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Dr. Hibberd>> So now, let's fast forward into the
microbiome and omics revolution of the last few years.
I'm sure everybody here knows the excitement about the
Human Microbiome Project, which was launched in 2008,
basically facilitated because of culture independent methods
to characterize the microbial communities
living within us and on us.
Because there are a hell of a lot of these microbes living on
us or in us, the standard line is at least 10 times more
microbes than we have cells at least in the GI tract.
And they have a lot of genes.
And they're probably doing things.
And we need to know about this.
Our microbes are mostly bacteria but they include archaea,
eukaryotes, and viruses.
This is a fairly simple approach to understanding what's going on
in the GI tract.
Here is your nice happy epithelial level,
until you get over here, that is protected by mucus,
and then on top of that, you've got these nice happy commensal
organisms, some of these sort of heading towards probiotics.
Then there are these pathobiomes,
which are commensal type organisms who can start causing
trouble and disease in the right circumstance,
and then these are the horrible exogenous pathogens
that come along and wipe out all the good protection
of the epithelial layer.
And obviously a huge concern is the overuse of antibiotics in
our country, and actually around the world,
resulting in depleted microbiota,
overgrowth of pathobiomes and disrupted mucosa.
And the idea here is, let's throw in a probiotic and
hopefully we're going to take care of everything.
It really is way too simplistic, and one of the other concepts
I want to introduce is the concept of keystone species.
I'm sure you've heard a lot of about this
in the last year or so.
The idea here that there are certain microbes potentially in
the GI tract and elsewhere that are more influential than their
numbers would suggest, and one of the ideas is that there could
be stabilizer keystone species and maybe that's the concept of
probiotic we're looking for.
But there are also keystone species that are pathogens that
we need to learn from as well.
So the whole concept here is that we can now start to
understand the microbial community in a sample.
And mostly our samples are coming from poop.
The poop is not necessarily telling us exactly where each of
the bugs reside, but it is a sample.
And what we can do is extract the DNA,
then get to the 16S RNA, amplify and recognize the sequences in
this ribosomal RNA, so this is just a small part of the RNA of
the bacteria, and then come up with those organisms that are
present in a specimen.
And this work comes from Morgan and Huttenhower most recently
who are based at the School of Public Health.
They also show that we can take that same microbial community
sample, extract DNA, and then do much better sequencing
based on all the RNA.
And I think what we're going to find is the information from the
16S is often not going to agree, not surprisingly,
with the entire RNA in terms of what organisms are present.
But again, the concept is the same.
We understand what genes are present,
and then we match them up with known databases
to figure out what the community can do
based on this fuller genetic potential.