The Human Microbiome Flashcards
definition of microbiota
The microorganisms that typically inhabit a specific environment
definition of microbiome
the totality of microbes, their genomes and environmental interactions in a defined environment. e.g. the gut of a human, soil sample
HMP – Human Microbiome Project
Highly parallel DNA sequencers combined with high throughput mass spectrometers enable characterisation of whole microbial communities : genomes, proteins, metabolic products
“A strategy to understand the microbial components of the human genetic & metabolic landscape, and how they contribute to normal physiology & predisposition to disease”
The role of 16S rRNA in the HMP
identifies the genus
16S rRNA is a component of the small subunit (30S)
Contains highly conserved & highly variable regions making it very useful for identifying taxonomic groups
HMP specific aims
Can changes in the human microbiome be correlated with changes in human health
How stable is the microbiome
o what extent to factors such as genetics, diet & socio-economic background influence the composition of the microbiome
Does the microbiome contribute directly to human health & disease
Steps of 16S rDNA analysis
Extract rDNA from sample
Perform PCR analysis on this DNA using universal 16S rDNA primers
Sequence this mixture, and identify the species present based on the 16S rDNA sequences
definition of metagenomics
‘whole gut’ genomics
the study of genetic material recovered directly from environmental samples: Extracting DNA from sample and sequencing everything (no PCR)
Host + microbial DNA
Essential for defining the microbiome
The major advantage of metagenomic techniques is
that they don’t rely on laboratory cultures of organisms.
RNA sequences taken directly from the environment have suggested that culture-based methods find less than 1% of the bacteria and archaea species in a given sample
the gut microbiota have been implicated in a variety of human conditions:
Obesity Childhood-onset asthma Inflammatory bowel disease (colitis) Colorectal carcinomas Cardiovascular disease Multiple sclerosis
in the mouse model of obesity (mutation in leptin gene)
Obesity was associated with a shift in the relative abundance of taxa present
50% reduction in Bacteroidetes
Significant increase in Firmicute
A similar shift was observed in obese humans - Abundance of bacteriodetes increased when dieting - change in abundance correlated with weight lost
Obesity associated microbiome has more capacity for energy harvest in mammalian cells
concept of a microbiota mediated transmission of obesity
Microbiota-mediated ‘transmission’ of obesity
“Conventionally-raised” (CONV-R) mice fed various different diets before being sacrificed
The microbiota from these different sacrificed mice was transplanted into mice that had been raised in a germ-free environment
Assessed weight gain in these recipient mice, as well as monitoring microbiota composition etc.
An “obese microbiome” promoted weight gain when transplanted to a germ-free mouse, compared to comparable transplantation of a “lean microbiome”
Shifting microbiota alters metabolic potential
in obese mice
Increase in genes encoding enzymes involved in the breakdown of dietary polysaccharides
A lower amount of energy remained in the faeces of obese mice compared to lean counterparts
Increased capacity of the obese microbiome for energy extraction
see helicobacter
cards
Microbiota and CVD
A high fat diet rich in phosphatidylcholine produces TMA (trimethylamine) by the gut flora
The liver converts TMA into TMAO (trimethyl amine N-oxide)
A high level of TMAO promotes athlerosclerosis
Metabolites of the lipid phosphatidylcholine (including choline and trimethylamine N-oxide, TMAO) were found to be risk factors for cardiovascular disease (CVD) in a large clinical cohort.
The gut flora played a role in generating these metabolites.
Suppression of intestinal flora in mouse model protected against CVD
Gut microbiota & multiple sclerosis
In multiple sclerosis (MS), the myelin coat that surrounds nerve fibres gets damaged as a result of an autoimmune response
Experimental autoimmune encephalomyelitis, (EAE) is a well-established mouse model of multiple sclerosis
EAE mice DO NOT develop disease if the mice are raised germ-free
Gut microbiota influences the balance between pro- and anti-inflammatory immune responses during EAE
Microbiota and Parkinsons
Used mice genetically programmed to develop Parkinson’s disease.
Mice reared normally developed symptoms, but germ-free mice remained healthy.
Transplanting bacteria from Parkinson’s patients to mice led to mice developing more symptoms than if they received bacteria from healthy people.
HMP therapeutics - FMT
Faecal microbiota transplantation (FMT)
used for C diff infection
Traditional antibiotic therapy has limited efficacy; doesn’t correct the imbalance and generally exacerbates the problem - pseudomembranous colitis
Expanding indications for faecal transplant
Extensive clinical trials:
- Ulcerative colitis
- Crohn’s disease
- Irritable bowel syndrome
Isolated case reports:
- Multiple sclerosis
- Parkinson’s disease
- Chronic fatigue syndrome
- Rheumatoid arthritis
Anti inflammatory gut organisms such as Faecalibacterium might be an effective probiotic for CD
Example additive microbiota therapies
A - vaginal commensale Lactobacillus jensenii engineered to produce antiviral protein cyanovirin-N: colonisation by recombinant bacteria inhibits host infection by SHIV in simian model
B - Lactococcus lactis genetically modified to produce anti inflammatory cytokine interleukin-10 (IL10): administration in mice with colitis shown to reduce inflammation during gut transit
C - Probiotic Escherichia coli engineered to synthesise N-acyl-phosphatidylethanolamines (NAPEs): host mediated conversion of NAPEs to N-acylethanolamides (NAEs) prevents obesity in mice (through inc. satiety)
D - Endogenous urease (Ure+) activity of mouse microbiota can exacerbate hyperammonemia caused by liver injury, depletion of native microbiota via antibiotics and polythene glycol: replacement with urease deficient (Ure-)microbiota can protect from hyperammonemia and associated neurotoxicity
Potential strategies for therapeutic microbiome manipulation:
- Antibiotics
- Bacteriophage
- Probiotics
- Prebiotics
- Synbiotics
- Nutritional therapy
- Microbiota restoration
Metabolic approaches to microbiome manipulations and therapies
Bacterial gut metagenome produces primary and secondary metabolites
Secondary metabolites are called ‘specialised metabolites’
Specialised metabolites can produce molecules that have effects in the body, e.g. GABA produced by bacteria can have neurological effects
Lactobacillus rhamnosus produces GABA: probiotic treatment increases GABA receptor expression in the hippocampus and reduces anxiety and depression behaviours in the mouse model
