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Full summary digesting the microbiome 2024
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Full summary for the course digesting the microbiome (NWI-BM081), given in 2024 - Radboud University, Nijmegen.
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Digesting the Microbiome – LE108-04-2024 – Introduction, Secretion and Absorption
Introduction
The functioning of the intestinal tract can be divided into four parts: motility, secretion,
digestion and absorption. We will mainly be going over the secretion and absorption
part.
Food is broken down in the
mouth, stomach, duodenum (by
enzymes secreted by the
pancreas and liver), and the
epithelium of the small intestine.
It is also absorbed in the
intestines.
The microbiome is very important
in the gut, as it helps us digest
otherwise indigestible food
components and prevents
disease.
Our gut microbiome is affected by host genetics, exercise, stress, antibiotics, age,
gastric motility, antimicrobial peptides and IgA, gastric secretion, diet, mode of delivery
at birth and our geographical location.
Our gut is not the only place where a microbiome is present. Different microbiomes can
be found in our mouth, pharynx, respiratory system, skin and the urogenital tract.
Visualization can be done through microbiome time series, phylogenetic analysis, PCA
followed by cluster analysis/heatmap, etc.
,Mini Quiz
1. The main function of the parietal cell in the stomach is to produce gastric acid.
2. Somatostatin inhibits gastric acid secretion.
3. Carbohydrates are broken down by enzymes (pancreatic amylase and
disaccharidases) and then absorbed as monosaccharides.
4. Protons can provide the driving force for transport of small peptides (co-
transport).
5. Lipase can digest lipids.
6. Chloride ions are actively secreted in the intestinal lumen during secretory
diarrhoea.
7. Bicarbonate ions are secreted in the duodenum to neutralize the pH.
8. Fibers stimulate the growth of the microbiome and are therefore considered a
prebiotic.
9. The alpha diversity of the microbiome is the variation of microbes in a single
sample.
10. Ribosomal RNA is generally sequenced to determine the microbiome
composition.
Secretion
The digestive system’s functions are motility,
secretion, absorption and digestion of
carbohydrates, protein and fats, as well as
absorption of water and ions.
Secretion comes in the form of enzymes, mucus,
H2O, ions, H+ and HCO-3. A total of 9 litre is put into
the lumen on a daily basis; 7.5L of this is absorbed in
the small intestines, 1.4L in the large intestine and
0.1L is excreted via faeces.
Digestion can be divided into four phases: the cephalic phase, oral phase, gastric phase
and the intestinal phase.
, Biomolecule Digested by Into Enzyme Location
Carbohydrate
Starch Amylase Maltose Saliva, pancreas
Disaccharides Intestine
- Maltose - Maltase - 2 glucose
- Lactose - Lactase - glucose +
- Sucrose - Sucrase galactose
- glucose + fructose
Proteins
Interior/terminal Endo/exo- Peptides / amino Stomach, intestine,
peptide bonds peptidases acids pancreas
NH2-terminal aminopeptidase
end
COOH-terminal Carboxypeptidase
end
Fats
Triglycerides Lipase Monoglyceride and Mouth, stomach,
free fatty acids pancreas
Phospholipids Phospholipase Lyso-phospholipid Pancreas
and free fatty acids
Cephalic and Oral Phase of Digestion
The cephalic phase is started by the anticipation of food.
The oral phase starts when food is located in the mouth.
During these two phases, saliva is produced by 3 pairs of
salivary glands (parotid, sublingual and submandibular
glands). It is a mixture of water, mucoprotein and salivary
amylase. It serves to dilute and transport food, but also
to dissolve tastants for the sensors (taste buds). It is the
start of starch digestion. Saliva has an antimicrobial and
cleansing effect.
The composition of the final secretion of saliva depends
on the secretion rate. The primary secretion secretes a
primary isotonic fluid rich in NaCl, whereas the
secondary secretion reabsorbs NaCl and secretes K+ and
HCO-3 instead. This is regulated by the parasympathetic
nervous system.
During these two phases, there are two types of reflexes: long reflexes through the
central nervous system and short reflexes in the cells of the intestine. There is also
secretion and motility active in the digestive tract.
, Gastric Phase of Digestion
Different types of cells are present
in the gastric mucosa. There are
the superficial epithelial cells, the
mucous neck cells, the
stem/regenerative cells, the
parietal/oxyntic cells, the chief
cells and the endocrine cells. The
endocrine cells are located in the
deepest part of the gastric gland,
as to protect them from the low pH
in the stomach. The cells below
the top layer regulate HCl
secretion.
The stomach is there for
• Storage
• Digestion
o HCl, secreted by parietal or wall cells
o Lipase, secreted by chief cells
o Pepsinogen, secreted by chief cells
• Protection of the stomach wall
o HCO-3 and mucus, secreted by mucus neck cells and goblet cells
• Diverse
o Production of intrinsic factor (complexes with vitamin B12) to permit
absorption.
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