How we study the microbes living in your gut | Dan Knights

If I asked you to name a microbe
that’s living in your gut, many of you would probably say E. coli. A lot of people say this.
It’s the best-known of the gut microbes. But it turns out that E. coli
is outnumbered in your gut about a thousand to one by other species, many of which
you probably haven’t heard of. These are Bacteroides;
Prevotella is another example. Those are the two that dominate
the modern human gut. There are about a hundred trillion
microbes living inside you. We call this your microbiome, so it’s like a little world
living inside you — actually more like a universe. A hundred trillion means
if you took a blade of grass and planted it for every microbe
living in your gut, that could fill a million football fields. So it’s incredibly complex. But interestingly, as our bodies have been adapting
to life in modern society, we’re losing some of our normal microbes, and at the same time, there are quite a few diseases
related to the gut that are skyrocketing
in developed nations all around the world. And many of you probably know
someone who suffers from obesity, diabetes, Crohn’s disease
or ulcerative colitis, allergies and asthma. Every one of these diseases and many others related to metabolism
and autoimmunity are linked to a loss
of healthy diversity in the gut. My lab got our first indication of this when actually we were studying
non-human primates. We wanted to find out what happens
to a monkey’s microbiome when they move from the jungle to a zoo. Does their microbiome change?
Do they pick up new bugs? Do they lose some?
Does it get better or worse? We tracked two different
species in the jungle, one in Vietnam, one in Costa Rica, and then we sequenced
the DNA from their stool. This is how we study the microbiome
in my research lab. And what we found in the DNA
is that in the wild, these two species had
totally different sets of microbes. It was like a fingerprint for the species. But in the zoo, they had lost
most of that diversity and had acquired
some other set of microbes. So this was very curious. We’ve got these two different microbiomes. In the wild, picture a lush
tropical rainforest living the guts of these monkeys. That’s the kind of diversity
that we’re talking about. Then in the zoo, they’ve lost diversity. Picture a rainforest
that’s been burned to the ground and taken over by a few invasive species. That’s more like the microbiome
in a captive primate. Now, in the meantime, many of the animals in the zoo
are not doing so well. They have issues with obesity, wasting, gastroenteritis, diarrhea, bloating, and some of them were barely
holding onto their lives. Now, of course, we were
very interested to find out what are these so-called invasive species
that are taking over in the zoo. So we went back to the DNA,
and what the DNA told us is that every monkey in the zoo had become dominated
by Bacteroides and Prevotella, the same microbes that we all have
in our guts as modern humans. We wanted to find a way to visualize this, and we used some tools
from multivariate ecology to put all of the microbiomes
we were studying onto an axis. And what you’re seeing here
is a distance plot where every point
is a different animal’s microbiome. So every point represents
a whole zoo of microbes. And the microbiomes
that have a lot of microbes in common are close to each other. The ones that are very different
are farther apart. So this is showing you that the two groups of wild monkeys
are over on the left. The top left are these
highly endangered monkeys called the red-shanked douc in Vietnam. And at the bottom left
are monkeys from Costa Rica. So you can see that they have
totally different microbiomes in the wild. And then the same two species
of monkey in the zoo are converging, so their microbiomes change and they become
much more similar to each other, even though these are zoos
on different continents, different geographical regions,
and they’re eating different diets. Now, we did study
some other species of primate. What species of primate
do you think is even more divergent from the wild primates
than the captive primates? Modern humans. These are humans
living in developing nations. So they were more different
from the wild primates than those in the zoo. And the final group that we studied,
all the way on the right, is people living in the USA. And when I saw this figure, the hairs raised up
on the back of my neck, because one way to think about it is,
“Oh, that’s interesting, captive monkeys are sort of on their way
to becoming like Americans.” (Laughter) But the other way to think about it is that Americans
are like super-captive monkeys. And I was actually looking
at this figure on my computer screen when I got the news
that four of the red-shanked doucs had died in the zoo of gut-related issues. So for some of these animals, having the right microbes
living inside them may be a matter of survival. Now this brings us
to the human part of the story. Obviously, the microbiomes in the USA aren’t causing premature death
as frequently as in the zoo, but we have major risk
of obesity, diabetes, a number of these other diseases. And this applies not just to people
who have been living in the USA for many generations, but also to immigrants and refugees, who, for most immigrant
and refugee groups, arrive in the USA metabolically healthy, and then within a few years, they become just as high-risk
for obesity and diabetes as other Americans. And we discussed
this issue with two groups that have been coming to the USA
from Southeast Asia: the Hmong, who started coming
in the mid-1970s as refugees from the Vietnam War
and the US secret war in Laos; and the Karen, who have been coming
more recently as refugees from Myanmar. So we’ve been working for a few years with these local
communities and clinicians to study what happens
to the Hmong and Karen microbiomes when people move from refugee camps
and villages in Thailand to the USA. And what we found is that when people
come to the USA from these groups, they lose a large fraction
of their microbiome, somewhere around 20 percent, and those who come to the USA
and become obese lose about a third of their microbes. So we know that moving to the USA is sufficient to cause
a dramatic change in your microbiome, probably not for the better. Are these microbes
actually causing the obesity, or is the obesity causing
a change in the microbes? This is something
that we’re following up on, and the evidence we have now in my lab combined with evidence
from a number of labs around the world tells us that certain changes
in the microbiome do lead to obesity, and a number of other modern,
kind of Westernized diseases. The good news is that
your microbiome can actually change. Unlike your own genome, it’s a living, breathing thing, and there’s a broad front
of research happening right now to better understand
how we can restore our microbiomes when something goes wrong, using diet, using live microbes. And in fact, one of the next steps for us is collecting and preserving microbes
from healthy people around the world so that they can be kept
as cultural assets for those groups to potentially protect them
as they adapt to modern society, and to protect future generations who are currently growing up
to have increased risk of these diseases with every generation. I’m looking forward to a future where we have the tools that we need
to restore and replenish our microbiomes, and in that world, the monkeys
will live happier and healthier lives, and so will we. (Applause)


