Lectures digesting the
microbiome
Theme 1: intestinal physiology
Week 1: introduction (09/04/2021)
The microbiome in the digestive system is mainly present in the colon, and a little in the jejenum and
ileum. However, be aware that bacteria are present in the mouth, duodenum, and even in the
stomach. The microbiome is important for digesting fibers and human health in general. The
microbiome plays an important role in colonic cancer, and the microbiome determines health of the
brain as well. The microbiome can be disturbed by obesity and certain types of drugs, e.g. antibiotics.
The microbiome changes somewhat with age, but changing the microbiome is not easy: the
composition of the microbiome is largely determined during the first years of life.
Be aware that the microbiome is not only present in the intestines, but also on the skin, in the
urogenital tract (bladder, genitals), and in the mouth. The composition of the microbiome differs in
these different parts of the body.
Test yourself: answers
1 What is the main function of the parietal cell in the stomach?
- Production of gastric acid.
2 Which hormone inhibits gastric acid secretion?
- Somatostatin. Histamine, gastrin, and acetylcholine stimulate secretion of gastric acid.
3 By which mechanism are carbohydrates absorbed?
- Carbohydrates cannot be immediately absorbed, first there needs to be luminal breakdown
by enzymes. Then, these monosaccharides can be absorbed.
o Transcytosis for peptides.
o Emulsification by bile for lipids.
o Microbial breakdown for fibres.
4 Which ions can provide the driving force for small peptides (co-transport)?
- Protons and sodium.
5 Which enzyme can digest lipids?
- Lipase can digest lipids. Bile is important for the emulsification of lipids.
6 Which ions are actively secreted in the intestinal lumen during secretory diarrhea?
- There is osmotic and secretory diarrhea. Secretory diarrhea is a response of the body to a
pathogen, often bacteria. During secretory diarrhea chloride ions are secreted in the
intestinal lumen. Sodium will follow the chloride. This attracts water into the intestinal tract,
and the bacteria are excreted with the water.
7 Which ions are secreted in the duodenum to neutralize pH?
- The stomach has an acidic pH but this needs to be neutralized at the beginning of the
duodenum via bicarbonate. When producing gastric acid, water and CO 2 are used to produce
H+ and HCO3- (bicarbonate). H+ is secreted directly in the stomach, while bicarbonate is
transported into the duodenum. When bicarbonate and H + from the stomach meet, water
and CO2 can be produced again.
8 What is a prebiotic?
- Fibres stimulating the growth of the microbiome (food for the bacteria and microbiota in the
intestine).
o The ingested microbial organisms are called probiotics.
9 What is referred to as the alpha diversity of the microbiome?
, - Variation of microbes in a single sample.
o Beta diversity: variation of microbial communities between samples.
10 Which genetic material is generally sequenced to determine the microbiome composition?
- Ribosomal RNA. The s-subunit of rRNA is present in all microbiota, but all microbiota have a
different type of this subunit. By sequencing this subunit the type of bacterium can be
determined.
Week 1: secretion (09/04/2021)
Overview functions of the digestive system
- Motility.
- Secretion.
- Absorption and digestion of carbohydrates and
fats.
- Absorption water and ions.
Colon cancer is getting more prominent in the western
world. Therefore, in the Netherlands people are screened
for colon cancer from a certain age. It is hypothesised that
the incidence of colon cancer is increasing because of the
western diet. Also, proton pump inhibitors, which inhibit
gastric acid secretions, are more widely used. Proton pump
inhibitors have side effects as well.
Secretion
Within a day 9 litres passes through the intestines: 2 L of food and drinks and 7 L are added by the
body, including saliva and enzymes. The small and especially the large intestine has to reabsorb all
these fluids the faeces are only 0.2 L.
These fluids contain enzymes, mucus, water, ions, H + and bicarbonate. Enzymes are important to
digest the components of food. Each group of nutrients has their own enzyme to digest these
nutrients. These enzymes are produced at different locations in the body.
Biomolecule Digested by Into Enzyme location
Carbohydrate
Starch Amylase Maltose Saliva, pancreas
Disaccharides
Maltose Maltase 2 glucose Intestine
Lactose Lactase Glucose + galactose Intestine
Sucrose Sucrase Glucose + fructose Intestine
Proteins
Interior peptide bonds Endopeptidases Peptides Stomach, intestine,
pancreas
Terminal peptide Exopeptidases Amino acids Stomach, intestine,
bonds pancreas
At NH2-terminal end Aminopeptidase
At COOH-terminal end Carboxypeptidase
Fats
Triglycerides Lipase Monoglyceride and Mouth, stomach,
free fatty acids pancreas
Phospholipids Phospholipase Lysophospholipid and Pancreas
, free fatty acids
Be aware that acid is not the only thing being produced in the stomach peptidases and gastric lipase
are produced here as well.
Because foods are already digested in the mouth, the foods have a stronger taste – this is especially
true for carbohydrates.
Phases of digestion
- Cephalic phase.
- Oral phase.
- Gastric phase.
- Intestinal phase.
Cephalic and oral phase of digestion
The cephalic phase is the anticipation of food. Thinking about what you are going to eat may give a
reaction in the production of saliva. The oral phase is the phase were eating has started and food is
present in the mouth.
Saliva is produced by 3 pairs of salivary glands: the sublingual gland, the parotid gland and the
submandibular gland. Saliva contains:
- Water.
- Enzymes. One of the enzymes is salivary amylase, which is important for carbohydrate
digestion.
The food is diluted by the saliva, so the mouth is cleaned, and taste is better spread through the
mouth.
Saliva enters the mouth via two types of secretion: secretion in
the gland and secretion in the mouth. The composition of the
final secretion depends on the secretion rate. There are two
phases of saliva secretion:
- Primary secretion: composition when the blood
contains high levels of sodium. Sodium will attract
water. In this water enzymes can be secreted.
- Secondary secretion: absorption of sodium and
secretion of potassium and bicarbonate.
Saliva secretion is regulated by the parasympathetic nervous
system.
In the oral phase aside from the parasympathetic nervous
system the reflexes in the intestine and in the mouth are
important as well a pressure sensor in the intestinal cells will
increase secretion of saliva and gastric acid. This means that
gastric acid is already produced when the food is still present in
the mouth.
- The oral phase is a preparation of the whole digestive
system for food.
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