Host-microbe interactions
Lecture 1
There is a functional signi cance of microorganisms colonizing our bodies
Human microbiota = types of organisms present in an environmental habitat
Human microbiome = genome collection of microbes particular environmental system, which refer
to their function
The human microbiome is comprised of di erent microbiota that colonies di erent habits of the
body. Microbiota colonizing the skin is di erent from that of the gut
- Microbes can for example digest food that the human body cannot
- Can degrade xenobiotics, e.g. drugs (foreign compounds)
- Protection from new microbes
- Regulation of epithelial homeostasis
It is important to know the human microbiota:
- Development of biomarkers to predict predisposition to speci c diseases (e.g. COVID)
- Design of therapies targeting selected microbial species in particular body site
- Personalized diet/drug therapies
- Tailor-made probiotics
How to identify the gut microbiota?
- Culturing; however, the majority of microorganisms can not be cultured or enumerated using
growth-dependent approaches (many also need anaerobic conditions)
- 16S ribosomal RNA
Fusion of culture and molecular-based analyses
The focus on molecular sequences in microbiome studies does not diminish the importance of
cultivation in the study of of the human microbiome -> the development of appropriate culture
conditions for isolation is being guided by meta genomic sequencing, which provides insight into
the nutritional requirements of the uncultured
microorganisms
• Do individuals share core human microbiome?
• Is there a correlation between the composition
of microbiota colonizing a body site and host
genotype?
• Do di erences in the human microbiome
correlate with di erences in human health?
• Are di erences in the relative abundance of
speci c bacterial populations important to
either health or disease?
Oral cavity
- The oral cavity is a complex, heterogeneous
microbial habitat
- Saliva contains antimicrobial enzymes
- High concentrations of nutrients near surfaces in the mouth promote localized microbial growth
Gastrointestinal
- Humans are mono gastric and omnivorous
- Microbes in the gut a ect early development, health, and predisposition to disease
- Colonization of gut begins at birth
ff
fiff ff ff fi ff ff fi ff
,Small intestine has larger surface area due to crevices -> more absorption of
nutrients
Many organisms already die due to enzymes in oral cavity or stomach acids;
however, there are a few that can withstand the acidity
Large intestine -> most diversity of microbes; mainly bacteroidetes and rmicutes
Microbes help in the production of metabolites through their metabolic reactions ->
mainly in the large intestine
- The colon is essentially an in vivo fermentation vessel, with the microbiota using
nutrients derived from the digestion of food
- Most organisms are restricted to the lumen of the large intestine, while others are
in the mucosal layers (cover endothelial cells)
Our diet shapes the metabolic outcome of the
microbes
The things that cannot be further digest are secreted as feces
The interlining of the column is covered by a mucus layer ->
prevents translocation of the microbes into the epithelial layer
(would give an immune response) (IUD: bowel disorders)
Mucus layer has two layers:
- Inner most layer; completely sterile, no bacteria
- Outer layer; bacteria can attach to it
In stomach -> not may microbiota due to low pH (= 2): digestion of
macromolecules from the food
Small intestine (duodenum, jejenum, ileum) -> pH rises; continuing
digestion & absorption
Large intestine -> absorption of water
The majority of all human gut phylotypes fall into one of 3 major
bacterial phyla: Firmicutes, Bacteroidetes, and Proteobacteria
- Individuals may have mostly Firmicutes, mostly Bacteriodetes, or a mix of the two. This
regulates the metabolism and the host’s propensity for obesity
Processes of microbiota:
- Vitamin synthesis
- Amino acid synthesis
- Gas production
- Odor production
- Organic acid production
- Glycosidase reactions
- Steroid metabolism (bile acids)
Urogenital tract
- Lower diversity than gastrointestinal tract
- Altered conditions can cause potential pathogens (E. Coli) in the urethra -> cause UTI’s
- E. Coli is naturally found in the gut, but is pathogenic in urogenital tract
Vaginal bacterial diversity -> if diversity increases, it indicates a
disease
- It has mostly Firmicutes
- Has low pH -> death of many other microorganisms
Skin
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,- Main entrance between inside body and outside world
- Varies greatly in chemical composition and moisture content
- Three microenvironment: dry skin, moist skin, sebaceous skin (oily)
- Composition of microbes is a ected by environmental factors (e.g. weather),
host factors (e.g. age, personal hygiene), each microenvironment has own unique
microbiota
Human Microbiome Project (HMP) determined a baseline for healthy human microbiomes; lacks
data on diets/other life style attributes
Mouse models -> there are signi cant di erences between mice & humans
- mice have larger cecum than humans
