The World Within
Micro-organisms in the Digestive
Tract:
Friends, Foes, and Visitors
Janice M. Joneja, Ph.D 2002
The
Internal
Landscape
2
The Digestive Tract
 Each site within the digestive tract is designed for
optimal function:
 Digestion of food
 Protection against invading disease-causing microorganisms
 Maintenance of healthy balance (homeostasis)
 In the lower bowel, micro-organisms play an active role
in all these functions
 Sometimes, conditions favour colonisation by
microorganisms; others are hostile to their survival
 The proper functioning of the resident microflora is
essential to the health of the body
3
Digestive Enzymes
Mouth:
Salivary -amylase
Lingual lipase
Stomach:
Acid hydrolysis
Gastric pepsins
Small intestine:
Pancreatic
-amylase
Lipase
Colipase
Trypsin
Chymotrypsin
Elastase
Carboxypeptidases
Large bowel
Microbial metabolism
Small intestine:
Gall bladder:
Bile salts
Small intestine:
Brush border:
Lactase (ß galactosidase)
Glucoamylase (-glucosidase)
Sucrase-isomaltase
Amino-oligopeptidases
Dipeptidyl-peptidase
4
Microbial Colonisation
Mouth:
Saliva
Microbial colonisation
Esophagus:
Micro-organisms present
Stomach
High acidity
Usually sterile
Small intestine
Neutral or slightly alkaline
No resident microbial population
Micro-organisms populate lower ileum
Large bowel
Dense microbial population
Mostly anaerobic organisms
Rectum
Faeces
Dense microbial population
5
Microbial Colonisation of the
Digestive Tract
 Factors allowing micro-organisms to live:
 Body defences (immune system)
 Determines who stays, who goes
 Environment:
 Acidity and alkalinity (pH)
 Level of oxygen present
 Diet:
 Provides nutrients for microbial growth and
reproduction
 Interactions between different types of microorganisms
 Survival of the fittest
6
Colonisation by Microorganisms
The Mouth
 Micro-organisms enter through the mouth from
the external environment
 Nutrients and salivary secretions in the mouth
allow colonisation:
 Crevices around the teeth
 Pockets in oral tissues
 Bacterial plaque on the surface of teeth
 Numbers and persistence of micro-organisms
depends on:
 Available nutrients
 Hygiene
 Speed of transit of contents
7
Micro-organisms in the Esophagus
 Micro-organisms pass with the oral contents
through the esophagus
 The environment of the esophagus is the same
as in the mouth, but it is a conduit, not a
“vessel”
 Material passes through, but does not remain in
location, and therefore micro-organisms have no
opportunity to colonise the area
8
Micro-organisms in the Stomach
 In the healthy individual the stomach is sterile
 The process of eating triggers release of
gastric secretions and acid
 After a meal the pH can be as low as 3.0
 Most micro-organisms cannot survive this
 Gastric secretions and hydrochloric acid kill off
most micro-organisms passing from the
esophagus
 Rate of flow of food through stomach also
influences microbial survival
9
Micro-organisms in the Stomach
 Low acidity (higher pH) allows some microorganisms to survive
 Conditions that may allow bacteria to live:
 Achlorhydria (lack of gastric acid), especially in
the very young, and the elderly
 Neutralizing substances that reduce acidity of
contents, e.g.:
 sodium bicarbonate
 other antacids
 Most common pathogen: Helicobacter pylori
10
Survival of Micro-organisms in the
Stomach
 Rapid movement of food material through
before pH is low enough to kill them:
 Before a meal, pH of stomach is 4-5
 Drops to pH 3 while eating
 Rate of flow of stomach contents influenced by:
 Composition of meal:
 Fat passes through slowly
 Liquid passes through quickly
 Micro-organisms that survive through the
stomach pass into the small intestine
11
Micro-organisms in the Small Intestine
 Very few micro-organisms live in the first part of the
healthy small intestine
 Numbers increase as the digesta passes into the
terminal ileum
 Conditions that influence microbial multiplication:
 Rate of flow of digesta:
 Flow rate greatest at the beginning
 Slows as material reaches distal end
 Normal length of time food material takes to transit small
intestine: 3-4 hours
 Water is absorbed
 Consistency is more solid and allows organisms to
stay in place long enough to multiply
12
Micro-organisms in the Small Intestine
 Under normal circumstances several processes
inhibit adherence and colonization in the small
intestine, and kill micro-organisms surviving
from the stomach:
 Mucus coats bacteria and disallows contact
with the intestinal wall
 Antibodies, especially secretory IgA, neutralize
bacteria
 Lysozyme in secretions is bactericidal (kills
bacteria)
 Bile salts are bactericidal
13
Micro-organisms in the Small Intestine
 Micro-organisms can colonise the small intestine
and cause infection if they can adhere to the
intestinal wall
 Usually, contents pass through too rapidly to
allow this
 Some situations may predispose to colonization:
 Motility disorders that interfere with the
normal passage of material through
 Material becomes lodged within tissue pockets
(diverticulae)
14
The Large Bowel
 Most of the micro-organisms that colonise the
human body live and thrive in the large intestine
 Digesta from small intestine enters the caecum
where microbial activity begins in earnest
 As the contents pass from the caecum to the
rectum, microbial numbers increase dramatically
 Adult eating typical Western diet:
 Total contents: 220 grams dry weight
 Bacterial dry matter: 18 grams
15
Micro-organisms in the Large Bowel
 Contents of the large bowel pass from the body
as faeces
 Micro-organisms in faeces same as in terminal
part of large bowel
 Bacteria in faeces:
 Approximately a trillion per gram dry weight
 The longer the material remains in the colon,
the greater the number of micro-organisms
 Several hundred different microbial species
 About 99% of these belong to only 30-40
species
16
Micro-organisms in the Large Bowel
 Food material remains in the colon approximately 70
hours
 Inter-individual variation: 20 - 120 hours
 Many species multiply rapidly: some double every
twenty minutes
 Type and species of micro-organisms is surprisingly
stable for each individual
 Even when infection changes the nature of the species,
after pathogens are removed, microflora tends to revert
to its original composition
17
Micro-organisms in the Large Bowel
 Conditions that influence type and numbers of
micro-organisms:
 Amount of oxygen available (many are strict
anaerobes and are killed by exposure to oxygen)
 Competition for nutrients
 Type of nutrients available
 Type of micro-organisms present:
 Organisms that can break down food material and
use nutrients fastest will multiply fastest
 Confined space
 Organisms that multiply fastest, crowd out others
18
Micro-organisms in the Large Bowel
Inter-Species Competition
 Space and nutrients are limited
 Species that break down and use available
nutrients most efficiently achieve the highest
numbers
 Advantage to species that can:
 Use substrates most other species cannot process
 Use waste products of other species, e.g.
 Hydrogen sulphide
 Organic acids
19
Source of Nutrients in the Large Bowel
 Material that has not been completely digested
and absorbed in the small intestine:
 Food matter consumed in diet
 Cells and tissues sloughed off from digestive tract
 Enzymes and other material from body processes
such as:
 saliva
 intestinal secretions such as mucin
 blood cells
 Dead micro-organisms
20
Micro-organisms in the Large Bowel
Nutrient Substrates
 Most important nutrient substrates are:
 Carbohydrates
 Starch
 Plant storage material
 Non-starch polysaccharides (dietary fibre)
 Plant structural material
 Oligosaccharides (long chain sugars)
 From partial digestion of carbohydrates
 Sometimes disaccharides (sugars)
 Most are broken down in small intestine
 Proteins
 Diet
 Body secretions, including digestive enzymes
 Dead micro-organisms
21
Microbial Use of Material in the Large Bowel:
Carbohydrates
 Majority of bacterial species in the large bowel
act on carbohydrates
 Carbohydrates entering the colon of the average
adult eating a Western diet per day include:
 Dietary fibre…………………………12 grams
 Undigested starch…………………30-40 grams
 Material from the digestive tract
(mucins, enzymes and dead microorganisms)…………………...……….3-4 grams
22
Carbohydrates
 Dietary fibre
 Structural parts of plants
 Have beta-glycosidic linkages between molecules
 Indigestible by human enzymes
 Includes:





