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Microbiome - Coggle Diagram
Microbiome
Why learn about the microbiome?
Composition of the microbiota increasingly linked to numerous diseases
Diabetes
Depression
Crohn’s
Obesity
Certain cancers (?)
Modulating this microbiota could therefore have massive impact on human health
The role of the GM in IBS
Butyrate
Primary energy source for intestinal epithelial cells.
Increases mucin production
Increases mucosal blood supply
Improves tight junction function in intestinal epithelial cells and reduces inflammation.
*Decrease in butyrate producing bacteria (including bifidobacteria) shown to be detrimental in IBD patients by contributing to inflammation.
Adding up the genetic numbers
How many genes do we have?
Human genome around 20,000
How many genes does our microbiome contain?
Around 4.4 million
What functions do bacteria carry out that we can’t?
How can we determine what species are present?
Environmental sample selection and collection
Library preparation
16S rRNA sequencing
DNA quality/quantity check
16S bacterial rRNA universal primer design and synthesis
PCR amplification
Amplification purification and assessment
Sample multiplexing
Shotgun sequencing
DNA quality/quantity check
NGS shotgun library preparation
Library purification and assessment
Metatranscriptomics
RNA quality/quantity check
rRNA removal
NGS total RNA library preperation
Library purification and assessment
Total DNA/RNA extraction
NGS sequencing
Data analysis
16S rRNA
16S rRNA detection, clustering and identification
Taxonomic classification (up to genus level)
Diversity analysis
Statistical analysis
Functional predictions
Shotgun
Read mapping and assignment
Taxonomic classification (up to species and stain levels)
Genome assembly
Statistical analysis
Functional predictions
Meta
Read mapping and assignment
ORF identification
Gene expression profiling
Functional annotation
Statistical analysis
Taxonomic predictions
Why is it important to characterise the microbiome?
What species are present?
What are genes are present and being expressed?
What effect is this having to the host (i.e. you)
What proteins and chemical stimuli are they producing?
The role of the GM in Metabolism
The GM helps break down carbohydrates that the host can not digest themselves.
50-70% ingested cellulose broken down by gut bacteria.
SCFAs by intestinal microbial fermentation of mainly undigested dietary carbohydrates.
SCFA’s include butyrate and acetate.
The role of the GM in Parkinson’s
Parkinson's disease is characterized pathologically by degeneration of the mid brain and widespread neuroinflammation.
1) Changes in SCFA production
Butyrate was significantly lower in parkinsons patients relative to age-matched healthy controls.
Butyrate strengthens the blood-brain barrier (BBB) by promoting increased expression and organization of BBB tight junction proteins.
The role of the GM in behaviour
Current evidence suggests:
Rodent behaviour altered when you modify the gut microbiota
GF mice demonstrate reduced anxiety like behaviour.
Increased exploration of aversive zones in laboratory testing.
Our microbial fingerprint
Your microbiome is unique
It is a consequence of a complex interplay between the microorganisms present, your genes and external stimuli
The interplay is multidirectional
The role of the GM in obesity
Role of SCFA’s in obesity
Butyrate is mainly anti-obesogenic
Acetate appears to be predominantly obesogenic
WHY?
Anti-inflammatory potential of butyrate due to intestinal epithelial increased barrier function.
Butyrate stimulates anorexigenic gut hormones which decrease appetite
Acetate is a substrate for lipogenesis and cholesterol synthesis.
Role of LPS in obesity
Increased Bacteroidetes (gram-negative) found in obesity
LPS endotoxin found in gram negative bacteria
LPS increases low grade inflammation.
Reduction in butyrate leads to leaky gut and increases LPS in bloodsteam
Low grade inflammation leads to cytokine production
Cytokines target fat cells increasing adiposity and kupffer cells causing insulin resistance.
Cont.
Overall decrease in butryate and increase in acetate producing bacteria.
Acetate increases lipogenesis.
Drop in butyrate leads to "leaky gut"
Increased inflammation due to gram negative LPS getting through "leaky gut" into blood stream leading to cytokine production.
Inflammatory cytokines increase adiposity and insulin resistance
Transfer of gut microbiota from germ free to wild-type mice results in a weight gain!
The influence of fat on the GM
The typical Western diet is both high in saturated and trans fats while low in mono an polyunsaturated fats
Consumption of high saturated and trans fat diets is thought to increase the risk of cardiovascular disease through upregulation of blood total- and LDL-cholesterol
Studies on humans are limited, most interesting studies done in rodents
High fat diets increase the propionate and acetate producing genus Bacteroides (gram-negative).
LPS increased leading to inflammation and vascular dysfunction.
White adipose tissue inflammation key factor in obesity.
Predominant species present in the GM
In the human gut
Firmicutes (Gram positive)- Lactobacilli, Streptococci and Clostridia
Bacteroidetes (Gram negative)- Bacteroides
Actinobacteria (Gram positive)- Bifidobacteria
Most of the human adult microbiome lives in the gut. Only in the human colon does microbial cell density exceed 1011 cells/g contents, being equivalent to 1–2 kg of body weigh
The influence of carbohydrates on the GM
Sugar from fruit (dates) increased bifidobacteria (reduce inflammation) and reduced clostridia species
Refined sugars mediate the overgrowth of opportunistic bacteria like C. difficile and C. perfringens
How can we measure activity?
'omics' technology
Genomics-what genes are present?
Transcriptomics-what genes are being transcribed and to what level?
Proteomics-what proteins are being translated and to what level
Metabolomics-what metabolic pathways are active and to what level?
The role of the GM in cancer
The relative proportion of bacterially-produced short chain fatty acids (SCFA) differs significantly between stool of healthy adults and individuals with colorectal cancer.