- Most fermentation is completed in the mouse cecum, rather than the human large intestine
-> mice have short life cycle and well-de ned genetic lines; can be raised in a germ-free
environment (antibiotic therapy; strict dietary control; fecal transplants; germ-free environment)
Microbial activities in rst year of life
- Colonization begins at birth, with transfer from mother to infant
- Early colonizing microbes are a source of vitamins and tend to be facultative rather than
obligate anaerobes
Variable determine the nature of the gut microbiome:
- Vaginally born infants have a microbiome more similar to that of their mothers than those born
via Cesarean section
- Breastfed infants have more of a certain type of commensal bacteria (Bi dobacteria), as breast
milk has oligosaccharides that promote their colonization
Stability of adult microbiome and transitions with age:
- Early experiences determine gut microbiome
- Aging and frailty are associated with decreased microbial
diversity
Role of gut microbiota in obesity: mouse models
- Normal mice have 40% more fat than germ-free mice
with the same diet. When germ-free mice were give
normal mouse microbiota, they started gaining weight
- Mice that are genetically obese have more Firmicutes
- Also obese humans have more Firmicutes
More Firmicutes = obese (00:55)
Methanogens produce CH4
Lean: food is fermented to SCFAs and nutrients, but also hydrogen gasses -> the
hydrogen gives negative signal; stops fermentation and production of SCFAs
Obese: besides production of hydrogen, there’s also methane (CH4); then the
hydrogen is not enough to stop fermentation
The nature and transferability of gut microbiota is dependent on diet as well as genetics
Relative vs. absolute abundance
- Relative abundance = the percentage of a certain taxa compared to the microbial community
- Absolute abundance = the absolute number; not relative to the numbers of other
taxa
Diseases often show changes in relative abundance
fi ff fi fffi fi
, Dental Caries and periodontitis
- Cells form a bio lm called dental plaque, which has Streptococccus and other fermenting
bacteria (is also found in the gut, but is not pathogenic there)
- These fermenters produce acid, which wears down the tooth enamel
- Periodontal disease is thought to contribute to several systemic conditions, including
cardiovascular disease and arthritis
Antibiotics
- Oral antibiotics decrease ALL microbes in the human gut (both target and non-target)
- Use of antibiotics during the rst few months of life increases the risk of developing
in ammatory bowl disease and other disorders related to dysbiosis
- Clostridium di cile infections are associated with antibiotics use -> is a spore-former and
generally antibiotic resistant; a newer therapy is a fecal transplant
Normal situation -> other microbes make sure C.
Di cile doesn’t grow too fast
Antibiotics -> organisms die and C. di cile is no
longer inhibited
Probiotics are live organisms that confer a health bene t to the host
- Bi dobacterium and Lactobacillus are commonly used probiotics found in yogurt and probiotic
drinks
- They may work by taking up space of nutrients, limiting the ability of pathogens to colonize the
gut
Prebiotics are typically carbohydrates that are indigestible by human hosts, but provide nutrition
for fermentative gut bacteria
The gut microbiome is a biomarker of di erential susceptibility to SARS-CoV-2
Lecture 2
Metagenomics
Analysis of ribosomes (1970s) -> ribosomes could be used to nd
relations between di erent types of bacteria
16S rRNA-gene pro ling is based on sequencing variable regions of 16S
rRNA of ribosomes (small-subunit)
Ribosomes are encoded in operons; contains all the fragments, including
tRNAs necessary for ribosomal constructs
- After transcription of the complete operon, separate parts are cleaved of out
of the pre-RNA
- Bacteria can have more than one operon; the number varies
- E. Coli has 7 ribosomal operons
Secondary structure of 16S is conserved among microbes
- around 1540 nt’s
- 48 loops and hairpins
- 9 variable regions V1-V9 -> can identify bacterial species by its variable regions
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ffifi fiff fi ffi ff fi fi
Lecture 1
There is a functional signi cance of microorganisms colonizing our bodies
Human microbiota = types of organisms present in an environmental habitat
Human microbiome = genome collection of microbes particular environmental system, which refer
to their function
The human microbiome is comprised of di erent microbiota that colonies di erent habits of the
body. Microbiota colonizing the skin is di erent from that of the gut
- Microbes can for example digest food that the human body cannot
- Can degrade xenobiotics, e.g. drugs (foreign compounds)
- Protection from new microbes
- Regulation of epithelial homeostasis
It is important to know the human microbiota:
- Development of biomarkers to predict predisposition to speci c diseases (e.g. COVID)
- Design of therapies targeting selected microbial species in particular body site
- Personalized diet/drug therapies
- Tailor-made probiotics
How to identify the gut microbiota?