Pectin
Cellulose
Gums
Beta-glucans
Fructans
23
Dietary Fibre
 Usually separated into two types depending how it
interacts with water:
 Soluble fibre:
 Forms gel or gum
 Insoluble fibre:
 Remains unchanged in water
 Both types present in plants, e.g in legumes:
 Hard outer skin is insoluble type
 Inner “pulse” higher in soluble type
 Cooking and processing does not change the nature of
fibre
24
Carbohydrates
 Starches
 Previously thought all starch was digested and
absorbed in the small intestine
 Enzymes break alpha-glycosidic linkages
between molecules
 Recent research shows 15%-20% of dietary
starch passes undigested into the colon from
high starch foods such as:
 potato
 pasta
 rice
 banana
 grains (wheat, corn)
25
Starch
 Undigested starch is called
“resistant” starch
 Starch that is readily digested and
absorbed in the small intestine is
called “non-resistant”
 Resistant starch is resistant to digestive enzymes
 Passes into the colon where it is fermented by gut
microflora
 Unlike fibre, resistant starch is affected by cooking and
processing
26
Resistant Starch
 Process of digestion in the small intestine can be
speeded up by cooking - starch is gelatinized
 Cooling causes a process of crystallization
(retrogradation) that renders the molecules
non-digestible by enzymes
 Undigested material passes into the large bowel
 Freezing and drying can also cause changes in
starch that makes it resistant to digestion
 Research on contents of ileostomy bag
27
Comparison of Dietary Starch
A comparison of dietary starch:
a) Fed
b) Recovered after digestion in the small intestine
Food
Starch
Fed
(grams)
Starch
Recovered
(grams)
Percentage
Starch
Recovered
(%)
White bread
62
1.6
3
Oats
58
1.2
2
Cornflakes
74
3.7
5
Banana (raw)
19
17.2
89
Potato
freshly cooked
cooled
reheated
45
47
47
4.5
5.8
3.6
3
12
8
Englyst and Kingman 1994
28
Factors Affecting Amount of Starch in
the Colon
 Physical accessibility




