expression of taste receptors, making certain foods taste better; they may release hunger-inducing hormones; or they may manipulate the vagus nerve (which connects the stomach to the brain) to control their hosts’ eating behavior.

Are you sure you really want that extra side of chips? Or has your gut biome decided it wants that extra fat, and influences you to eat it.

Additionally, you can "reseed" your gut biome by changing your diet. Do you crave greasy food? Go vegan for 2 weeks. The new gut biome that develops and takes hold may soon have you start craving healthier foods. A change in diet can change your biome in as little as 4 days. (2) You can witness this phenomena in the movie Super Size Me. At the start of the movie Spurlock is disgusted by eating McDonalds for every meal. But, by the end of his experiment, his gut biome has significantly changed, and you can literally see his mood darken when he is not eating greasy fries and burgers. He craves, or should I say, his microbiome craves those happy meals, and is influencing both his taste receptors, health, and general mood in order to manipulate him in to a trip to the drive though.

1. http://www.theatlantic.com/health/archive/2014/08/your-gut-b... 2. http://www.scientificamerican.com/article/the-guts-microbiom...

> One topic that was not mentioned in the article that I have found fascinating is that your gut microbiome can actually affect your cravings

It's worth noting that the study[1] does not suggest that. It says that there has been some "circumstantial evidence for a connection between cravings and the composition of gut microbiota" and notes that there would be evolutionary pressure on microbes to be able to influence cravings, but gives no evidence on this point.

The thing the study was actually researching was ways microbes could influence cravings, not whether or not any of them actually were.

Meanwhile, it does appear you can noticeably change the expression of your microbiome by long term changes in your diet, but the effects we've actually found are still fairly subtle (at least in terms of metabolic outputs), and I've found no studies that indicate you can change cravings due to those changes. For example, in [2], "chocolate desiring" subjects had noticeably different microbiomes than "chocolate indifferent" subjects, but that difference was significant even when on the exact same diet (which was necessary for the study's methods).

You have to be careful not to extrapolate from actual data to "what makes sense". Spurlock's stuff appeals at a gut instinct level, but that's often the most dangerous kind of thing for science since our brains desperately want to make patterns out of data even when there isn't one.

[1] http://onlinelibrary.wiley.com/doi/10.1002/bies.201400071/fu...

[2] http://pic.plover.com/chocolate.pdf

I'm not sure about chocolate cravings. The scientist I heard talk had done some experiments on her self that eating chocolate for a while produced cravings but I guess that could be psychology rather than bacteria. There have been solid studies on gut bacteria making people fat and thin, presumably by effecting their desire to eat. See eg http://www.nytimes.com/2013/09/06/health/gut-bacteria-from-t...

The experiments basically fed gut bacteria from thin creatures, (mice / humans) to fat ones (mice) and they lost weight and visa versa for fat to thin. I guess you could extend that experiment quite easily to mice and chocolate though I'm not sure it's been done yet. Maybe if anyones got some experimental mice and bars of chocolate knocking around they could report back?

I think cravings are mostly an expression of a finely tuned feedback mechanism of the body to tell you what kinds of nutrients and minerals are currently lacking the most. The better you train this system by eating very varied, trying out all kinds of non processed foods, the better it works. Search for 'magnesium deficiency and cravings' for a start. There should be other papers on the topic but i can't find anything right now.

But i'm not saying that there is no such thing as the microbiome directly influencing your brain, bacteria produce a wide array of by-products. In which way these by-products affect our bodies is exactly the question. I just want to point out that there are types of dysbioses that can reduce the ability to absord certain nutrients and by that could exacerbate the problem of cravings.

Would love to see this tested in a more detailed way, what if your vegan diet consists of high amounts of non-animal oils, would you still crave oily burgers eating a vegan diet with high amounts of canola or olive oil? Would you lose the cravings with lower oil intakes on the same vegan diet?

Somewhat interesting and different look at what different types of foods do to us by focusing on our guts and those little things that help us digest. His recommendation seems to be more complex carbohydrates, less sugar... same old conclusion, different way of getting there I guess. It's still "Eat food, not too much, mostly plants."

The take-away, to me, is to append one more variable when we consider wehat goes in our mouth: the bioavailability / effect in your microbiome.

