1. The gastrointestinal tract contains over 100 trillion microorganisms that play an important role in human health and disease. The microflora composition varies along the GI tract and is influenced by factors like age, diet, pH, and antibiotic use. 2. Common commensal bacteria in the mouth include streptococci and anaerobes like fusobacteria, while the stomach typically contains lactobacilli and streptococci due to its acidic environment. The small intestine contains fewer bacteria than the colon. 3. The colon harbors over 500 bacterial species, predominantly anaerobic bacteroides, bifidobacteria, and clostridia. This dense microflora aids nutrient absorption and maturation of

1. Microbiology of the
Gastrointestinal Tract
Dr. Eskindir Molla GSR1
Moderator
Dr. Henok Seifu (Consultant Hepatobilliary and
General surgeon)

2. Outline of the presentation
• Introduction
• Factors determining the distribution of GI microflora
• Distribution of microorganisms by specific anatomic region
• Clinical significance of MO in the GI tract
• Special disease entities,
• Antibiotic use and the MO
• Bowel Preparation
• Summary
• References

3. Introduction
• Microorganism is a broad term encompassing organism of
microscopic or ultramicroscopic size including bacterias, viruses and
fungi.
• Normal floras are organisms living on the hosts skin or mucosal
surface of a healthy individual.
• There are 2 classes of GI Microflora
Allocthonus (transient)
Autocthonus (indigenous)

4. Metabolism of bacteria

5. Host – Microorganism relation ship types
• Host is the organism that microorganisms colonize
• Symbiosis is an intimate, long-term, and specific association
between organisms of two or more species. There are three
types
1. Mutualism:- a symbiosis beneficial to both partners
2. Parasitism:- a relationship harmful to one partner
3. Commensalism is beneficial to one partner and largely
neutral for the other

6. Introduction
• The normal flora outnumber human cells 100 to 1000:1
• The GI tract holds on most share of these
• Normal floras are the microorganisms that live on another
living organism (human or animal) without causing disease

7.  Factors determining the distribution of GI microflora
Mode of delivery
Age
Diet
PH
Constipation
• Nutrition
• Redox potential
• Bacterial antagonism
• Bacterial adhesion
• Antibiotic use
• Sexual practice

9. Factors determining …
• Infants who are breast fed have more lactobacillus and
Bifidobacterium in the GI tract than those of formula fed.
• People who consume meat frequently have more Bacteroides their
stools than those on a predominantly vegetable or fish diet

10. Distribution of microorganisms by specific
anatomic region
• Normal floras in the mouth
The warm and moist environment of the mouth is ideal for microorganism
harboring and multiplication
Gingival crevices and crypts in various location of the mouth creates ideal
environment for anaerobic organisms.
Saliva usually contains a mixed flora of about 108 organisms per milliliter

11. Normal floras in the mouth
Both aerobes and anaerobes and also some fungi exist
Some of the anerobic bacterias are actinomyces, Arachnia,
Bacteriodes, Bifidobacterium, Eubacterium, Fusobacterium,
Lactobacillus, Leptotrichia, Peptococcus, Peptostreptococcus,
Propionibacterium, selenomonas, veillonella.

12. Normal floras …
• The facultative aerobic organisms common in mouth are Nisseria
species, streptococcus viridans, Moraxella and haemophilus species.
• In addition, there are also a number of fungi found in the oral cavity,
including: Candida, aspergillus, fusarium, penicillium and
cryptococcus.

13. Normal flora in the Esophagus and Stomach
• Esophagus has a mixed microflora of the mouth and stomach
• These organisms cause esophagitis rarely.
• The stomach has a unique acidic and lytic media that kills most of
mouth and esophagus’s microorganisms. The bacterial load is 103 to
106/g of contents
• But the stomach isn’t sterile.

14. • The common resilient organisms that survive in the stomach are
Lactobacillus and Streptococcus spp.
• H.pylori is the pathogenic bacteria there causing gastritis, PUD,
Maltoma and their complications.

15. Normal floras in the small intestine
• The anerobic organisms dominate again here. The terminal ileum
resembles that of the colon.
• Some of the organisms are Peptostreptococcus, Porphyromonas, and
Prevotella.
• In normal hosts the bacterial load of duodenum is (0 to 103/g of
contents).
• The ileum contains a moderately mixed flora (106 to 108/g of
contents).

16. Normal floras of the Large Bowel
• The flora of the large bowel is dense with a load of 109 to 1011/g of
contents
• 90% are anaerobes predominantly from genera Bacteroides,
Fusobacterium, Bifidobacterium, and Clostridium.
• facultative anerobic organisms like non pathogenic strains of
Escherichia coli and enterococci fecalis and enterococci feceum are
very common.

17. • The biliary tree, the pancreatic ducts are sterile.
• Any organism there is an infection.

18. Clinical significance of GI microflora
• Priming of the immune system:- study done on rats raised under
aseptic conditions feeding sterile foods showed poor humoral and
celluar immunity. Thus normal flora are responsible for maturing and
sensitizing the immune system.
• The GI normal flora prevents other pathogenic organisms from
colonizing the tract by competing for space and nutrition.

19. Clinical …
• Thiamine, folate, biotin, riboflavin, and panthothenic acid are water-
soluble vitamins are also synthesized by gut bacteria.
• vitamin A and k from and from fat soluble vitamins absorption and
synthesis is aided by bacteria.
• Aids synthesis of vitamins by fermentation‐based or enzymatic
biocatalytic processes.