Cell walls of plant cells entrap starch
Prevents its swelling and dispersion
Delays or prevents digestion by enzymes
Includes whole grains, nuts, seeds:
 vegetables with “skins”: sweet corn, peas, beans
 partly milled grains and seeds: “whole grain” breads
and cereals
 If the rigid structures of the plant are physically
removed, more of the alpha-glycosidic bonds of the
starch are exposed to the action of enzymes in the
small intestine
29
Factors Affecting Amount of Starch in
the Colon
 Cooking
 Disrupts starch granules
 Facilitates digestion by enzymes in saliva and the
small intestine
 When foods with a high level of resistant starch are
eaten raw, more undigested starch passes into the
colon
 e.g. Banana
 Retrograded starch increases on cooling: eat foods
with high level of resistant starch when it is hot
30
Factors Affecting Amount of Starch in
the Colon
 Chewing
 Amylase (ptyalin) in saliva is first enzyme to start
process of starch digestion
 The more the food is chewed, the greater the
exposure of the starch to enzymes in the mouth and
the small intestine
 Speed of transit of food
 The faster the food transits the small intestine, the
less exposure to enzymes
 High fat slows transit
 High fluid (water with the meal) speeds the transit
31
Oligosaccharides




Polymers of glucose 3 - 8 hexose units in length
Exist in plant materials as oligosaccharides
Or are derived from partial digestion of starches
Trisaccharides are most “notorious”
 Raffinose
 Stachyose
 Principally in legumes such as dried peas, beans,
lentils
 Proficient in generating excessive amounts of
intestinal gas and flatus
32
Oligosaccharides
 Fructo-oligosaccharides
 Polymers of fructose - called inulins
 Made by plants such as:








onions
garlic
artichokes
chicory
Appearing as “health foods”
Resist human digestive enzymes
Promote growth of Bifidobacteria in the large bowel
Tend to reduce growth of “undesirable” bacteria
33
Fructo-oligosaccharides and
Bifidobacteria
 Bifidobacteria are beneficial because they:




