Eubiosis and Dysbiosis

Question 1

Human GIT microflora contains how many viable microorganisms?

Answer 1

10 to the 14 power from over 1000 species; 100 x that of human body cells

Question 2

Three Main Enterotypes of microflora?

Answer 2

 Bacteroides (enterotype 1)
◦ associated with diets rich in animal protein and
saturated fats
 Prevotella (enterotype 2)
◦ associated with a predominantly plant-based diet
 high in carbohydrates & low in meat and dairy
 Ruminococcus (enterotype 3)
◦ originally believed as most prevalent, now appears
least prevalent (Guinane & Cotter, 2013

Question 2

Three Main Enterotypes of microflora?

Answer 2

 Bacteroides (enterotype 1)
◦ associated with diets rich in animal protein and
saturated fats
 Prevotella (enterotype 2)
◦ associated with a predominantly plant-based diet
 high in carbohydrates & low in meat and dairy
 Ruminococcus (enterotype 3)
◦ originally believed as most prevalent, now appears
least prevalent (Guinane & Cotter, 2013

Question 3

What are the health benefits of the colonic microflora?

Answer 3

1. Enhanced GIT motility & function
2. Modulate the immune system
3. Improved digestion and nutrient
   absorption
4. Production of Vitamins
   ◦ B group
   ◦ Vitamin K
5. Xenobiotic metabolism
6. Colonisation resistance
   ◦ ‘the protection against colonisation of the intestinal
   tract with potentially pathogenic bacteria afforded by
   the intestinal flora
7. Production of SCFAs
8. Production of polyamines
    polyamines (putrescine, spermidine, and spermine)
   participate in a large number of cellular processes, such
   as:
    cell growth and differentiation
    regulation of RNA, DNA and protein synthesis
    improve GIT microcirculation
    can be utilised as an instant energy source by intestinal cells
9. Weight management

Question 4

Physiological Activity of SCFAs

Answer 4

◦ 3 main SCFAs
 butyrate, propionate, acetate
◦  colonic pH
◦ improves colonic epithelial barrier function
mainly from butyrate
◦ protect against colon carcinogenesis
◦ have trophic effects on small intestine
◦ improve laxation
◦ improve circulation to colon and liver
◦ improve mineral absorption
◦ decrease colonic and systemic inflammation

Question 5

What is the pH and microbial biomass along the GI tract, mouth, stomach, duodenum, jejunum, ileum, colon

Answer 5

Mouth: 100 million to billion cells/ml
Stomach: pH 1.5-5; 100-1000 cells/ml
Duodenum: pH 5-7; 1000-10,000 cells/ml
Jejunum: pH 7-9; 10,000 - 100,000 cells/ml
Ileum: pH 7-8; 100 million cells/ml
Colon: pH 5-7; 100 billion cells/ml

Question 6

In what ways does the colonic microflora modulate the immune system?

Answer 6

1. GIT flora promotes secretion of intestinal secretory IgA

2.shift T-helper cell balance towards Th-1
  production of IgE and eosinophils
 dampens hypersensitivity reactions and intestinal inflammation
 induces oral tolerance
 prevents development of atopic diseases

3. may modify antigens to less antigenic forms
    induces & maintains oral tolerance

4.Non-specific immune stimulation
 in vitro - ↑ production of cytokines, tumor necrosis factor
α and interleukin 6 (reflecting stimulation of nonspecific
immunity)
 Increases production of macrophages and stimulates
phagocytosis

Question 7

How colonic microflora enhances GIT motility and functions?

Answer 7

1. gastric emptying, small intestinal transit, and colonic
   transit have all been found to be more rapid in
   conventional animals than in their germ-free
   counterparts
2. ‘normal’ GIT propulsive activity is determined to a
   significant degree by the presence of the normal flora
    microbial production of nitric oxide, short-chain fatty acids, and polyamines may play a role

Question 8

How does colonic microflora improve digestion and nutrient absorption?

Answer 8

1. provides about 10% of daily energy needs via fermentation in colon
2. salvages energy from unabsorbed carbohydrates
   in the colon → SCFAs
3. improves the absorption of calcium, magnesium
   and trace minerals

Question 9

Colonic microflora produces which vitamins?

Answer 9

B group, K
- note: high dose abx&raquo_space; to vit K deficiency&raquo_space; incr risk of clots

Question 10

The colonic microflora produce polyamines. What do they do for health?

