12. Disease as an Imbalance of Microbes

Question 1

Define ‘dysbiosis’

Answer 1

• imbalance in microbial community associated with disease
• can be due to gain or loss of community members or changes in relative abundance of members

Question 2

How to measure dysbiosis?

Answer 2

• DNA analysis of complex microbial populations
• involves sequencing 16S rRNA gene for bacteria
• metagenomics involves sequencing all DNA in sample and using bioinformatics to predict source and function of DNA sequences

Question 3

… is one of the most diverse microbial communties in the body

Answer 3

gut microbiome

Question 4

… to … species in gut microbiome
Variation between people is high/low

Answer 4

500-1000
high

Question 5

Why are we still unclear what a healthy gut microbiome looks like?

Answer 5

• large differences in healthy individuals (genetic, environmental, lifestyle)
• differences in study parameters (experiemental design, bioinformatics analysis approaches)
• lack of large scale studies (30 mill people genome sequences vs 10,000 publicly available microbiome data sets)

Question 6

3 things that influence gut microbiome

Answer 6

• mother
• environment
• lifestyle

Question 7

How much of your gut microbiome is determined by environment?

Answer 7

20-25%

Question 8

How does your mother influence your gut microbiome?

Answer 8

• first microbes you encounter are key
• acquired as you pass along birth canal
• breast feeding
• skin to skin contact

Question 9

How does environment influnce gut microbiome?

Answer 9

• pets/rural upbringing
• drugs (antimicrobials)

Question 10

How does lifestyle influence gut microbiome?

Answer 10

• diet (switch from eastern to western lifestyle can modify it and fibre consumption)
• urban vs indigenous lifestyle

Question 11

Differences between microbiota have been linked to what factors?

Answer 11

• obesity
• colorectal cancer
• inflammatory bowel disease
• systemic conditions

Question 12

Microbiome analysis measures … and therefore can’t be used for what?

Answer 12

• composition
• attribute certain organism to disease
• hard to compare studies too as diff experimental methods and bioinformatics

Question 13

3 models of the gut microbiome in colorectal cancer

Answer 13

• model 1 is that the key microorganisms can drive tumorigenesis (F.nucleatum promotes cancer cell proliferation and inhibits anti-tumour immunity)
• model 2 is that collective mirobiota drives tumerigenesis (metabolism of fats by microbial communtiies releases carcinogens)
• model 3 is that key microbes shape microbiota (individual organisms can shape overall microbiota promoting model 2)

Question 14

Explain IBD
Link to gut microbiome

Answer 14

• Chron’s disease and ulcerative colitis affects over 3.6 million people increasing in last few decades
• host genetics are key but less than 50% concordance with mono twins
• gut microbiome is a protagonist (no single causative organism, dysbiosis of microbial comms)

Question 15

Difference between IBD and new-onset paediatric Crohn’s disease

Answer 15

• not changes in species present
• but the changes in metabolic functions in microbial community that drives disease

Question 16

Changes in microbial composition in IBD

Answer 16

• decrease in alpha diversity
• decrease in bacteroides and firmicutes
• increase in gammaproteobacteria
• presence of E.Coli
• presence of fusobacterium

Question 17

Changes in microbial function in IBD

Answer 17

• increase in auxotrophy
• increase in sulfate transport
• increase in amino acid transport
• increased oxidative stress
• decrease in amino acid biosynthesis

Question 18

How do treatments target the microbiome?

Answer 18

• careful selection of antibiotics to minimise unwanted shifts in microbiota e.g avoids repeated use of single antibiotic
• repopulation of gut with healthy bacteria (pre and pro biotics, faecal microbiota transplantation)
• manipulation of microbiome from birth by vaginal seeding for C-section babies

Question 19

Explain faecal microbiota transplantation

Answer 19

• encouraging results for relapsing C-difficile infection
• not so clear yet for IBD

Question 20

Healthy oral microbiome is the … … community of humans with … to … species colonizing both … and … tissue

Answer 20

• second largest
• 400-700
• hard and soft

Question 21

How do we acquire oral microbiota?

Answer 21

• oral bacteria from mother train fetal immunity
• vertical transmission during birth
• diet-breast feeding
• horizontal transmission - family members and pets

Question 22

Dysbiosis of the oral microbiome drives what issues?

Answer 22

• periodontal disease
• caries
• oral cancer
• peri-implantitis
• mucosal diseases like leukoplakia and lichen planus

Question 23

Periodontal disease is a … … disease

Answer 23

destructive inflammatory

Question 24

Explain ‘non-specific plaque hypothesis’

Answer 24

• simple idea
• that plaque mass at gingival margin equates to disease status

Question 25

Explain ‘specific plaque hypothesis’

Answer 25

• presence or an increase in specific pathogenic bacteria
• considered periodontal pathogen Socransky modified Kochs postulates
• pathogenicity of specific bacteria based on association with disease, treatment elimination, pathogenicity of animal models, induction of a host immune response and production of virulence factors

Question 26

Explain ‘microbial shift hypothesis from specific plaque’

Answer 26

• decrease in number of beneficial commensal species an increase in number of specific pathogens associated with periodontitis
• identification of specific microbial groups within dental plaque

Question 27

Why is dysbiosis sometimes not accurate for disease detection?

Answer 27

• putative periodontal pathogens like P.gingivalis are frequently found in healthy periodontal sites
• doesn’t mean they’re active players

Question 28

Explain the ‘ecological plaque theory’

Answer 28

• subgingival environment dictates or selects specific microbial composition
• in turn this drives change from health to disease

Question 29

Explain ‘keystone pathogen hypothesis’

Answer 29

• keystone pathogen supports and stabilises dysbiotic state
• triggers immune reaction
• even when present at low numbers

Question 30

Explain polymicrobial synergy and dysbiosis model

Answer 30

• periodontitis is initiated by synergistic and dysbiotic microbiota
• fulfil different roles that converge and shape and stabilize disease-provoking microbiota

Question 31

Explain dental caries

Answer 31

• most prevalent biofilm-dependent infectious disease
• causes tooth destruction leading to pulp infection and systemic infection
• through dysbiosis of supragingival plaque in a high sugar diet

Question 32

Studies into caries

Answer 32

• small scale (8 with, 4 without)
• most species of bacteria common in caries and caries free - only a few associated with caries but acid production
• organisms most abundant in plaque showed diffs in caries and caries free (acidgenic and aciduric bacteria )

Question 33

Explain extended caries ecological plaque hypothesis

Answer 33

• clinically sound enamel surfaces - mainly non-mutans strep and
  actinomyces
• add sugar and acidification enhances acidurance/genity of non-mutans bacteria and colonises more aciduric strains
• this acid-induced adaptation shifts demineralization/remineralization balance towards net mineral loss - dental caries
• prolonger acidic conditions means aciduric become dominant and promote greater demineralisation