Stimulate immune function
Enhance synthesis of B vitamins
Restore normal microbial flora after antibiotic therapy
Prevent colonization by potential pathogens,
especially Clostridia
 Fructo-oligosacchardies:
 Reduce triglyceride and cholesterol levels in rats and
diabetic humans
34
Disaccharides
 Principally:
 Lactose; sucrose; maltose
 Usually broken down to monosaccharides (“single
sugars”) and absorbed in the small intestine
 When enzymes deficient, disaccharides pass undigested
into the colon
 Have several effects:
 Change osmotic pressure
 Act as substrate for microbial fermentation
 Results in symptoms typical of lactose intolerance;




Diarrhea
Abdominal bloating
Gas
Pain
35
Products of Microbial
Fermentation of Carbohydrates
 Any carbohydrate entering the colon acts as
substrate (nutrient) for microbial fermentation
 Principal products are short-chain fatty acids
(SCFAs):
 Acetic acid
 Propionic acid
 Butyric acid
 These three account for 85-95% of SCFAs in the
colon
36
Other Sources of SCFAs
 A smaller percentage of SCFAs come from
proteins
 Up to 40% of SCFAs are derived from protein,
depending on the diet
 Branched chain amino acids are converted to
branched chain fatty acids
 Contribute to the total SCFAs in the colon
resulting from microbial activity
37
Products of Microbial Fermentation of
Carbohydrates
 In converting the carbohydrates to these SCFAs
intermediate products are formed:
 Lactate
 Succinate
 Ethanol
 Most do not accumulate, but are converted to
SCFAs in the colon
 However, occasionally ethanol may accumulate:
 Results in “autobrewery syndrome” resembling
alcohol intoxication
38
Function of SCFAs
 SCFAs absorbed into the body through the colonic
membrane (wall), and can be measured in blood
 SCFAs serve a variety of functions in the colon:
Provide source of energy
Preserve the integrity of the colonic mucosa (lining)
Stimulate absorption of water and sodium
Reduce intestinal pH
Aid in protection against bacterial infection
Butyrate thought to be particularly important in protection
against colon cancer
 May also protect against inflammatory bowel diseases such as
ulcerative colitis






39
Proteins in the Colon
 12 – 13 grams of protein enter the large bowel
each day
 Material comes from:




Diet (even a vegan diet)
Secretions from the digestive tract
Dead bacteria
Tissue cells
 Much of the material is digested by pancreatic
enzymes in the small intestine
40
Proteins in the Colon
 Pancreatic enzymes continue digestion in the
large bowel as they pass in with the digesta
from the small intestine
 Bacterial enzymes actively attack the undigested
proteins
 Bacterial species Bacteroides are particularly
active in this process
 These species are also the most active
degraders of fibre in the colon
41
Protein breakdown in the Colon
 Proteins are first broken down to polypeptides
 Some bacteria use these directly as nutrients
 Other bacteria produce enzymes to break down
the polypeptides into dipeptides
 Dipeptides are then broken down further into
single amino acids
 20 amino acids make up all dietary proteins
42
Amino Acids in the Colon
 Bacteria utilize the amino acids in a variety of
ways:
 Deamination to ammonia
 Decarboxylation to amines and carbon dioxide
 Both systems are important in maintaining a
healthy colon
43
Ammonia in the Colon
Large quantities almost always present in the colon
High levels can be toxic
Can be a risk factor in the development of colon cancer
Colon bacteria use ammonia as a source of nitrogen in
their metabolism
 These strains are important to maintain a healthy colon
 These bacteria use carbohydrate, and especially fibre as
a course of energy
 Fibre in the diet thus aids in growth of the ammoniautilizing bacteria, which is thought to reduce the risk of
colon cancer




44
Biogenic Amines in the Colon
 Sometimes the amines are detrimental to a
person’s health, e.g.
 Histamine:
 Migraine headaches
 Symptoms resembling allergy






Hives
Tissue swelling (angioedema)
Rhinitis(“stuffy nose”)
Itching
Reddening and flushing
Increased heart rate
45
Biogenic Amines in the Colon
 Tyramine
 Migraine headaches
 Hypertensive crisis