- Culturing; however, the majority of microorganisms can not be cultured or enumerated using
growth-dependent approaches (many also need anaerobic conditions)
- 16S ribosomal RNA
Fusion of culture and molecular-based analyses
The focus on molecular sequences in microbiome studies does not diminish the importance of
cultivation in the study of of the human microbiome -> the development of appropriate culture
conditions for isolation is being guided by meta genomic sequencing, which provides insight into
the nutritional requirements of the uncultured
microorganisms
• Do individuals share core human microbiome?
• Is there a correlation between the composition
of microbiota colonizing a body site and host
genotype?
• Do di erences in the human microbiome
correlate with di erences in human health?
• Are di erences in the relative abundance of
speci c bacterial populations important to
either health or disease?
Oral cavity
- The oral cavity is a complex, heterogeneous
microbial habitat
- Saliva contains antimicrobial enzymes
- High concentrations of nutrients near surfaces in the mouth promote localized microbial growth
Gastrointestinal
- Humans are mono gastric and omnivorous
- Microbes in the gut a ect early development, health, and predisposition to disease
- Colonization of gut begins at birth
ff
fiff ff ff fi ff ff fi ff
,Small intestine has larger surface area due to crevices -> more absorption of
nutrients
Many organisms already die due to enzymes in oral cavity or stomach acids;
however, there are a few that can withstand the acidity
Large intestine -> most diversity of microbes; mainly bacteroidetes and rmicutes
Microbes help in the production of metabolites through their metabolic reactions ->
mainly in the large intestine
- The colon is essentially an in vivo fermentation vessel, with the microbiota using
nutrients derived from the digestion of food
- Most organisms are restricted to the lumen of the large intestine, while others are
in the mucosal layers (cover endothelial cells)
Our diet shapes the metabolic outcome of the
microbes
The things that cannot be further digest are secreted as feces
The interlining of the column is covered by a mucus layer ->
prevents translocation of the microbes into the epithelial layer
(would give an immune response) (IUD: bowel disorders)
Mucus layer has two layers:
- Inner most layer; completely sterile, no bacteria
- Outer layer; bacteria can attach to it
In stomach -> not may microbiota due to low pH (= 2): digestion of
macromolecules from the food
Small intestine (duodenum, jejenum, ileum) -> pH rises; continuing
digestion & absorption
Large intestine -> absorption of water
The majority of all human gut phylotypes fall into one of 3 major
bacterial phyla: Firmicutes, Bacteroidetes, and Proteobacteria
- Individuals may have mostly Firmicutes, mostly Bacteriodetes, or a mix of the two. This
regulates the metabolism and the host’s propensity for obesity
Processes of microbiota:
- Vitamin synthesis
- Amino acid synthesis
- Gas production
- Odor production
- Organic acid production
- Glycosidase reactions
- Steroid metabolism (bile acids)
Urogenital tract
- Lower diversity than gastrointestinal tract
- Altered conditions can cause potential pathogens (E. Coli) in the urethra -> cause UTI’s
- E. Coli is naturally found in the gut, but is pathogenic in urogenital tract
Vaginal bacterial diversity -> if diversity increases, it indicates a
disease
- It has mostly Firmicutes
- Has low pH -> death of many other microorganisms
Skin
fi
,- Main entrance between inside body and outside world
- Varies greatly in chemical composition and moisture content
- Three microenvironment: dry skin, moist skin, sebaceous skin (oily)
- Composition of microbes is a ected by environmental factors (e.g. weather),
host factors (e.g. age, personal hygiene), each microenvironment has own unique
microbiota
Human Microbiome Project (HMP) determined a baseline for healthy human microbiomes; lacks
data on diets/other life style attributes
Mouse models -> there are signi cant di erences between mice & humans
- mice have larger cecum than humans