Answer 10

 cell growth and differentiation
 regulation of RNA, DNA and protein synthesis
 improve GIT microcirculation
 can be utilised as an instant energy source by intestinal cells

Question 11

How are colonic microflora related to weight management?

Answer 11

microflora plays a vital role in energy
homeostasis
 obese microbiota has an increased capacity to
harvest energy from the diet

Question 12

Define “dysbiosis”

Answer 12

1. ‘qualitative and quantitative changes in the
   intestinal flora, their metabolic activities or their
   local distribution that produces harmful effects on
   the host
2. growth of potentially pathogenic microorganisms
   over their beneficial counterparts and/or alterations
   in the metabolic activities of the flora

Question 13

Dysbiosis plays role in what chronic/degen diseases?

Answer 13

e.g., rheumatoid arthritis, ankylosing
spondylitis, IBS, IBD, atopic eczema, obesity

Question 14

How does microflora of IBS patients differs from
that of healthy controls?

Answer 14

◦ lower faecal concentrations of bifidobacteria and
lactobacilli
◦ higher concentrations of Enterobacteriacea

Question 15

How is dysbiosis presented in ulcerative colitis?

Answer 15

  colonic concentration of lactobacilli
 toxic strains of Escherichia coli may play a role
  populations of Faecalibacterium prausnitzii
 95% of UC sufferers are colonised by sulphate-reducing
bacteria (SRB)
 active UC is associated with  production of luminal hydrogen
sulphide

Question 16

How is dysbiosis presented in Crohn’s Disease?

Answer 16

  in faecal bifidobacteria
 toxic strains of E. coli may play a role
 elevated numbers of Bacteroides spp.
  populations of Faecalibacterium prausnitzii

Question 17

How does Dysbiosis in Atopic Eczema present?
 Babies who later developed AE

Answer 17

◦ ↓ enterococci
◦ ↓ bifidobacteria
◦ ↑ clostridia
◦ ↑ Bacteroides spp.
◦ ↑ E. coli

Question 18

How does dysbiosis incr risk of kidney stones?

Answer 18

Presence of colonic Oxalobacter formigenes
(OF) reduces the risk of kidney stones (Kaufman et
al, 2008)
◦ OF utilise oxalate as sole food source
 thereby decreasing amount of oxalate available for
absorption
◦ After triple antibiotic therapy (Kharlamb et al, 2011)
 of subjects who were OF positive at baseline, only 37%
continued to be colonised by OF after 1 and 6 months

Question 19

How does dysbiosis present in obesity?

Answer 19

◦ obese people have:
 lower Bacteroidetes and more
Firmicutes than lean subjects (Ley et al,
2006)
 higher proportion of gram-negative
bacteria in the microflora

Infant antibiotic exposure is a risk factor
for childhood obesity

Question 20

Causes of dysbiosis?

Answer 20

1. Antibiotics
2. Chemotherapy
3. Stress
4. Cesarean section
5. birth location (hospital vs home)
6. Formula feeding
7. Diet

Question 21

What dietary patterns are assoc with dysbiosis?

Answer 21

 sulphates and sulphites
 high protein diets
 high animal protein diets
 high fat diets
 high in refined carbohydrates

Question 22

Products of protein putrefaction in the colon?

Answer 22

SCFAs
BCFA
Phenols and Indoles - co-carcinogens
Ammonia - mutagen, cellular poison
Amines: neurotransmitter and mutagen precursors
HS and thiols: cellular toxins

Question 23

high protein diet and dysbiosis changes?

Answer 23

 Induces changes to the ecosystem: (Duncan et al, 2007)
◦ Decreases in faecal concentrations of bifidobacteria
 50% decline on a high-protein + low-carb diet in
just 4 weeks!
◦ Decreases in concentrations of butyrate-producing species
 Roseburia spp. and Eubacterium rectale
◦ Decreases in faecal butyrate

Question 24

How does high animal protein diet >> dysbiosis?

Answer 24

Diets high in animal protein →  activity of certain bacterial enzymes, such as beta–glucuronidase, azoreductase, nitroreductase and 7--hydroxysteroid dehydroxylase →  release of potentially toxic and unwanted metabolites in the bowel  can be attenuated through prebiotic consumption

Question 25

HIgh fat diet and dysbiosis?