Serotonin
Piperidine
Pyrrolidine
Cadaverine
Purescine
 Have adverse effects only in excess and in
sensitive individuals
46
Fate of Microbial Products
 Most microbial products enter circulation by
being absorbed through the colon wall
 Taken to the liver
 Cleared and excreted in the urine
 Examples:




Phenol and p-cresol from amino acid tyrosine in proteins
50-100 mg per day in the healthy adult urine
Level increases with increase in protein in the diet
Decreases when bran added to the diet – bran acts as
energy source for bacteria that use tyrosine to build
bacterial protein
47
Fate of Microbial Products
 Products of microbial activity normally cleared in
the liver and excreted in the urine without
adverse effects
 Scientific data about the fate of many byproducts of microbial metabolism is presently
lacking in many cases
 There is suspicion that in sensitive individuals
some “psychological disturbances” following
ingestion of certain food materials might be
caused by these microbial by-products
48
Protection Against Invading
Pathogens
 Because of its ideal environment, the large bowel
may be the site of invasion by disease-causing
microorganisms
 Various factors protect against this:
 Resident microflora protect their own space
 SCFAs act as antagonists to many pathogenic microorganisms:




Salmonella
Shigella (dysentery)
Vibrio (cholera)
E.coli (enteritis)
49
Invading Pathogens
 Antibiotics taken by mouth kill off many of the
resident species
 Less SCFAs are produced
 pH rises
 Pathogens can now invade and colonize more
readily
 Takes time for the resident micro-flora to reestablish
 Symptoms of irritable bowel syndrome not
uncommon following enteric infections
50
Protection Against Invading
Pathogens
 Diarrheal diseases also decrease SCFAs
 Microbial infection
 Lactose intolerance
 Magnesium-based laxatives
 Fibre increases level of SCFAs because bacteria
that produce them also use fibre as a substrate,
which increases bacterial numbers
51
GAS
 Fermentation always leads to production of
various types of gases
 80% of the gas from fermentation is released as
flatus
 20% is absorbed into the body and excreted in
breath
 Volume of gas depends on composition of diet:
from 0.5 to 4 litres per day in the adult human
52
Gas
 Healthy people pass flatus an average of 14 times
per day
 25 – 100 ml on each occasion
 Can rise to 168 ml per hour when >50% of the
diet is in the form of non-starch fibres and nonabsorbable sugars:




Beans
Whole grains
Some vegetables
Some fruits
53
Gases in Breath
 Principal gases in breath are:
 Hydrogen
 Carbon dioxide
 Small quantities:




Methanediol
Ethanediol
Ammonia
Hydrogen sulphide
 Occasionally
 Methane
 Type of gas depends on the presence of the
specific bacteria capable of producing it
54
Colonic Gases
 Some bacteria use gases for their metabolism:
 Hydrogen metabolized to:
 Methane
 Hydrogen sulphide
 Acetate
 These may be:
 utilized by micro-organisms
 excreted as flatus
 passed into circulation and breath
 Amount of hydrogen even from the same amount
of substrate is not constant: it depends on:
 Type of micro-organisms present
 Speed of fermentation
 Utilization by other micro-organisms
55
Hydrogen Breath Test for Lactose
Intolerance
 Results of hydrogen breath test used in the
diagnosis of lactose intolerance varies depending
on type of micro-organisms in the bowel
 Rationale for test:
 If lactose is not digested by brush-border lactase, it
passes into the large bowel
 Here it will be fermented by the resident microorganisms, with the production of hydrogen
 The hydrogen is absorbed, taken in blood to the lungs
where it is excreted
 Amount of hydrogen collected from breath is measured
and used as an indication of the degree of lactase
deficiency
56
Methane
 Methane-producing bacteria convert hydrogen to
methane
 30-50% of healthy adults have methane-producing
bacteria in their colon
 Gas is excreted in the breath
 Not detectable in children under the age of two years
 In methane-producers, adult level of methane reached
by age 10 years
 Tends to be familial
 Methane production does not vary with diet
 May be associated with:
 large bowel cancer
 intestinal polyps
 ulcerative colitis
57
Hydrogen Sulphide
 Sulphate-reducing bacteria in the colon convert
hydrogen to hydrogen sulphide
 Methane-producing and sulphide-producing
bacteria compete for hydrogen in the colon
 When the diet is high in foods that contain
sulphates, hydrogen-sulphide producing bacteria
have an advantage
 Another source of sulphate is body secretions
such as mucins that contain sulphated
glycoproteins
58
Sulphate-Containing Foods
 Sulphates may occur naturally:
 Some fruits
 Some vegetables
 Sulphates may be used as clarifying agents and
stabilizers in manufactured foods, such as:









