Lecture 1: Opening lecture
The colon has
a very high
density of
bacteria (1011-
1012/mL). This
is mainly
because water
is extracted
out of the
colon, so the
bacteria are
concentrated.
Approximately
80-90% of the
calories are absorbed in the small intestne, the rest is mainly absorbed in the colon.
The microbiota contribute to the digeston of food components, producton of essental nutrients
(e.g. certain B-vitamins), complements and infuences human “biochemistry” (they have more
different enzyymes than humans), metabolic capacity and actvity comparable to the liver, immune
system training and maintenance, colonisaton resistance against pathogens. So the microbiota have
an important role in health and disease.
The human is a superorganism, we never walk alone. The mutualistc relatonship between humans
and bacteria is “robust” but also “fragile”. The intestne provides a nutrient rich and stable
temperature habitat for its microbiota, and the microbiota provides biochemical complement and
environmental training to its host.
The intestne should be both open (for maximal absorptve capacity) and closed (as a barrier
functon). A resilient balance should be there. eomeostasis is very important. The recovery rate
should be fast.
The epithelial cells in the small intestne are every 4-6 days renewed. This layer is only one cell thick.
The Goblet cells create a mucus layer on top of the epithelial layer. In the crypts stem-cells and
Paneth-cells are present. Paneth-cells play a role in innate immunity.
The interactons between host, microbiota, and diet are very complex. It is a multvariate intertwined
system.
The human intestne microbiota is dominated by Bacteria, but also small populatons of Archaea and
Eukarya are present. The Bacteria and Archaea are members of the Prokaryote.
Microbiota compositon analyses can be “classical” culture based approaches, but only 20-35% of
cultured species can be grown in the laboratory. Nowadays, culture independent molecular methods
are present, such as 16S rRNA approaches. 16S rRNA is universally present in bacteria. It is a
sequence based phylogenetc marker, it has variable and conserved regions. There are several
molecular analyses for 16S rRNA.
Bacterial phylogeny goes the following: phylum class order family genus species
(OTU). It does not stop with species (e.g. strain). For example humans (Homo sapiens) are not all the
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,same. 80% of the bacteria in the human intestne (but also pigs and mice) are Bacteroidetes,
Firmicutes, and Actnobacteria. This are three different phylums. The microbiota are stable over tme,
resilient (the bacteria mostly come back afer an antbiotc therapy), and subject-specifc.
The diet, pre/probiotcs, host genotype, lifestyle, and pharmaceutcals are examples of factors
infuencing the compositon and functon of microbes. The compositon and functon of microbes
again has an affect on energy harvest (obesity and diabetes), intestnal functon (IBS and IBD),
immune functon (auto-immunity, allergies, and oral-tolerance), and brain functon (pain anxiety,
autsm, and cognitve performances). eowever, it could also be that the relatonship goes the other
way around (e.g. intestnal functon affects the microbes). Faecal transplantaton could give
indicatons to the causality.
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,Lecture 2: 16S rRNA proflingg Metagenomicsg
Metatranscriptomics
Species boundaries have for more
than 98% the same identty, this
means that only approximately 30
nucleotdes in the entre 16S rRNA differ. Variatons are not distributed equally along the variable
regions. Species assignment is not reliably possible on partal 16S rRNA sequence. Genus boundaries
have <92 or 97% the same identty, which means that approximately 45 to 120 nucleotdes differ, so
there is a much stronger separaton.
The Bacteroidetes, Firmicutes, and Actnobacteria are the most dominant (80%). eowever, the gut is
dominated by bacteria not yet sequenced (approximately 70%).
All vertebrate guts are dominated by Firmicutes and Bacteroides and some smaller contributons of
other phyla. Carnivores express the least variety whereas the herbivores have a large variety of OTU.
The principal approach of metagenomics is isolaton of total DNA from ecosystem, cloning in
heterologous host (functon mining), direct sequencing (sequence mining), sequence assembly to
construct gene catalogue, and microbiota-functon inventory (microbiome).
There are different
enterotypes, and the
majority of the people
belong to one of the
following groups:
Bacteroides, Prevotella
(ofen seen in natve
Africans), and
Ruminococcus.
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, Lecture 3: Metatranscriptomicsg Bacterial genomicsg
Cornerstone bacteria
The colon has a good accessibility and
well studied microbiota. The small
intestne is poorly accessible and
relatvely unexplored. iith ileostomy
subjects sampling of the luminal
microbiota of the distal ileum is
possible and non-invasive.
It is very important to know individual
isolate genomes because it generates
vital basic informaton to understand
microbes in ecosystems. It is not a
trivial task to need multple isolates
(strains), but “single representatves” are good enough. iith such informaton the accuracy of
metagenome mapping increases drastcally and allows beter functon reconstructon of ecosystems.
Probiotcs are living microorganisms that when administered in adequate amounts confer a
benefcial health effect on the host. Examples of probiotc products are Yakult, Actvia, and Actmel.
Probiotcs are dominated by Lactobacilli and Bifidobacteria. There is a limited clarity for (some)
health benefts, and a lack of EFSA approval of health claims on probiotc products. An example of a
probiotc bacteria is Lactobacillus plantarum. This bacteria is a nomadic microbe and has frequent
migraton between niches. Today’s fermentng fruit is tomorrow’s Drosophila (fy) isolate, and
today’s sauerkraut is tomorrow’s faecal isolate. There is virtually no value in “niche of isolaton” label
with the Lactobacillus plantarum, and this is valid for other lactobacilli with nomadic lifestyle (e.g. L.
rhamnosus and L. casei). This does not mean that strain specifc nice ftness is equal, but it probably
means that niche ftness can only be assessed in competton models.
The Bacteroides are obligate anaerobes, bile resistant, non-spore forming, gram negatve rods.
Approximately 25% of the commensal anaerobes in the human colonic fora are Bacteroides, and
more than thirty species are identfed, including B. fragilis (important commensal with proven host
interacton capacity, dependent on polysaccharide A) and B. thetaiotamicron (extensively studied
commensal microbe, host responses analysed in depth). Capsular polysaccharide loci are scatered
around the B. fragilis genome. B. fragilis can change its CPS “coat”. There is a phase variaton of
seven out of eight B. fragilis capsular polysaccharides, PSA is the most studied one, and strongly
interacts with immune cells. Bacteroides thetaiotamicron is a strongly saccharolytc microorganism. It
is an effectve degrader of complex glycans, and this bacteria lives in close contact with the epithelial
mucins layer.
The Actinobacteria includes the Bifidobacteria (e.g. Bifidobacterium longum) , which are effectve
saccharolytc microbes (“prevents spilling of food”). They are refected in the genome by multple
glycan utlisaton “islands”.
The Firmicutes include the Segmented Filamentous Bacteria (SFB). SFB in animal models are among
the early colonisers in the infant gut. They strongly stmulate the adaptve immune development:
Te17, and enhance protecton against infecton. No SFB homologues are known for humans, but they
are known in mice, pigs, chicken, and many other animals. They have prominent saccharolytc
capacites, and have mucin degradaton as primary food-sourcing. They have close contact with
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