Digesting the microbiome
Lecture 1 – Introduction
Content
• Introduction to intestinal physiology
• Introduction to the microbiome
• Test yourself!
• Course set-up
• Final assignment
• Examination
Intestinal tract
Secretion, digestion and absorption mostly.
What is secreted to the intestinal tract? About
80% of the fluid in the intestinal tract, that all
needs to be absorbed.
Secretion & absorption
We will look at how we digest carbohydrates, lipids and proteins. You see that whatever
nutrient we eat we want them to the most basic building block (monosaccharides, fatty acids
and amino acids). That’s what we eventually absorb in the intestinal tract. We need a lot of
digestion.
Microbiome
There are nutrients that we cannot digest
ourself, such as fibers. Than the microbiome
comes in play. Then we can eventually also
absorb the building blocks that they break
down. If you look at the microbiota in the
intestinal tract then the highest number of
microbiota are in the colon (cecum) but there
are also microbiota in our stomach (low pH).
The microbiome is personal, a lot of factors
have influence on the microbiome.
,You develop microbiome in first three years of your life. After that it’s much more difficult to
change your microbiome. If you see changes in the microbiome then it will return to the
basics again. After that there are a lot of factors playing a role (antibiotics, diet, exercise) in
the health of your microbiome.
Mostly intestinal microbiome in this course, but there is
more: skin, respiratory, urogenital tract microbiome. The
species living there are different depending on the
conditions.
Example antibiotics
If you have a starting point then you will see that you have a quite diverse microbiota in the
intestines but once you start with antibiotic treatment then you see that a lot of these die. You
affect also microbiota that you need when you have microbiota treatment.
Microbiome: real life
In real life it looks more like this. Every dot is one
microbiota. If you look into data of the microbiome
you normally look in an omics dataset. Then you can
cluster those and see if there are changes into
certain conditions.
Microbiome: visualisation
As these datasets are quite rich, there are many
ways to visualise the microbiome.
,Pre course quiz
1. What is the main function of the parietal cell in the stomach?
Production of mucus
Production of gastric acid
Production of pepsinogen
Production of gastric lipase
2. Which hormone inhibits gastric acid secrestion
Histamine
Gastrin
Acetylcholine
Somatostatin
The other 3 are hormones that stimulate gastric acid secretion. Somatostatin is the inhibitory
one.
3. By which mechanism are carbohydrates absorbed?
Luminal breakdown by enzymes and absorption and monosaccharides
Small sugar chains are absorbed by vesicles (transcytosis)
Emulsification of sugars by bile and absorption in droplets
Microbial breakdown and absorption via transporters
Transcytosis is for small peptides, so not for saccharides. Emulsification of sugars by bile
does not exist, it should be emulsification of lipids. Microbial breakdown is for fibers.
4. Which ion can provide the driving force for small peptides (co-transport)?
Potassium
Calcium
Proton
Chloride
We see in the intestinal tract often cotransport of solutes. Sodium is a common one and
protons is a common one that is driving that.
Co-transport of solutes is common in the intestine
5. Which enzyme can digest lipids
Lipase
Bile
Amylase
Pepsin
Bile does not digest lipids, it emulsifies the lipids to make them more available for enzymes.
The enzymes are more hydrophilic. Amylase and pepsin are involved in carbohydrate and
peptide breakdown.
6. Which ions are actively secreted in the intestinal lumen during secretory diarrhea?
Potassium
Chloride
Bicarbonate
Calcium
, There are 2 types of diarrhea; secretory and osmotic. If you have osmotic diarrhea you have
a reason why here is a high osmotic value in the intestinal tract that will attract water. In
secretory diarrhea you create the high osmotic value yourself by secreting a lot of chloride
and sodium will follow. You create a high sodium chloride concentration in the intestinal tract
that will also attract water.
When do you need diarrhea? When you have an infection and you want to expel pathogens
then you will get secretory diarrhea.
7. Which ions are secreted in the duodenum to neutralize the pH?
Bicarbonate
Sodiumhydroxide
Ammonium
Chloride
You create protons from CO2 and H2O in the stomach and you will create bicarbonate and
that you will secrete in the duodenum to neutralize the pH again.
8. What is a prebiotic?
Fibers stimulating the growth of the microbiome
Ingested microbial organisms
Antibiotic substance
Predigestion of fibers by pancreatic enzymes
9. What is referred to as the alpha diversity of the microbiome?
Variation of microbial communities between samples
Ratio between healthy microbes and pathogenic microbes
Variation of microbes in a single sample
Number of microbes in a sample
That’s the alpha diversity. If you compare it between samples, then it’s the beta diversity. So
it’s the variation rather than the number.
10. Which genetic material is generally sequenced to determine the microbiome
composition?
Messenger RNA
Genomic DNA
Mitochondrial DNA
Ribosomal RNA
You capture all the ribosomal 16s RNA subunits, this is being sequenced and based on the
sequence of that we know from which origin that is.