"We realize a diet like this doesn’t lend itself to being packaged and sold. It emphasizes how to think about food in the context of one’s microbiome, rather than prescribing a narrow choice of foods, counting calories, or advocating “dieting” as a daily activity. This advice is far from sexy and certainly not earth-shattering."

My favourite way of phrasing that is: "Athletes don't diet and workout, they eat and train."

How you get there is up to you. Calorie counting and avoiding simple carbs works for me. As does training for at least an hour a day.

Agreed, but I liked that he walked through the reasoning and the processes that inform that conclusion. The more something looks like a mystery, the less we understand it / the less scientific it really is.

Be careful how much you take at face value, though. While a lot of what he has to say is accurate, there's some stuff in there, like a reference to "leaky gut syndrome" which treats it as a legitimate health concern rather than the totally unfounded alternative-medicine BS that it is, which you'd be ill advised to take seriously.

While "leaky gut syndrome" as imagined by pseudoscience believers is a little ridiculous, the general idea of chronic low grade inflammation of the intestinal epithelium due to a breakdown of the innate immune system is not. If anyone is interested, checkout out David Artis' work on commensal bacteria on barrier surfaces.

Rolled out this idea in a thread long ago about Apple not including a Period Tracker in their health app and it was taboo then, but here is as best a place to try again... There should be a poop tracking app. It would help a user track their waste over time, identify important red flags, act as an incredibly detailed source of diagnostic data for health care professionals, and promote healthy and happy living. Two topics that people seem so afraid of discussing are shitting and masturbating which seems so silly to me, as those are two things all humans do. If you want to be healthy, start with your poo; understanding your waste will tell you how to eat, sleep, exercise, and live better.

Um..."very solid today", "kind of soft today"...what exactly would you track, without more tools to analyze it?

Color, texture, odor, amount, frequency, duration, experience, to start off. Chromotagraphy and good ol' regular image capture might be super useful, too. Pairing the app with a food intake tracker would be ideal. There could be different options of detail in terms of data collection. Known illnesses could be factored in. Worrisome trends could be identified. Uncomfortable conversations could be avoided, thereby helping medical professionals more easily asses the root causes of problems. Anonymous communities could be established based on chronic ailments and religiously health minded folks alike. There are a diarrhea of options for this idea (I couldn't fuckingbhelp myself... so many poop puns wanted to come out...)

"never eating Taco Bell again."

Actually, you could track cohesion, firmness, gassiness, possibly odor, etc. Unfortunately there's already an online community of people who do this kind of thing.

It's nice to see an article that explains that too much animal protein can be bad for your health, without advocating a 100% plant-based/vegan diet. We humans are apes, and when you look at other apes, they eat mostly plants, but not always only plants. For example, chimpanzees eat small amounts of meat.

I'm a bit skeptical to the claim that whole grains is a nearly perfect food, though. Think about it - we apes have not eaten huge amounts of grains for most of evolution. Also grains contain various anti-nutrients, otherwise they would have been eaten by insects. It does not seem inconceivable that some of these insect-harming anti-nutrients could also be harmful for humans.

Many dietary studies are done with rodents, but I think (I'm not an expert here) rodents have eaten far more grains than apes during most of evolution. So studies with rodents showing that high-grain diets are healthy, are perhaps showing just that - that high-grain diets are healthy for rodents (and not necessarily apes).

What? Looking at other apes is a poor indicator. What an animal eats has to do with it's environment and it's digestion mechanisms. Some apes largely ate grasses. Nutrients matters, but largely is solved by eating a varied diet.

You might have noticed that we do something other species don't. Cooking! It's a pre-digestion mechanism that saves a lot of work. Combined with our omnivorous digestive system we can probably be considered radically distinct from our ape ancestors (in a good way).

So, I googled for grass eating apes and found this: https://www.nsf.gov/news/news_summ.jsp?cntn_id=128106

Is this what you were thinking about?

The evidence seems rather sketchy, though. From the article:

"If early humans ate grass-eating insects or large grazing animals like zebras, wildebeest and buffalo, it also would appear they ate C4 grasses.

If they ate fish that ate algae, it would give a false appearance of grass-eating because of the way algae takes up carbonate from water, Cerling says.

If they ate small antelope and rhinos that browsed on C3 leaves, it would appear they ate C3 trees-shrubs."

Seems more likely that they ate the animals, though. I mean, otherwise, shouldn't our teeth have been different by now?

