- Jacques, thank you so much for inviting me to your home.
- Thanks so much for coming.
We got so much information during our trip,
I though it would be nice to go over
some of the interesting pieces we had to cut out.
- Absolutely. A debrief would be great.
You know, there was just so much good stuff,
if we had to include everything,
the episode would be an hour long.
- This is meant to be a supplement to the main episode
in Adventures in Genomics.
- So if you haven't checked out our main episode,
please be sure to check that out first.
The link will be in the description below.
It was really interesting to talk to Cecil Lewis
and Christina Warinner at the University of Oklahoma.
There's a lot more to metagenomics than I ever realized.
- Metagenomics is a brand new field
that only took off about five years ago
with the development of next-gen sequencing,
and now we realize there's a whole world of microbes
that play a critical role in our health
and in our environment.
- And it is even more important to understand,
now that our urbanized lifestyles are moving
further and further away from our natural environment,
now that we also have
these so-called diseases of civilization.
- To me, the greatest insight was that we, as humans,
had millions of years to adapt to a
hunter-gatherer lifestyle, and that should be our reference.
It seems obvious in retrospect, but it's so easy to forget.
- And it was surprising just how unique
and well-adapted their metagenomes are.
I mean, they even have unique microbes
that help and protect them.
- The problem is that these authentic hunter-gatherer groups
are disappearing very fast, and that makes this work
so much more urgent.
- Metagenomics is such a new concept that it is useful
to define exactly what it means.
- And the term metagenome was coined in 1998,
and it refers to collecting and sequencing
microbial genes from the environment.
- Often, that is taken to mean bacterial genes,
but it really includes viruses and eukaryotes as well.
- And, yes, and that's very important to remember
because bacterial phages play an important role
in controlling bacterial populations.
- The eukaryotes can include things like fungi,
protists, algae, as well as eggs in juvenile stages
of some of the larger metazoans.
That's code for parasites.
- Fortunately, you can get all of those
from shotgun sequencing.
- Shotgun sequencing refers to fractionating
and then sequencing all the DNA fragments in the sample,
regardless of origin.
- Other techniques like 16S ribosomal RNA sequencing
gives you much less information and will miss the viruses.
- As sequencing is becoming less expensive,
and there is a clear benefit to shotgun sequencing,
that seems to be the direction the field is going.
- Their primary sources of protein is fish
with the occasional monkey, sloth, capybara, or alligator
and so on, so on.
- And the people from Tunupuku in the Peruvian Highlands
ate tubers, like potatoes, oca, and mashua.
- And, once in awhile, tukush, which is a delicacy
of fermented potatoes that they ferment in wet soil.
- You know, it is just amazing that the researches
got such good cooperation from these groups.
Without them, this work would not have been possible.
- You know, that is a very good point.
The researchers worked very closely with the government
and also the elders.
Cecil also mentioned how important it is
that this research should not just benefit the wealthy
nations, but also these groups,
whose lifestyles are changing so fast.
- The open question is, how the microbes moved
from one continent to another
over a period of 10s of thousands of years.
- You know, the microbes could have been carried
along by the first humans,
or they could have been lost and reacquired
from the environment.
- The test will be if the same microbes are present
in human remains or coprolites along the route.
- It was surprising that one of the unique microbes
would be Treponema.
I think of Treponema as a spirochete
that causes diseases like syphilis and yaws.
- You know, these Treponema strains are not
directly related to the pathogenic clades.
The closest known member is Treponema succinifaciens,
a known carbohydrate metabolizer in swine.
- Treponema is also present in the termite gut,
so there may be a metabolic role for it.
- There's a huge variety of Treponemas
and we actually know very little about them.
In the coming years, we can expect to learn
a lot more about these microbes
and the role they play in human health and disease.
- You know, Jacques, the point Christina makes
about diversity creating resilience
is really important.
- You know, you see that in the environment as well
in places like ponds and forests,
where diversity is naturally maintained.
- And the diversity in microbes could also be
as a result of diversity in diets.
- You know, when you look beyond the things
we obsess about in industrial societies
like starch and protein and so on,
the difference between the diets really
is the hunter-gatherers eat a highly varied diet,
whereas the diet from the agricultural group
is really very monotonous.
- It's true, and in industrial societies,
we have access to a huge variety of foods
and, regardless of season or where we live,
we tend to buy the same foods over and over again.
- You know, that's certainly true
when I look at my grocery list,
but the foods are also so much more processed.
- It's true, but you know,
ultimately, our food also feeds our microbiome
and the solution at the end of the day
is up to us.
- You know, that's absolutely true,
and where this work comes in,
if we understand what an optimum microbiome really is,
and how it functions,
it can guide us in the right direction.
- So the question is, where does our microbiome
come from?
And that is a very interesting question.
In the middle ages, people decided
bathing was not very healthy,
and that did not turn out well at all.
So, you know, what do you do?
- You know, I know the story about King Louis XIV
- And at the time, the Russians were considered
to be perverts because they bathed once a month.
- You know, I was wondering where do you have
to draw the line between living in dirt
and not washing at all,
or our obsessive modern hygiene,
where everything is sanitized
and we run around with this bottle of hand sanitizer
wherever we go.
- Well the problem with a lot of these sanitizers
is that, if you read the bottle
they say it will kill 99% of all the germs,
but they forget to tell you that they leave
the most resistant 1% behind,
and that is ultimately the problem,
so, with all this hygiene, ultimately we are building
more and more resistant microbes.
- Absolutely, and you know, that is why some of the
most dangerous microbes come from the cleanest places,
like hospitals.
- Now, on the other hand,
we need microbes to build a healthy immune system,
and you can actually see that
with our increased hygiene,
there is an increase in autoimmune diseases.
- And you know, we have to rethink about
our relationship with microbes.
They're not all good, but they're not all bad either.
- You know, we've had an intimate relationship
with our microbiome for millions and millions
of years.
Now, finally, we have the tools to understand
this relationship better
and to build a healthier relationship with our microbiome.