Welcome to Module 1: The Human Microbiome.
In this clip, I'll talk about omics approaches.
The field of the gut microbiota research went through very exciting scientific developments.
We are now able to study millions of molecules in a snap shot.
This so called ’omics techniques’
stand for collective characterisation and quantification of
pools of biological molecules.
So let me guide you through these ‘omics approaches’.
A gram of feces contains approximately 10 to the 12th of microbes.
These are not all different microbes.
Some microbes are present in high quantities,
while others are only presented in low numbers.
The total amount of different microbes within a fecal sample is estimated to be around a 1000.
Now visualise all these microbes as ping-pong balls.
10 to the 12th balls in a room, and all of different colours.
Each colour represents a microbial species.
Some balls will be very well represented
while others will be rare.
If you would pick 10 balls,
what would this tell you about the total composition of balls?
And if you would pick a million balls would this give you a fair representation of the total composition?
This is exactly what omics techniques in the microbiome research is about.
By taking a sample and analysing it,
you get a snap shot of the composition at a certain time point.
The amount of information you gather is important to estimate how much it can tell you about the sample.
The most widely used technique to study the microbiome
is ‘16S rRNA DNA profiling’.
By using primers that amplify the 16S rRNA gene of all microbes
you can create a database of DNA sequences.
From one fecal sample, we are able to generate a thousand to a million of those 16S DNA sequences.
The microbes that are most abundant in your sample,
will be found back the most in terms of 16S DNA sequence reads.
Microbes that are low abundant,
will not be detected or will only generate a few of those 16S DNA sequences.
The sequence information will tell you which DNA is there.
This information can be used to find out what microbes are there.
It also tells you what microbes are very well represented,
and which are present in low numbers.
To study the genetic potential of the microbiome, we can use the information of the complete genomes of
all microbes in a fecal sample.
This technique is called metagenomics.
With metagenomics, a set of primers is used that can amplify any gene of any microorganism.
In this case, the ping-pong balls are coloured by gene.
And this will give you many more different colours.
After sequencing, a database of DNA is generated
that can hold again millions of reads.
These reads can be grouped in batches, depending on what information you are interested in.
As such, batches can be made of similar genes, for example.
This way, it could tell you how much antibiotic genes are present in the microbiome.
Another advantage of metagenomics
is that the genes can be used to assemble genomes.
This way, you can extrapolate complete genomes from your fecal sample.
This also makes it possible to discover complete genomes of bacteria that are not yet cultured.
The genome information could be used again to understand what a microbe needs for its physiology.
And this information can help to design a culture media for an uncultured microbiota member.
Another approach that is used with metagenomic databases,
is to compare the complete set of genes of the microbiome between
groups of individuals.
This way differences in microbiota composition can be taken to the next level.
Do the different microbes indeed harbour different functions between the bodies of healthy people
compared to those with diabetes type II for example.
This can help to understand the actual functional involvement of the microbiome in states of disease.
The creation of big databases of microbial products
through the sequencing can be done for DNA, RNA, proteins and metabolites.
Each of these different approaches will give you clues
about the function of the microbiota.
It will also tell you what is most abundant,
and if there are differences between samples.
The generated results and the findings are, however, merely predictions and a snap shot of a
certain sampling point.
On top of this the amount of data generated from a sample,
needs to be taken into account to understand
if the complete microbial community is represented.
So in short,
omics approaches are techniques that generate big databases of molecular data
from the microbiome.
These omics approaches are a big advantage in culture independent studies on the microbiome.