Cheeses
Egg products
Pickles
Candied and glazed fruit
Flours; breads; cereals; pastas
Sugars
Wine; beers
Nutritional supplements
Laxatives; homeopathic remedies; medications
59
Acetate
 If methane-producing and sulphide-producing
bacteria are absent, bacteria may convert
hydrogen and carbon dioxide to acetate
 The extent to which this occurs is unknown
 Acetate may be used by the body as a source of
energy in certain metabolic processes
 The type of gases excreted as flatus or in breath
depends more on the species of micro-organisms
colonising the bowel than on the composition of
the diet
 Components of the diet determine the amount of
gas produced
60
Vitamins Produced by Bacteria
 Bacteria not only break down food material
(catabolism), they synthesise nutrients
(anabolism) from these building blocks
 Vitamin K
 Required in blood clotting
 Menaquinone component of the vitamin is derived
from bacterial action on vegetable material mostly in
the ileum from where it is absorbed
 Taken to the liver, where it is complexed with
prothrombin
61
Vitamins Produced by Bacteria
 Vitamin B12
 Made solely by micro-organisms in ruminant digestive
tract
 Absorbed through small intestine
 Passes into meat and milk of the animals
 Human bacteria (Pseudomonas and Klebsiella) also
synthesise B12
 5 mcg excreted in feces daily
 Site of synthesis in humans is large bowel but
absorption from here is poor
 Some people have micro-organisms capable of
synthesising B12 in the small intestine
62
Vitamins Produced by Bacteria
 Biotin
 Synthesised by bacteria in animals and humans
 Absorbed in lower ileum
 Antibiotics can reduce biotin levels in urine, indicating
significant reduction in biotin synthesis when bacteria
are killed
 Folic acid
 Thiamine
 Produced by bacteria, especially in the large bowel
 Amount absorbed is inadequate alone, and the
vitamins must be provided in food to avoid deficiency
63
Changing the Microbial Flora of the
Bowel
 Diet has very little influence on the types of
micro-organisms that colonise the digestive tract
 Attempts to alter the gut microflora by direct
dietary manipulation tend to be frustrating
 Differences in types and numbers in the bowel of
one individual compared to another in the same
community, eating the same diet
 Microflora can be changed by use of oral
antibiotics
 Microflora tends to return to pre-antibiotic types
over time
64
Probiotics
 Food supplement containing live bacterial
culture
 Trials in disease situations such as :
 Diarrheal diseases
 Re-establishment of normal flora after antibiotic
therapy
 Inflammatory bowel diseases
 Fungal disease (e.g. candidiasis)
 Cancers
 Cholesterol lowering
65
Probiotics
 Examples of bacteria:
 Lactobacilli
 Bifidobacteria
 Examples of food supplements containing live
culture:







Yogurts
Fermented milks
Fortified fruit juice
Powders
Capsules
Tablets
Sprays
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Prebiotics
 Non-digestible food ingredients that selectively
stimulate a limited number of bacteria, to
improve health
 Examples:
 Fructo-oligosaccharides
 Lactulose
 Galacto-oligosaccharides
 Provided in:




Beverages and fermented milks
Health drinks and spreads
Cereals, confectionery, cakes
Food supplements
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Synbiotics
 Combine prebiotics and probiotics
 Prebiotic substrate should enhance survival of
probiotic bacteria
 Example:
 Bifidobacteria + fructo-oligosaccharide
 In order to establish the new species, need to
continue to provide live culture, and appropriate
substrate
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