Answer 25

◦ increases in the ratio of gram-negative to gram-positive (Cani et al, 2008)  e.g., an increased proportion of lipopolysaccharide-containing microbiota in the gut  greater pool of luminal endotoxin  LPS represents ~80% of the cell wall mass of gram-negative bacteria ◦ decreases in bifidobacteria concentrations (Cani et al, 2007) ◦ increases in E. coli populations (Martinez-Medina et al, 2013) ◦ increases in Desulfovibrionaceae (Hildebrandt et al, 2009) Meals high in fat increase endotoxin absorption (Laugerette et al, 2011)  → postprandial endotoxaemia → low-grade systemic inflammation ◦ the higher the fat content the higher the serum level of endotoxins ◦ saturated fat appears to further enhance endotoxin absorption (Mani et al, 2013)  whereas omega-3 fats attenuate postprandial endotoxaemia ◦ concurrent consumption of fibre (30g) also attenuates postprandial endotoxaemia

Question 26

Diets High in Milk Fat and dysbiosis?

Answer 26

Animal models have found that ingesting increased amounts of milk fat (but not safflower oil) triggers blooms of an otherwise rare gram-negative bacterium – Bilophila wadsworthia ◦ went from nearly 0% of flora to 6% ◦ B. wadsworthia consumes sulphur-rich bile salts produced to help breakdown the milk fat  → ↑ in H2 S production and gut inflammation

Question 27

sucralose and dysbiosis?

Answer 27

◦ Causes significant changes in the microflora  Reductions in:  total anaerobes  total aerobes  beneficial bacteria:  bifidobacteria  lactobacilli ◦ Increased faecal pH

Question 28

how is dysbiosis diagnosed?

Answer 28

1. Primarily based on the patient’s medical and diet history * recent history of antibiotic use, or multiple courses of antibiotics; recent chemotherapy or radiotherapy; long-term PPI or NSAID use * suffer from one or more of the diseases detailed earlier * high stress levels * dietary risk factors * SAD; Ketogenic diet; High fat-low carb; high protein-low carb; high processed carb; low fibre diets; low FODMAP diet; diets low in plant food diversity 2. Specialised stool testing

Question 29

Stool Test Summary

Answer 29

* Culture has no role to play in assessing GI microbiota composition – so don’t use it! * Most accurate and comprehensive results come from combining a molecular stool test using 16s RNA or shotgun metagenomic sequencing with a CDSA/CSA (complete digestive stool analysis/comprehensive stool analysis) * broad overview of ecosystem and diversity scoring * all important genera highlighted and more! * microbe metabolic pathways (shotgun only) * digestive & microbial markers – faecal fat, pancreatic elastase, stool pH, total SCFAs & ratios, β-glucuronidase * inflammatory & immune markers – calprotectin, sIgA, mucous, lactoferrin, occult blood * however – ignore the microbe section on culture-based CSAs/CDSAs!

Question 30

Tools used to treat dysbiosis?

Answer 30

 Prebiotics  Probiotics  Colonic foods  Antimicrobial herbs?

Question 31

What probiotics to use for dysbiosis?

Answer 31

 Bifidobacterium lactis HN019 (Ahmed et al, 2007) ◦ increases in faecal concentrations of bifidobacteria (P<0.0005), lactobacilli (P<0.005), and enterococci (P<0.005) compared to baseline; ◦ decrease in coliforms (P<0.005)  Lactobacillus rhamnosus GG (Benno et al, 1996) ◦ increases in faecal concentrations of bifidobacteria and lactobacilli (both P<0.05) ◦ decrease in clostridia concentrations

Question 32

Define colonic foods?

Answer 32

foods entering the colon and serving as substrates for the endogenous colonic bacteria, thus indirectly providing the host with energy, metabolic substrates and essential micronutrients.

Question 33

Colonic foods for dysbiosis examples?

Answer 33

*Brown rice *Carrots *Cocoa *Green tea

Question 34

General Dysbiosis Treatment Approaches

Answer 34

General Dysbiosis Treatment Approaches  Selective Weeding - if deemed necessary, choose selectively-acting antimicrobials first before using broad-spectrum options ◦ Garlic  preferably raw ◦ Green tea extract  ~300mg catechins/day ◦ Pomegranate husk

Question 35

General Dysbiosis Treatment Approaches

Answer 35

 Leave more broad-acting, potentially microflora-damaging options as last resort ◦ Berberine-rich herbs  Coptis chinensis (10% in 1:2 tincture)  Phellodendron amurense (6%)  Hydrastis canadensis (3%)  B. vulgaris and M. aquifolium too low in berberine to have significant impacts as antimicrobials ◦ Enteric-coated essential oils  Oregano, thyme, clove, cinnamon ◦ Antibiotics Would you p