Introduction to the Microbiology of the Gut
The basic pathogenic mechanisms involved in the damage of and
malfunction of the alimentary tract
The macroscopic and microscopic structure of the alimentary system
and the mechanism of fluid and electrolyte transport
The distribution of normal bacterial flora in the alimentary tract
A definition of the following: commensal, normal flora, pathogen,
anaerobe, acute diarrhoea, chronic diarrhoea, food-poisoning,
malabsorption, dysentry, gastroenteritis
2 beneficial functions of normal gut flora
How pathogens can induce diarrhoea by 3 different pathogenic
mechanisms and the type of pathogen responsible for each
mechanism
The microbiome is the complex mixture of microbes that live in our gut.
Normal flora
Normal flora describes the flora of microorganisms that normally live within our
intestines.
We have microorganisms on all our surfaces, this includes the gut.
Resident flora are flora that are there for life, transient flora are organisms that
colonise us but can temporarily be reduced, carried or changed according to various
factors including the environment we live in.
An example of a change in transient flora, is baby -> adult, where there is a change
from bifidobacter which likes breast milk. Other changes could be stress, hormones,
age etc.
We see this in baby faecal transitions. The first time a baby defacates (sterile
meconium) it is sterile, we then see a change in the stools as the baby aquires
microbial flora.
In the beginning we may start with facultative anaerobes (organisms that live
anaerobically but can live in presence of oxygen also).
There then ends up being a strictly anaerobic gut (survive in oxygen free
environments) that live in the colon.
Bifidobacter is an example of a strict anaerobe. They metabolise breast milk sugars
that gives itself energy and produces nutrients for the baby.
As we wean off the breast milk, the microorganisms change, we quite adult-like gut
microbiota.
Importantly, no one species of gut flora is a commensal, but together the flora may be
regarded as commensal (no harm to the host). This is a product of extensive co-
evolution.
Symbiosis includes: commensalism, parasitism, mutulism.
, Bacteria are distributed throughout the GI tract. There are very few in the stomach
due to the high acidity.
As we move through the duodenum and ileum and get to the terminal ileum we see
much more bacteria here and a more complex mixture.
The colon, which is an anaerobic environment, contains facultative and obligate
anaerobes. There are a very large amount of bacteria here and a very complex mixture.
e.g. bacterioides, clostridia, E.coli
In someone with inflammatory bowel disease the distribution of bacteria in the gut is
very different.
Microbiome alterations are associated with disease states,
e.g. Crohn’s disease, Inflammatory bowel disease, IBS, C.difficle etc.
Properties of intestinal physiology affected by microbiome
Changing the microbiome of the gut will substantially change the physiology of the gut
e.g. the hormones it releases.
Exposure to antibiotics can affect the microbiome leading to a change in gut
physiology.
Host Defences and Normal Flora
If we have so many microbes living in the gut how are we not overwhelmed by them?
There must be a balance in place whereby we can control our gut flora.
To appreciate this we have to look at the defence mechanisms of our gut:
Structural:
- A seamless epithelium surface, with tight junctions, there is rapid
turnover/sloughing
The basic pathogenic mechanisms involved in the damage of and
malfunction of the alimentary tract
The macroscopic and microscopic structure of the alimentary system
and the mechanism of fluid and electrolyte transport
The distribution of normal bacterial flora in the alimentary tract
A definition of the following: commensal, normal flora, pathogen,
anaerobe, acute diarrhoea, chronic diarrhoea, food-poisoning,
malabsorption, dysentry, gastroenteritis
2 beneficial functions of normal gut flora
How pathogens can induce diarrhoea by 3 different pathogenic
mechanisms and the type of pathogen responsible for each
mechanism
The microbiome is the complex mixture of microbes that live in our gut.
Normal flora
Normal flora describes the flora of microorganisms that normally live within our
intestines.
We have microorganisms on all our surfaces, this includes the gut.
Resident flora are flora that are there for life, transient flora are organisms that
colonise us but can temporarily be reduced, carried or changed according to various
factors including the environment we live in.
An example of a change in transient flora, is baby -> adult, where there is a change
from bifidobacter which likes breast milk. Other changes could be stress, hormones,
age etc.
We see this in baby faecal transitions. The first time a baby defacates (sterile
meconium) it is sterile, we then see a change in the stools as the baby aquires
microbial flora.
In the beginning we may start with facultative anaerobes (organisms that live
anaerobically but can live in presence of oxygen also).
There then ends up being a strictly anaerobic gut (survive in oxygen free
environments) that live in the colon.
Bifidobacter is an example of a strict anaerobe. They metabolise breast milk sugars
that gives itself energy and produces nutrients for the baby.
As we wean off the breast milk, the microorganisms change, we quite adult-like gut
microbiota.
Importantly, no one species of gut flora is a commensal, but together the flora may be
regarded as commensal (no harm to the host). This is a product of extensive co-
evolution.
Symbiosis includes: commensalism, parasitism, mutulism.
, Bacteria are distributed throughout the GI tract. There are very few in the stomach
due to the high acidity.
As we move through the duodenum and ileum and get to the terminal ileum we see
much more bacteria here and a more complex mixture.
The colon, which is an anaerobic environment, contains facultative and obligate
anaerobes. There are a very large amount of bacteria here and a very complex mixture.
e.g. bacterioides, clostridia, E.coli
In someone with inflammatory bowel disease the distribution of bacteria in the gut is
very different.
Microbiome alterations are associated with disease states,
e.g. Crohn’s disease, Inflammatory bowel disease, IBS, C.difficle etc.
Properties of intestinal physiology affected by microbiome
Changing the microbiome of the gut will substantially change the physiology of the gut
e.g. the hormones it releases.
Exposure to antibiotics can affect the microbiome leading to a change in gut
physiology.
Host Defences and Normal Flora
If we have so many microbes living in the gut how are we not overwhelmed by them?
There must be a balance in place whereby we can control our gut flora.
To appreciate this we have to look at the defence mechanisms of our gut:
Structural:
- A seamless epithelium surface, with tight junctions, there is rapid
turnover/sloughing