20. Causative Agents for Diarrhea

21. Clinical …

22. Surgically relevant microflora
Helicobacter Pylori
Gram negative spiral bacteria with flagella
is microaerophilic bacteria with catalase, oxidase and urease enzymes.
Can survive in the acidic medium of the stomach because of the
following virulence factors

23. Surgically ...
• Urease (urea amidohydrolase) catalyzes the hydrolysis of urea to yield
ammonia and carbon dioxide
• hydrolyzes gastric luminal urea to ammonia that helps it neutralize
gastric acid and form a protective cloud around the organism,
• attaches to gastric epithelial cells by means of specific receptor-
mediated adhesion on receptors on epithelial cell

24. • H. pylori then attaches to gastric epithelial cells by means of specific
receptor-mediated adhesion Although attachment is dependent upon
binding of bacterial surface adhesins to specific epithelial cell
receptors

25. • Causes inflammation and ulcer by Colonization which always leads to
infiltration of the gastric mucosa in both antrum and corpus with
neutrophilic and mononuclear cells causing gastritis and ulcer.
• Also when the organism maintains direct contact with the endothelial
cells inciting inflammation.
• It causes acute and chronic gastritis, PUD with its all complications
and incriminated to cause gastric cancer.

26. • It causes acute and chronic gastritis, PUD with its all complications
and incriminated to cause gastric cancer.

27. Tuberculuos Enteritis
• Both M. tuberculosis and M. Bovis are incriminated for
the disease.
• The route of infection is
a. Swallowing infected sputum
b. Hematogenous spread from active pulmonary or
miliary TB
c. Ingestion of contaminated milk or food
d. Contiguous spread from adjacent organs

28. Tuberculuos …
• The ileocecal junction is the commonly affected area.
• Manifestations are broadly divided to 3 major groups
1. Ulcerative:- the commonest one
2. Hypertrophic includes scarring, fibrosis, and
pseudotumor lesions. Commonly causes intestinal
obstruction.
3. Ulcero-hypertrophic the overlapping of the above two

29. Tuberculuos …
The symptom complex of TB are also part of the
presentation.
Commonest differential to to Chron’s disease.

30. Intra-abdominal Infections
Hepatic Abscesses: broadly there are two sources of infections
a. Pylephlebitis due to neglected appendicitis and diverticulitis
Common in previous years now decreasing
b. Infections of the biliary tract and manipulation of the biliary tract
Commenest cause now.
Commonly incriminated aerobic organisms are E coli, K pneumoniae,
enterococci, and Pseudomonas spp.,
anaerobic bacteria are Bacteroides spp and Fusobacterium spp.

31. Intra-abdominal Infections
• Microbial contamination of the peritoneal cavity is termed peritonitis or intra-
abdominal infection
Primary peritonitis:- occurs when microbes
invade the peritoneal cavity via hematogenous dissemination from a distant
source of infection
• Common in patients with ascitis
These infections invariably are monomicrobial
Incriminated organisms are E coli, K pneumoniae, andS pneumoniae
•

32. Secondary peritonitis occurs due to perforation or severe inflammation
and infection of an intra-abdominal organ.
Examples include appendicitis, perforation of any portion of the
gastrointestinal tract, or diverticulitis
• E faecalis and faecium, S epidermidis, C albicans, and P aeruginosa
commonly are identified

33. Tertiary(persistent) peritonitis
• common in immunosuppressed patients
• Inability to clear the organisms of secondary peritonitis after
receiving appropriate treatment
• Incriminated organisms are E faecalis and faecium, S epidermidis, C
albicans, andP. aeruginosa

34. Antibiotics and the GI microflora
• Each species of GI microflora are in equilibrium with each other.
• Irrational and aggressive use of antibiotics can wipe out the normal
flora and lead to colonization by pathogenic organisms or disturbance
of the equilibrium.
• For instance antibiotic use result in candidiasis of the mouth, vagina
and anus because it creates proliferation of C.Albicans which is a
normal flora but in small quantity.
• The same holds true for clostridium defficile.

35. Antibiotics and …
• For instance antibiotic use result in candidiasis of the mouth, vagina
and anus because it creates proliferation of C.Albicans which is a
normal flora but in small quantity.
• The same holds true for clostridium defficile.
• Clostridium difficile causes diarrhea and a more severe syndrome of
pseudomembrane colitis

37. Bowel Preparation
• Aim is to reduce bacterial load of the colon in colon surgery so that
post op infection can be reduced
• has an additional benefit of easily manipulated colon and avoidance
of stool column if anastomosis is to be done
• But now an area of controversy
• Broadly of 3 types

38. a. Mechanical bowel preparation
• Use of catheritics like PEG, magnesium citrate, or castor oil
• Patients are ordered to take large amount of fluid in order to have
good effect
• Can cause fluid and electrolyte disturbance

39. b. antibiotics
• Using broad spectrum po antibiotics covering both aerobes and
anaerobes
• Usually neomycin and metronidazole are prescribed the night before
surgery

41. c. Cleansing enema
sodium phosphate, glycerin, or saline solutions.
low-residue liquid supplements/meals

42. References
• Sherris Medical Microbiology, 7th edition
• Schwartz principles of Surgery, 11th edition
• Uptodate, 2018