The World Within

Micro-organisms in the Digestive Tract:Friends, Foes, and Visitors

Janice M. Joneja, Ph.D 2002

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TheInternal Landscape

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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

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Digestive Enzymes

Stomach:Acid hydrolysisGastric pepsins

Mouth:Salivary -amylaseLingual lipase

Small intestine:Pancreatic-amylaseLipaseColipaseTrypsinChymotrypsinElastaseCarboxypeptidases

Small intestine:Gall bladder:Bile salts

Small intestine:Brush border:Lactase (ß galactosidase)Glucoamylase (-glucosidase)Sucrase-isomaltaseAmino-oligopeptidasesDipeptidyl-peptidaseLarge bowel

Microbial metabolism

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Microbial Colonisation

Mouth:SalivaMicrobial colonisation

Esophagus:Micro-organisms present

StomachHigh acidityUsually sterile

Small intestineNeutral or slightly alkalineNo resident microbial populationMicro-organisms populate lower ileum

Large bowelDense microbial populationMostly anaerobic organisms

RectumFaecesDense microbial population

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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 micro-organisms Survival of the fittest

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Colonisation by MicroorganismsThe 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

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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

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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

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Micro-organisms in the Stomach

Low acidity (higher pH) allows some micro-organisms 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

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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

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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

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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

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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)

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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

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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

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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

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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

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Micro-organisms in the Large BowelInter-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

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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

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Micro-organisms in the Large BowelNutrient 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

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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 micro-organisms)

…………………...……….3-4 grams

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Carbohydrates

Dietary fibre Structural parts of plants Have beta-glycosidic linkages between

molecules Indigestible by human enzymes

Includes: Pectin Cellulose Gums Beta-glucans Fructans

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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

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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)

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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

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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

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Comparison of Dietary Starch

A comparison of dietary starch:a) Fedb) Recovered after digestion in the small intestine

Food StarchFed(grams)

StarchRecovered(grams)

PercentageStarchRecovered(%)

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

454747

4.5 5.8 3.6

312 8

Englyst and Kingman 1994

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 ammonia-

utilizing bacteria, which is thought to reduce the risk of colon cancer

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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

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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

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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

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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 by-products 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

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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

micro-organisms: Salmonella Shigella (dysentery) Vibrio (cholera) E.coli (enteritis)

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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 re-establish

Symptoms of irritable bowel syndrome not uncommon following enteric infections

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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

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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

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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 non-absorbable sugars: Beans Whole grains Some vegetables Some fruits

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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

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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

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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 micro-

organisms, 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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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