Host-microbe interaction
Joanna Falcao Salles:
The human gut biome is a representation of our environment, habits and diet. Thus it is a very
interesting thing to study. Still, a large percentage of microbes remain unknown and are yet to be
cultured.
We used to only be able to observe the microbes under a microscope, which differentiates little between
human. However, with new DNA techniques, of particularly, Carl Woese, who used ribosomal RNA to
explore phylogenecity of organisms, organisms can be traced back to its ancestry. This created a new
phylogenetic tree of life, which is dominated by microbes. The old tree sprouted into; plants, fungi and
animals, while in the new tree this is but a small branch.
“Our ancestors were multi-organismal before they were multicellular.”
This refers to the endosymbiosis theory, which states that the mitochondria and the chloroplast are
descendants from a bacteria that had a symbiotic relationship with the ancestral pre-eukaryotic cell,
Hologenome:
You are not 1, you are an ecosystem! You are a host to millions of microorganisms, that make a home of
your body. You, including all your symbiotes*, forms your hologenome. An organism can only be fully
understood when its microbiome is also taken into account. The host lives in homeostasis with its
microbiome. Stressors, like; temperature, toxins and pathogens, can affect both the host and the
microbiome, thus disrupting the homeostasis.
*symbiotes= microbes that interact with the host.
This is the hologenome theory of evolution, it means that:
1. All animals and plants have symbiotic relations with microbes.
2. Different host species contain different microbiomes.
3. Microbiomes differ between individuals, which leads to genotypic- and phenotypic variation.
4. Assosiations affect the host and the microbiome.
5. Microbial genetic information changes more rapidly than that of the hosts. This is because microbes
evolve more quickly.
6. There is vertical- horizontal gene transfer. The vertical gene transfer will happen from the mother
egg to the infant.
7. Natural selection takes places on the holobiont.
Page 1
,8. Microbiome variation can lead to host adaptations and specializations.
This theory does however have its criticisms:
1. Not all microbes have interactions with its host.
2. Not all microbes have a selective interest in fitness of the offspring.
3. Not all microbes are vertically transmitted.
Theory of disappearing microbiome:
It states that we lose bits of the diversity of our microbiome, this can be via a C-section or antibiotics.
Since vertical gene transfer best takes place during a natural birth, less of the maternal microbiome is
being transferred to the infant during a C-section.
The loss of diversity in our microbiome can lead to; autoimmune- and inflammatory diseases.
Human microbiome:
Humans only have a 1% difference in DNA, while the microbiome differs about 70-80% between
humans.
The human gut biome is correlated to a lot of things, like; sleep, allergies, depression, age and stress.
Although, the age and diet are the most important factors that determine
your gut biome.
The microbial cloud is the cloud of microbes left in the room after you
have left. This is because we exhale, we shed skin, because we live.
The human body has different microbiomes, e.g.; on the skin, in the gut
and in your mouth. The differences between these can be shown on a
graph.
On this graph, the axis don’t refer to actual measurement, but rather
indicate the relatedness.
Another important graph is this one;
- Resistant: this is when a pathogen enters the body,
and the microbiome acts as the secondary immune
response. The microbiome competes for nutrients,
and the pathogens probably lose. So, the perturbation
does not affect the biome.
- Resilient: this is when you take antibiotics to fight
an infection, so the microbiome lessens, this is the
perturbation. But once you stop taken them, the
biome goes back to normal.
- Collapse: this can be divided into a partial collapse
and total collapse. In case of the total collapse, the
Page 2
, microbiome is completely gone. The only
solution for this is to give them a new
microbiome with a poop-pill.
Microbial interventions:
There are certain interventions one can take
if ones microbiome is fucked up. Of these are;
targeted and untargeted. See all examples in
the picture;
Prebiotics: compounds in foods that foster
growth or activity for the microbes.
Probiotics: alive microbes that can be
consumed.
Synbiotics: combining prebiotics and
probiotics.
Postbiotics: soluble factors that are secreted
by live bacteria.
Metagenomics:
This is the application of modern genomic techniques used to study the communities of microorganisms
directly in their natural habitats.
There are 3 types; marker genes (amplicon), metagenomics (whole genome) and metatranscriptomics.
Marker gene sequencing/ Amplicon: this is to find out which microbes are there.
It gives your multiple fragments from 1 target gene.
With amplicon sequencing, you want to use the highly conserved genes 16S rRNA in bacteria and
archaea, and 18S rRNA in eukaryotes and ITS (internal transcribed spacer) in fungi. These genes consist
of conserved peaks, but also hyper variable regions (V1-V9). These hyper variable regions are able to
distinguish between species. These regions evolve at different rates and have unique sequences for each
species, acting like molecular fingerprints.
Pros Cons
Quick, simple and inexpensive No difference between live, dead or active
Can be used with low biomass Choice of primers magnifies biases
Large public data sets available for comparison Requires prior knowledge of the microbial community
Functional information is limited
Whole metagenome sequencing (WGS): this is to find out their genetic potential.
It gives you short sequence fragments from all DNA.
