Lecture 8 - Gut Microbiota Flashcards
Broad change in prevalence of diseases between 1950 and 2000
Reduction in incidence of infectious diseases
Increase in autoimmune, allergic, inflammatory disease
Hygiene hypothesis
Increased cleanliness associated with increased levels of autoimmune disease.
Reduced exposure to infectious agents leads to immune dysregulation
Hypotheses for why autoimmune diseases are increasing in prevalence in the Western world
1) Hygiene hypothesis
2) Microbiota hypothesis (human gut evolved to have bacteria)
3) Diet hypothesis (human microbiome changes according to diet)
Factors leading to altered diet in developed world
Economic
Demographic
Epidemiological
Aspects of Western diet that could lead to dysbiota
High in fat, sugar
Highly refined and processed
Low in fibre (important)
Factors potentially affecting microbiota composition
Host genetics Maternal transfer, early colonisation Antibiotics, medications Infection Inflammation Stress Hygiene Age
Is the microbiome uniform through the GIT?
No. Increases in bacterial density/g from the stomach to the colon.
Human vs microbial genome in human body
Human genome has ~23,000 genes.
Microbiome has over 100,000 genes
Advances in studying GIT microbiome 1) 2) 3) 4)
1) Generation of germ-free mice
2) High throughput DNA sequencing
3) Transcriptional and metabolomic tools, with which to measure microbiota impact on host physiology, immunity, development
4) Development of tractable experimental systems (C. elegans, drosophila)
Germ-free mice
Mice raised in a germ-free environment. Can be from different genetic lines, clonal, non-clonal.
Can selectively restore bacteria in microbiome
High throughput DNA sequencing effect on studying microbiome
Can generate metagenomic analyses to compare metabolic and taxonomic data from different microbiota
What is the human microbiome project?
1)
2)
3)
1) NIH
2) First phase (2007-2012). Characterised composition and diversity of human microbiome in skin, nose, mouth, GIT, UGT. Evaluated metabolic potential.
3) Second phase (2013-2015). Create the first integrated dataset of biological properties of host and microbiome from cohort studies of microbiome-associated diseases
What is a healthy microbiome?
1) Varies a lot between individuals
2) Predictions can be made loosely based on country, breast feeding, level of education
3) No core microbiotal genome, but broad metabolic characteristics are shared
Study into the diversity of microbiota
1)
2)
3)
1) 16S rRNA sequences compared in mono- and dizygotic twins
2) No core genome shared. High variability in species/phylum composition
3) Analysis of genes showed a similarity in metabolic capacities
Two major phyla in GIT microbiome
Firmicutes
Bacteroidetes
Study into diet-induced changes in GIT microflora 1) 2) 3) 4) 5)
1) Microbiota of children from Burkina-Faso and Florence were compared.
2) Bacteroidetes dominated in Burkina-Faso
3) Firmicutes dominated in Italy
4) Diet has a larger role in shaping microbiome than ethnicity, climate, sanitation, hygiene
5) More pathogenic bacteria, lower SCFA levels in Italian children
Functional members of non-pathogenic GIT microbiome
1) Probiotics
2) Autobionts
3) Pathobionts
Probiotics
Transiently-present bacteria.
Can be beneficial.
EG: bifidobacterium spp, lactobacillus spp
Autobionts
Permanent, symbiotic, immunomodulatory.
Part of normal microbiome.
Direct influence on host immune function
EG: Bacteroidetes fragilis, clostridium XIV
Pathobionts
Permanent, parasitic/infectious.
Don’t cause disease normally, unless microbiome is perturbed.
EG: Clostridium difficile, helicobacter
How are autobionts adapted to life in the GIT?
Express polysaccharide utilisation loci
Allows them to digest polysaccharides from plants.
Necessary for humans to be able to get nutrition from certain sugars (humans can only digest starch, maltose, sucrose).
Example of a polysaccharide utilisation locus in bacteroidetes ovatus
Xyloglucan PUL
Digestion of dietary fibre
1) Gut bacteria digest dietary fibre into short-chain fatty acids.
Bacteroidetes make acetate (2C), propionate (3C)
Firmicutes make butyrate (4C).