  1. Rency Santos

    August 8, 2018 at 8:23 am


  2. Music Lifee

    August 8, 2018 at 8:25 am


  3. Christian Bille

    August 8, 2018 at 8:26 am

    Interesting times we are living in!

  4. J J

    August 8, 2018 at 8:26 am

    Dan studied football field microbes in college. Then he got drafted and is now playing in the Pro Biotic League.

  5. Louis Slabbert

    August 8, 2018 at 8:34 am

    Hypothesis: if you investigate the microbiome of Italians in Sardinia (or vegetarians) you’ll find a healthy diverse microbiome.
    The USA is in grave danger with a large part of the population being overfed yet undernourished. (It affect the ability to think clearly…)

  6. phayke

    August 8, 2018 at 8:35 am


  7. Rubens Junior

    August 8, 2018 at 8:35 am

    Very nice! It's very interesting.

  8. Sage L

    August 8, 2018 at 8:40 am

    The heathiest gut bacteria come from eating a diverse diet of homegrown unwashed organic vegetables and fruits. This is because they have elevated microbiotics on their surface which will diversify your gut and keep you healthy. You can test this yourself. Test your gut before and after and you will see an enormous positive change as well as much better digestion. It is common for people from small villages in other countries to grow their own food but once they come to America, they eat processed food and lose their gut diversity.

  9. Nicolas Quay-cendre

    August 8, 2018 at 8:42 am

    I think at the end, he miss the principal point: feeling and thinking (human *being*). It's directly connected to your guts, collect data from a wise man in USA, I'm sure he would be as the non-western people, and even better!

    Plus, try meditation + yoga + gratitude during a month to compare before/after on the bacteria. (And not only food)

    I'm sure the best and beautiful solution is here if you wanna help / save western human (it's like 80% depressed people in America, no?). 
    Philosophy, Psychology, Spirituality, Wisdom…
    Knowing yourself then others then the world / universe 🌌.

  10. Koos Naamloos

    August 8, 2018 at 8:53 am

    If I could I would have legally changed my name to dan knights

  11. J Black

    August 8, 2018 at 9:05 am

    Fat people will use this as an excuse

  12. Brennos

    August 8, 2018 at 9:16 am

    Animals live far longer and older in zoos compared to their wild peers. Thanks to the good and abundant food, and to the medical care provided by the zoo staff and vet doctors.

  13. Fatih Altuntaş

    August 8, 2018 at 9:16 am

    Türkçe çeviri için teşekkürler Zeynep ve Figen.

  14. WCephei77HD

    August 8, 2018 at 9:34 am

    Go vegan!

  15. MAFIMA

    August 8, 2018 at 9:50 am

    want to better your gut? try plant based

  16. Rickbearcat

    August 8, 2018 at 10:03 am

    Not telling us how to replace the current gut microbes we have living in our guts with what should be there was a big fail on the part of this speaker. He really missed a big opportunity in this talk which I am not used to in a TED talk.

  17. Nathan Countyrman

    August 8, 2018 at 10:34 am

    Allergy’s is a disease?

  18. RemusKingOfRome5

    August 8, 2018 at 10:34 am

    ….. Sugar …… ???

  19. Doble Rollo

    August 8, 2018 at 10:44 am

    You can change the predominance of your microbiome from bacteroides to prevotella in just a couple weeks eating a whole foods, plant based diet.

  20. Rob Aldridge

    August 8, 2018 at 10:47 am

    Good talk Dan, Thanks.