- Most fermentation is completed in the mouse cecum, rather than the human large intestine
-> mice have short life cycle and well-de ned genetic lines; can be raised in a germ-free
environment (antibiotic therapy; strict dietary control; fecal transplants; germ-free environment)
Microbial activities in rst year of life
- Colonization begins at birth, with transfer from mother to infant
- Early colonizing microbes are a source of vitamins and tend to be facultative rather than
obligate anaerobes
Variable determine the nature of the gut microbiome:
- Vaginally born infants have a microbiome more similar to that of their mothers than those born
via Cesarean section
- Breastfed infants have more of a certain type of commensal bacteria (Bi dobacteria), as breast
milk has oligosaccharides that promote their colonization
Stability of adult microbiome and transitions with age:
- Early experiences determine gut microbiome
- Aging and frailty are associated with decreased microbial
diversity
Role of gut microbiota in obesity: mouse models
- Normal mice have 40% more fat than germ-free mice
with the same diet. When germ-free mice were give
normal mouse microbiota, they started gaining weight
- Mice that are genetically obese have more Firmicutes
- Also obese humans have more Firmicutes
More Firmicutes = obese (00:55)
Methanogens produce CH4
Lean: food is fermented to SCFAs and nutrients, but also hydrogen gasses -> the
hydrogen gives negative signal; stops fermentation and production of SCFAs
Obese: besides production of hydrogen, there’s also methane (CH4); then the
hydrogen is not enough to stop fermentation
The nature and transferability of gut microbiota is dependent on diet as well as genetics
Relative vs. absolute abundance
- Relative abundance = the percentage of a certain taxa compared to the microbial community
- Absolute abundance = the absolute number; not relative to the numbers of other
taxa
Diseases often show changes in relative abundance
fi ff fi fffi fi
, Dental Caries and periodontitis
- Cells form a bio lm called dental plaque, which has Streptococccus and other fermenting
bacteria (is also found in the gut, but is not pathogenic there)
- These fermenters produce acid, which wears down the tooth enamel
- Periodontal disease is thought to contribute to several systemic conditions, including
cardiovascular disease and arthritis
Antibiotics
- Oral antibiotics decrease ALL microbes in the human gut (both target and non-target)
- Use of antibiotics during the rst few months of life increases the risk of developing
in ammatory bowl disease and other disorders related to dysbiosis
- Clostridium di cile infections are associated with antibiotics use -> is a spore-former and
generally antibiotic resistant; a newer therapy is a fecal transplant
Normal situation -> other microbes make sure C.
Di cile doesn’t grow too fast
Antibiotics -> organisms die and C. di cile is no
longer inhibited
Probiotics are live organisms that confer a health bene t to the host
- Bi dobacterium and Lactobacillus are commonly used probiotics found in yogurt and probiotic
drinks
- They may work by taking up space of nutrients, limiting the ability of pathogens to colonize the
gut
Prebiotics are typically carbohydrates that are indigestible by human hosts, but provide nutrition
for fermentative gut bacteria
The gut microbiome is a biomarker of di erential susceptibility to SARS-CoV-2
Lecture 2
Metagenomics
Analysis of ribosomes (1970s) -> ribosomes could be used to nd
relations between di erent types of bacteria
16S rRNA-gene pro ling is based on sequencing variable regions of 16S
rRNA of ribosomes (small-subunit)
Ribosomes are encoded in operons; contains all the fragments, including
tRNAs necessary for ribosomal constructs
- After transcription of the complete operon, separate parts are cleaved of out
of the pre-RNA
- Bacteria can have more than one operon; the number varies
- E. Coli has 7 ribosomal operons
Secondary structure of 16S is conserved among microbes
- around 1540 nt’s
- 48 loops and hairpins
- 9 variable regions V1-V9 -> can identify bacterial species by its variable regions
flfiffi
ffifi fiff fi ffi ff fi fi
