
What Your Microbiome Wants for Dinner - dnetesn
http://nautil.us/issue/31/stress/what-your-microbiome-wants-for-dinner
======
asciimo
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?

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

~~~
kuschku
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.

~~~
Sargos
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.

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

~~~
mrob
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.

~~~
magicalist
> _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.

~~~
kuschku
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.

~~~
r00fus
More likely glycophosphates (roundup)

------
kefka
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.

~~~
shanusmagnus
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](http://www.dexcom.com/dexcom-g4-platinum-share)

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

~~~
kefka
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.

~~~
erkkie
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.

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

~~~
kefka
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.

------
_fs
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...](http://www.theatlantic.com/health/archive/2014/08/your-gut-bacteria-
want-you-to-eat-a-cupcake/378702/) 2\.
[http://www.scientificamerican.com/article/the-guts-
microbiom...](http://www.scientificamerican.com/article/the-guts-microbiome-
changes-diet/)

~~~
magicalist
> _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...](http://onlinelibrary.wiley.com/doi/10.1002/bies.201400071/full)

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

~~~
tim333
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...](http://www.nytimes.com/2013/09/06/health/gut-bacteria-from-thin-
humans-can-slim-mice-down.html?_r=0)

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?

------
blakesterz
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."

~~~
stevenkovar
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."

~~~
Swizec
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.

------
classicsnoot
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.

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

~~~
classicsnoot
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...)

------
jensen123
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).

~~~
Joof
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).

~~~
jensen123
So, I googled for grass eating apes and found this:
[https://www.nsf.gov/news/news_summ.jsp?cntn_id=128106](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?

~~~
Joof
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.

------
scholia
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...](http://www.amazon.com/The-Good-Gut-Control-Long-term-
ebook/dp/B00OZ0TOV2)

~~~
OldSchoolJohnny
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.

~~~
scholia
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.

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

Even the most brilliant people quite happily believe dumb things.

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

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

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

[http://sonnenburglab.stanford.edu/people.html](http://sonnenburglab.stanford.edu/people.html)

~~~
Joof
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.

~~~
scholia
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...

------
justinph
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.

~~~
magicalist
Ask your doctor: [http://arstechnica.com/science/2015/11/635-poop-pills-
cure-d...](http://arstechnica.com/science/2015/11/635-poop-pills-cure-deadly-
gastrointestinal-infection/)

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.

------
triangleman
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?

~~~
clock_tower
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).

------
edem
> 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?

------
coldcode
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.