  21. valerie joyce

    August 8, 2018 at 11:05 am

    Roundup??? 🌾🌾🌾 Epigenetics??? 😀🤔😢

  22. MrDami123

    August 8, 2018 at 11:22 am

    Very very important topic!

  23. mssummerrose1

    August 8, 2018 at 11:35 am

    What a sweet talker 😍…

  24. Aria Shirazi

    August 8, 2018 at 11:36 am


  25. knowitallll

    August 8, 2018 at 11:39 am

    I was hoping he would give me a cure for me ibs

  26. Blitzingtakin

    August 8, 2018 at 11:48 am

    Dank Nights

  27. Anti - Series

    August 8, 2018 at 11:55 am

    Dank nights

  28. Dindonmasker V

    August 8, 2018 at 1:34 pm

    that's SAD! (standard american diet)

  29. cashual k

    August 8, 2018 at 1:50 pm

    Interesting. should of been longer!!

  30. fjellyo32

    August 8, 2018 at 1:51 pm

    The USA is fucked!

  31. Meg Doyle

    August 8, 2018 at 2:08 pm

    I love that everyone is getting into gut health now!! So beneficial for overall knowledge of health

  32. Johnny B

    August 8, 2018 at 2:20 pm

    It's not just diet. Antibiotics are prescribed at basically the maximum possible level which destroys your entire microbiome. We grow monocrops rather than rotating crops, which means the soil becomes devoid of nutrients and becomes like a desert. We spray everything with glyphosate and other pesticides, which is water soluble so it's everywhere. It's on the food we eat. We even breathe it in when it rains. This chemical can disrupt the extremely delicate 1 cell thick lining of your gut. It creates a permeability in the lining of your digestive tract and allows microorganisms that would normally be blocked out by your gut lining to enter your body. When this happens, your immune system gets alerted and you get chronic inflammation. I think this is just the beginning of what I think is one of the biggest issues facing society right now.

  33. rexregalis

    August 8, 2018 at 2:46 pm

    Watching him talk about gut biomes is beautiful. And so is he. 😁

  34. Romanski

    August 8, 2018 at 2:48 pm

    Thumbs up for speaking positively about refugees!

  35. Edmond Cromwell

    August 8, 2018 at 3:04 pm

    Why are so many Ted viewers damn vegans?

  36. Jade Medallion

    August 8, 2018 at 3:15 pm

    Ted supports pedophiles! Boycott Ted Talks.

  37. MajkaSrajka

    August 8, 2018 at 3:27 pm

    I'm picturing the heck out of these rainforests in my gut.

  38. el chistoso murillo

    August 8, 2018 at 3:49 pm

    Now whenever you have a Gut feeling trust it! There’s a lot of biomes backing it up!

  39. Sandcastle •

    August 8, 2018 at 4:08 pm

    Liked this talk? Then by the book 'I Contain Multitudes'.
    Excellent read.

  40. Chris Comstock

    August 8, 2018 at 4:12 pm

    yep going vegan is the best

  41. KnightsWithoutATable

    August 8, 2018 at 5:58 pm

    Interesting research topic. Another line of research off of this one would be the difference that you see in European populations that don't have as high rates of obesity as the US. Unpasteurized cheeses, fresh fruits/vegetables, and unpasteurized alcoholic beverages would all add in different microbes. The use of different preservatives in foods could also be a factor.

  42. Steph Ss

    August 8, 2018 at 6:44 pm

    These are lifestyle diseases attached to nutrition. #govegan and check out nutritionfacts.Org …. stop polluting your body.

  43. memoryhero

    August 8, 2018 at 7:04 pm

    Eat raw Sauerkraut. That is all.

  44. Julie Gurley

    August 8, 2018 at 7:47 pm

    This information about gut research is so very promising. Wouldn't it be nice if we had optimal financial sourcing to make sure this research was optimized.

  45. Valentia

    August 8, 2018 at 7:49 pm

    Very interesting.

  46. r a

    August 8, 2018 at 7:57 pm

    Antibiotics in the food chain?

  47. r a

    August 8, 2018 at 8:02 pm

    I see the vegan evangelists have arrived…

  48. Vlad Macovei

    August 8, 2018 at 9:02 pm

    Are antibiotics found in food killing the good bacteria and then the gut is invaded by the other bacteria? Or does the invaders kill off the normal fauna? Does more radiation found in cities affect the equilibrium? Are micro particles influencing this war? We have tests for all those factors, let's combine those with machine learning and solve this.

  49. Cassandra Bankson

    August 8, 2018 at 10:41 pm

    No lie, gut microbes were huge when it come to controlling my acne.

  50. Adam Thomas

    August 8, 2018 at 11:13 pm

    Listen to this episode of Plant Proof Podcast for further information if this tickles your interest. So much to learn!