2) Short-chain fatty acids diffuse across lumen, are taken up by host transporters or bind to GPCR
Roles of short-chain fatty acids in GIT 1) 2) 3) 4) 5)
1) Stimulate mucus production by epithelial cells
2) Stimulate B cells to make IgA
3) Promote differentiation of Treg, leading to tolerance
4) Maybe lead to inflammosome activation, IL-18 release. This promotes epithelial integrity
5) Inhibition of inflammaroty NF-kB
Only source of nutrition for colonic cells
Short-chain fatty acids
Importance of the GIT microbiome 1) 2) 3) 4) 5)
1) ~10% of calorific intake
2) Vitamins B and K
3) GIT epithelial development
4) Immune system development and tolerance
5) Competition for pathogenic bacteria
Results of metagenome-wide association studies into microflora in T2DM patients
1)
2)
1) Decreased microbiome diversity associated with weight gain, insulin resistance, fatty liver, low-grade inflammation
2) Reduced butyrate products, increased pathogenic bacteria
Evidence for GIT microflora influencing adiposity 1) 2) 3) 4)
1) Gut microflora from obese/lean human twins transferred to mice
2) Tranfer of ‘obese’ microbiome resulted in greater adiposity
3) Presence of lean mice with a high-fibre diet or ‘lean’ microbiome led to decreased adiposity in obese mice (from coporophagy)
4) Transfer of microbiome from first trimester/third trimester pregnant women to mice. Mice that received first trimester remained lean. Mice that received third trimester became obese.
Modulation of host metabolism by short-chain fatty acid synthesis
1)
2)
3)
1) GPRC41 and GPRC43 stimulated. GPRC41 stimulation leads to peptide YY release. GPRC43 stimulation leads to hormone glucagon-like peptide release
2) Intestinal gluconeogenesis uses short-chain fatty acids as a carbon source
3) Inhibits fasting-induced adipose factor (FIAF).
Fasting induced adipose factor role
Inhibits lipoprotein lipase. Lipoprotein lipase leads to VLDL and chylomicron release of free fatty acids, leading to their storage in adipocytes.
Inhibiting FIAF might lead to increased adiposity
GPRC41
GPRC that binds short-chain fatty acids.
Binding leads to release of peptide YY, which regulates gut motility and intestinal transit rate
GPRC43
GPRC that binds short-chain fatty acids.
Binding leads to release of hormone glucagon-like peptide (GLP-1), which increase insulin-sensitivity
Critical GPRC regulators of obesity
GPRC43-deficient mice are obese on a lean diet.
Overexpression of GPRC43 in adipose tissue leads to leanness, regardless of calorie intake.
These effects were dependent on gut microbiome composition (absent in germ-free mice)
Effects of diet-induced dysbiosis 1) 2) 3) 4)
1) Local and systemic inflammation and inappropriate immune response
2) Change in Treg/Th17 balance
3) Increase in pathobionts, release of endotoxin (LPS)
4) Breakdown in gut barrier function, increased gut bacteria in blood
Immunosuppressive immune dysregulation from dysbiosis 1) 2) 3) 4)
1) Treg/Th17 ratio increased
2) Butyrate promotes formation of Treg
3) Increase in IL-10
4) Th17 activation suppressed
Inflammatory immune dysregulation from dysbiosis 1) 2) 3) 4) 5)
1) Treg/Th17 ratio reduced
2) Pathobionts promote Th17 differentiation
3) Associated with chronic autoimmunity
4) Induced by segmented, filamentous, G+, anaerobic bacteria
5) Segmented filamentous bacteria monocolonised mice don’t mount inflammatory response or colitis
Healthy microbiotal GIT response to a pathogen
1)
2)
3))
1) Commensal bacteria kill pathogen by competing for resources, reducing oxygen levels, suppressing virulence factors
2) B cells are stimulated to make IgA by SCFA release form commensals
3) IL-1b release from B cells leads to neutrophil entry into GIT, killing pathobionts, pathogenic bacteria
Dysbiotic GIT response to a pathogen
1)
2)
3)
1) Depleted autobionts leads to overgrowth of pathobionts
2) Epithelial damage from lack of SCFA
3) Pathogenic bacteria enter blood
Potential immunotherapy using microbiome 1) 2) 3) 4)
1) Less fat, more fibre in diet
2) Pre/pro biotics (pro - beneficial bacteria, pre - beneficial bacteria + undigestible food)
3) Faecal transplant
4) Targeted manipulation
When is the risk of immunoallergenic disorders highest for a migrant form a low-risk country to a high-risk country?
Risk decreases with age.
Greatest risk is when you move at a young age from a low-risk to a high-risk country
Do pre/probiotic supplements work?
Only when taken long-term
Successful treatment for refractory C. difficile infections
Faecal transplant from a healthy donor
Alternatives to a faecal transplant
1)
2)
3)
1) Use of cultured autobiotants
2) Inclusion of microbiota small molecules (such as acetate, butyrate)
3) Identify, administer antimicrobials produced by gut autobionts (EG: thuricin from bacillus thuringiensis kills C difficile)