Page 3
Joanna Falcao Salles:
The human gut biome is a representation of our environment, habits and diet. Thus it is a very
interesting thing to study. Still, a large percentage of microbes remain unknown and are yet to be
cultured.
We used to only be able to observe the microbes under a microscope, which differentiates little between
human. However, with new DNA techniques, of particularly, Carl Woese, who used ribosomal RNA to
explore phylogenecity of organisms, organisms can be traced back to its ancestry. This created a new
phylogenetic tree of life, which is dominated by microbes. The old tree sprouted into; plants, fungi and
animals, while in the new tree this is but a small branch.
“Our ancestors were multi-organismal before they were multicellular.”
This refers to the endosymbiosis theory, which states that the mitochondria and the chloroplast are
descendants from a bacteria that had a symbiotic relationship with the ancestral pre-eukaryotic cell,
Hologenome:
You are not 1, you are an ecosystem! You are a host to millions of microorganisms, that make a home of
your body. You, including all your symbiotes*, forms your hologenome. An organism can only be fully
understood when its microbiome is also taken into account. The host lives in homeostasis with its
microbiome. Stressors, like; temperature, toxins and pathogens, can affect both the host and the
microbiome, thus disrupting the homeostasis.
*symbiotes= microbes that interact with the host.
This is the hologenome theory of evolution, it means that:
1. All animals and plants have symbiotic relations with microbes.
2. Different host species contain different microbiomes.
3. Microbiomes differ between individuals, which leads to genotypic- and phenotypic variation.
4. Assosiations affect the host and the microbiome.
5. Microbial genetic information changes more rapidly than that of the hosts. This is because microbes
evolve more quickly.
6. There is vertical- horizontal gene transfer. The vertical gene transfer will happen from the mother
egg to the infant.
7. Natural selection takes places on the holobiont.
Page 1
,8. Microbiome variation can lead to host adaptations and specializations.
This theory does however have its criticisms:
1. Not all microbes have interactions with its host.
2. Not all microbes have a selective interest in fitness of the offspring.
3. Not all microbes are vertically transmitted.
Theory of disappearing microbiome:
It states that we lose bits of the diversity of our microbiome, this can be via a C-section or antibiotics.
Since vertical gene transfer best takes place during a natural birth, less of the maternal microbiome is
being transferred to the infant during a C-section.
The loss of diversity in our microbiome can lead to; autoimmune- and inflammatory diseases.
Human microbiome:
Humans only have a 1% difference in DNA, while the microbiome differs about 70-80% between
humans.
The human gut biome is correlated to a lot of things, like; sleep, allergies, depression, age and stress.
Although, the age and diet are the most important factors that determine
your gut biome.
The microbial cloud is the cloud of microbes left in the room after you
have left. This is because we exhale, we shed skin, because we live.
The human body has different microbiomes, e.g.; on the skin, in the gut
and in your mouth. The differences between these can be shown on a
graph.
On this graph, the axis don’t refer to actual measurement, but rather
indicate the relatedness.
Another important graph is this one;
- Resistant: this is when a pathogen enters the body,
and the microbiome acts as the secondary immune
response. The microbiome competes for nutrients,
and the pathogens probably lose. So, the perturbation
does not affect the biome.
- Resilient: this is when you take antibiotics to fight
an infection, so the microbiome lessens, this is the
perturbation. But once you stop taken them, the
biome goes back to normal.
- Collapse: this can be divided into a partial collapse
and total collapse. In case of the total collapse, the
Page 2
, microbiome is completely gone. The only
solution for this is to give them a new
microbiome with a poop-pill.
Microbial interventions:
There are certain interventions one can take
if ones microbiome is fucked up. Of these are;
targeted and untargeted. See all examples in
the picture;
Prebiotics: compounds in foods that foster
growth or activity for the microbes.
Probiotics: alive microbes that can be
consumed.
Synbiotics: combining prebiotics and
probiotics.
Postbiotics: soluble factors that are secreted
by live bacteria.
Metagenomics:
This is the application of modern genomic techniques used to study the communities of microorganisms
directly in their natural habitats.
There are 3 types; marker genes (amplicon), metagenomics (whole genome) and metatranscriptomics.
Marker gene sequencing/ Amplicon: this is to find out which microbes are there.
It gives your multiple fragments from 1 target gene.
With amplicon sequencing, you want to use the highly conserved genes 16S rRNA in bacteria and
archaea, and 18S rRNA in eukaryotes and ITS (internal transcribed spacer) in fungi. These genes consist
of conserved peaks, but also hyper variable regions (V1-V9). These hyper variable regions are able to
distinguish between species. These regions evolve at different rates and have unique sequences for each
species, acting like molecular fingerprints.
Pros Cons
Quick, simple and inexpensive No difference between live, dead or active
Can be used with low biomass Choice of primers magnifies biases
Large public data sets available for comparison Requires prior knowledge of the microbial community
Functional information is limited
Whole metagenome sequencing (WGS): this is to find out their genetic potential.
It gives you short sequence fragments from all DNA.
Page 3