Lecture 1 – Introduction
Content
• Introduction to intestinal physiology
• Introduction to the microbiome
• Test yourself!
• Course set-up
• Final assignment
• Examination
Intestinal tract
Secretion, digestion and absorption mostly.
What is secreted to the intestinal tract? About
80% of the fluid in the intestinal tract, that all
needs to be absorbed.
Secretion & absorption
We will look at how we digest carbohydrates, lipids and proteins. You see that whatever
nutrient we eat we want them to the most basic building block (monosaccharides, fatty acids
and amino acids). That’s what we eventually absorb in the intestinal tract. We need a lot of
digestion.
Microbiome
There are nutrients that we cannot digest
ourself, such as fibers. Than the microbiome
comes in play. Then we can eventually also
absorb the building blocks that they break
down. If you look at the microbiota in the
intestinal tract then the highest number of
microbiota are in the colon (cecum) but there
are also microbiota in our stomach (low pH).
The microbiome is personal, a lot of factors
have influence on the microbiome.
,You develop microbiome in first three years of your life. After that it’s much more difficult to
change your microbiome. If you see changes in the microbiome then it will return to the
basics again. After that there are a lot of factors playing a role (antibiotics, diet, exercise) in
the health of your microbiome.
Mostly intestinal microbiome in this course, but there is
more: skin, respiratory, urogenital tract microbiome. The
species living there are different depending on the
conditions.
Example antibiotics
If you have a starting point then you will see that you have a quite diverse microbiota in the
intestines but once you start with antibiotic treatment then you see that a lot of these die. You
affect also microbiota that you need when you have microbiota treatment.
Microbiome: real life
In real life it looks more like this. Every dot is one
microbiota. If you look into data of the microbiome
you normally look in an omics dataset. Then you can
cluster those and see if there are changes into
certain conditions.
Microbiome: visualisation
As these datasets are quite rich, there are many
ways to visualise the microbiome.
,Pre course quiz
1. What is the main function of the parietal cell in the stomach?
Production of mucus
Production of gastric acid
Production of pepsinogen
Production of gastric lipase
2. Which hormone inhibits gastric acid secrestion
Histamine
Gastrin
Acetylcholine
Somatostatin
The other 3 are hormones that stimulate gastric acid secretion. Somatostatin is the inhibitory
one.
3. By which mechanism are carbohydrates absorbed?
Luminal breakdown by enzymes and absorption and monosaccharides
Small sugar chains are absorbed by vesicles (transcytosis)
Emulsification of sugars by bile and absorption in droplets
Microbial breakdown and absorption via transporters
Transcytosis is for small peptides, so not for saccharides. Emulsification of sugars by bile
does not exist, it should be emulsification of lipids. Microbial breakdown is for fibers.
4. Which ion can provide the driving force for small peptides (co-transport)?
Potassium
Calcium
Proton
Chloride
We see in the intestinal tract often cotransport of solutes. Sodium is a common one and
protons is a common one that is driving that.
Co-transport of solutes is common in the intestine
5. Which enzyme can digest lipids
Lipase
Bile
Amylase
Pepsin
Bile does not digest lipids, it emulsifies the lipids to make them more available for enzymes.
The enzymes are more hydrophilic. Amylase and pepsin are involved in carbohydrate and
peptide breakdown.
6. Which ions are actively secreted in the intestinal lumen during secretory diarrhea?
Potassium
Chloride
Bicarbonate
Calcium
, There are 2 types of diarrhea; secretory and osmotic. If you have osmotic diarrhea you have
a reason why here is a high osmotic value in the intestinal tract that will attract water. In
secretory diarrhea you create the high osmotic value yourself by secreting a lot of chloride
and sodium will follow. You create a high sodium chloride concentration in the intestinal tract
that will also attract water.
When do you need diarrhea? When you have an infection and you want to expel pathogens
then you will get secretory diarrhea.
7. Which ions are secreted in the duodenum to neutralize the pH?
Bicarbonate
Sodiumhydroxide
Ammonium
Chloride
You create protons from CO2 and H2O in the stomach and you will create bicarbonate and
that you will secrete in the duodenum to neutralize the pH again.
8. What is a prebiotic?
Fibers stimulating the growth of the microbiome
Ingested microbial organisms
Antibiotic substance
Predigestion of fibers by pancreatic enzymes
9. What is referred to as the alpha diversity of the microbiome?
Variation of microbial communities between samples
Ratio between healthy microbes and pathogenic microbes
Variation of microbes in a single sample
Number of microbes in a sample
That’s the alpha diversity. If you compare it between samples, then it’s the beta diversity. So
it’s the variation rather than the number.
10. Which genetic material is generally sequenced to determine the microbiome
composition?
Messenger RNA
Genomic DNA
Mitochondrial DNA
Ribosomal RNA
You capture all the ribosomal 16s RNA subunits, this is being sequenced and based on the
sequence of that we know from which origin that is.