Sorry for not finding a name, but there's an early hominid (divergent from us, but not an ancestor) that ate C4 grasses and had the jaw shape for it. They are now extinct. Point being that we can't extrapolate from other species (apes) even if we share an ancestor.

Early humans were probably mostly scavengers anyway until fairly close to the agricultural period. Its unlikely they ate much meat.

It's a book extract: "Excerpted from The Hidden Half of Nature: The Microbial Roots of Life and Health by David R. Montgomery and Anne Biklé. Copyright © 2016 by David R. Montgomery and Anne Biklé. With permission of the publisher, W.W. Norton & Company, Inc. All rights reserved."

Based on that section, I would look for an extract from The Good Gut (1) instead. It leans more towards science and less towards popularization....

(1) http://www.amazon.com/The-Good-Gut-Control-Long-term-ebook/d...

I just read Good Gut, it's a very very very bad book. About 10% enlightening accepted science and about 90% rampant and very wild speculation. Filled with little chapters that take in many cases very tenuous unproven theories (they come out and say that) and then use weasel words to then write a whole speculative chapter about it.

I learned a lot about how digestion works and then a lot about how to make a book out of very thin gruel.

Views obviously differ. Both the authors (1) have very senior positions at the Sonnenburg Lab in the Department of Microbiology and Immunology at Stanford University, so I'd be quite surprised if the book is as bad as you claim.

Also, Amazon reviewers have given it 4.7 stars out of 5, which suggests quite a few people found it useful.

(1) Justin L. Sonnenburg. Principal Investigator, and Erica D. Sonnenburg. Senior Research Scientist.

Maybe, but remember that the process of review is removed.

Even the most brilliant people quite happily believe dumb things.

Sure. But brilliant people generally don't believe dumb things that in their core area of expertise....

Sure, but a PhD's area of expertise is increasingly narrow.

The authors are well beyond PhD level. They are supervising PhD students and post-doctoral fellows.


Look, I haven't read the book in particular. All I'm saying is that the success outcome of a book has completely different requirements than the success outcome of an academic paper. It's entirely possible that the most well-educated person in a field writes a book that is more interesting to read than it is well-proven.

Even so, I don't personally have enough background in the area to tell you much more than they publish in Journals with a reasonable impact factor. I can assume they know what they are talking about, but no matter the school, no matter the prestige, they could still be wrong and/or poor researchers and/or poor writers. They study ultra-specific things within an ultra-specific field.

Personally, I'd probably enjoy the book.

I don't understand why you're arguing about a book you haven't read.

> no matter the prestige, they could still be wrong and/or poor researchers and/or poor writers

Sure, but those are generalizations, and they don't apply in this case. As you would know if you could be bothered to read it...

As someone who's going through a not very fun period of C. Diff, this is pretty relevant. There is still so much we don't know about what makes a healthy and un-healthy biome, it's maddening.

Ask your doctor: http://arstechnica.com/science/2015/11/635-poop-pills-cure-d...

cost is relatively low (compared to typical C. diff treatments) and seems very effective, but isn't without it's risks. Research is still very early.

Ugh, went through that a couple years ago after a course of antibiotics due to a dog bite. Wouldn't wish it in my worse enemy. I'm also much more wary about ever taking antibiotics again.

What I would like to know is what happens to the colon when you go on a 20-day regimen of broad-spectrum antibiotics such as ciprofloxacin?

Nothing good, I'd imagine; intestinal flora tend to be antibiotics' first casualties. It's always a good idea to consume probiotic foods once you're off the medicine (or take intestinal-flora pills).

> The amount of meat in the Western diet can also pose problems. When consumed in relatively large quantities, animal protein is not completely broken down by the time it reaches the lower end of the small intestine. Eat too much meat and your overwhelmed small intestine delivers partially digested animal protein to the colon. When bacteria in the colon encounter intact or partially digested protein, a different kind of alchemy gets underway—protein putrefaction.

Do someone has any information on the "relatively large quantities" part? How much meat can I eat before protein putrefaction kicks in?

When I was in graduate school in the early 80's I wanted to get a PhD in toxicology (but didn't, became a programmer instead). Today if I was at that same stage I would study the microbiome, it's a fascinating melange of chemistry, microbiology and food science, and we still know very little about it, plus it can make a huge difference in the world. Toxicology seemed too much like slaughtering rats for a living.

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