  51. Tabtheperson

    August 9, 2018 at 12:15 am

    I love this ted talk. I deeply recommend Missing Microbes By Doctor Martin J. Blaser! He goes much more in detail. It’s truly amazing.

  52. lucabrazi36

    August 9, 2018 at 5:25 am

    It's the amount of Msg we use in our food. Fast food and processed food has loads of it. Glutamates from MSG attach to glutamate receptors along GI tract nerves and brain. Glutamates triggers nervous system to trigger smooth muscle around intestines. Persistals happens too fast then sops. At the same time Entero endocrine cells release serotonin to signal each nerve to fire. Food passes to fast from stomach to small intestine. Then the small intestine become stagnant once it depletes levels of Serotonin which then cause depression.. Food stops moving and gets fermented by bacteria. Bacteria multiply then immune system gets triggered and sends white blood cells to the intestine which then cause inflammation and sometumes auto immune diseases like Crohn's or ulcerative colitis. The constant triggerr of immune system will destroy the good Gut Flora in the GI tract. From then on you have bacteria over growth which cause gas and heartburn. The problem then is the amount of MSG that food manufacturers are adding into the food to enhance flavor and increase sales. They use various fifferent names for MSG to confuse the consumer.

  53. Taylor Jendras

    August 9, 2018 at 1:13 pm

    But what is it about the USA that changes it ? What can we do to get our gut microbiome back to what it is supposed to be! Chemicals? Toxins?

  54. YVRGunny

    August 10, 2018 at 3:38 am

    5:42 Non-western human still live in huts in the middle of the jungle

  55. Amanda Anderson

    August 10, 2018 at 8:07 am

    Eating healthy just means getting the processed foods out of your system. What diseases you are predestined to have are genetic based and not much you can do about it besides try to halt it for a few years. I have known healthy eating, active people drop dead of common diseases even after doing everything correctly. There is no genetic or health perfection. Do the best you can and deal with real life.

  56. PH10 AD600

    August 10, 2018 at 2:59 pm

    There now are also clinical pooptransplant treatments (no kidding) to treat colon disorders.

  57. Milie Andre

    August 10, 2018 at 8:04 pm

    Hmong live as well in French Guyana in Amazon's forest

  58. Thang Laka

    August 11, 2018 at 2:02 am

    Same time Dr Gibson is printing living cell with his BDS machine and planning to tele-transport to Mars

  59. HeBepo9lTHblu

    August 12, 2018 at 10:13 am

    Пожалуйста, добавьте русские субтитры на все ваши видео. Такие интересные темы у вас, но ничего не понятно. 🙁

  60. Magnicifent Vi

    August 12, 2018 at 4:24 pm

    This is really interesting! I’m Hmong-American and I’m first generation, born in the U.S when my parents came over. There are photos of my parents who looked very young and skinnier back in their prime. However, as time has passed, they’ve become different because of the foods they eat. My guess was because of their micro biomes and ours. With the introduction of many processed foods and such, it makes me wonder exactly the same question, Does the food we eat change our micro biomes? Or does the micro biome change because of the food we eat?

  61. Leonidas GGG

    August 12, 2018 at 7:59 pm

    Someone once tested that just by changing gut microbes animals (lab rats) can actually loose A LOT of weight "naturally".
    In a World with obesity so much on the rise, it is a research I would like to see more developed.

  62. Callum Gillman

    August 13, 2018 at 11:32 pm

    Is it the incorporation of modern day antibiotics in our foodchain, especially the US one, leading to more sensitive microbes dying off? Or is it more stress related or is it that those bacteria in the first world are hyper aggressive now?

  63. Filip Molin

    August 15, 2018 at 1:18 pm

    Question: Couldn't this have to do with the drinking water? I mean, we put Chlorine/Hypochlorous acid in our drinking water in order to kill any bacteria that might live in the pipes. The dosage is obviously too small to be harmful to humans, but couldn't it be harmful to the bacteria that live inside of us? The reason why we use it in the first place is to kill bacteria, so I'm just thinking that 1 + 1 = dead microbes. This would explain why we see this in both humans and animals in the first world. Because even tho we eat different food we still drink the same water.

    If any scientist happens to read this, have this hypothesis been tested? If not, I think it wouldn't be too difficult to do. Give one group of animals water with Chlorine and another group of animals water with no Chlorine and then test their gut bacteria. Or you could do a more direct test by exposing a diverse group of gut microbes to Hypochlorous acid and then see which microbes survive and if they fit the profile of the western gut biome.

    Just a thought from a layman.

  64. Idylchatter

    August 18, 2018 at 9:22 pm

    Dr. John Bergman on YT

  65. Mystee Pulcine

    August 21, 2018 at 7:45 pm

    But WHY does the microbiome of an immigrant change? Can it be prevented?

  66. Adiudicium 1776

    February 5, 2019 at 6:16 pm


Leave a Reply