Normal-Human-Microbiota.

1. Normal Human Microbiota

2. Learning objectives
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At the end of the session, the students will be able to understand:
▰ Microbiology of Normal Flora
▰ Role of Normal Microbiota, its beneficial and harmful effects
▰ Probiotics
▰ Prebiotics
Essentials of Medical Microbiology

3. INTRODUCTION
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▰ Normal microbial flora ( “indigenous microbiota”) refers to the diverse group
of microbial population that every human being harbors on his/her skin and
mucous membranes.
▰ In humans - normal flora is located in various sites – GIT, respiratory tract,
genitourinary tract and skin
▰ Two categories: resident flora and transient flora.
Essentials of Medical Microbiology

4. Resident Flora
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▰ Life-long members of the body’s normal microbial community.
▰ Very closely associated with a particular area.
▰ When disturbed, they again re-establish themselves.
▰ Example - Escherichia coli is a resident flora of the intestine - they do not
cause harm; rather they have beneficiary effect on the host.
Essentials of Medical Microbiology

5. Transient Flora
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▰ Inhabit the body surface or mucous membranes temporarily for a short
interval.
▰ Transient flora do not produce disease as long as the resident flora remains
intact.
▰ If the resident flora gets disturbed due to any reasons, transient flora may
colonize and produce disease, e.g. pneumococcus and meningococcus in
nasopharynx. Essentials of Medical Microbiology

6. Transient Flora (Cont..)
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▰ In hospitals, patients may acquire many resistant organisms as transient flora
from the HCWs and hospital environment.
▰ For examples, MRSA (Methicillin-resistant Staphylococcus aureus) in nose and
skin, MDROs such as Klebsiella, Escherichia coli, Pseudomonas, Acinetobacter
in respiratory tract
Essentials of Medical Microbiology

7. Transient Flora (Cont..)
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▰ In contrast to resident flora, they can be easily eliminated from the body
surface by following proper hand hygiene and other infection control
practices.
Essentials of Medical Microbiology

8. MICROBIOLOGY OF NORMAL
FLORA
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Essentials of Medical Microbiology

9. MICROBIOLOGY OF NORMAL FLORA
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▰ Humans acquire the normal flora soon after the birth and then continue to
harbor until death.
▰ The presence of the normal microbial flora in a given body site depends upon
various factors such as: Local temperature, moisture, pH, environmental flora
(hospital or community), immunity, and anatomical site (skin or mucosa.)
Essentials of Medical Microbiology

10. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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▰ Most of the normal flora predominantly contain bacteria and to a less extent
some fungi and parasites.
▰ The existence of viruses as normal flora is recently gained importance.
Essentials of Medical Microbiology

11. Human Viral Microbiota
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▰ Human viral microbiota or virome is the collection of viruses in and on the
human body.
▰ Viruses may get integrated into the human genome as proviruses.
▰ Every human being has a unique virome, which may get affected by age, life
style, diet, pre-existing immunity, geographic location and seasonal variation.
Essentials of Medical Microbiology

12. Human Viral Microbiota (Cont..)
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▰ With the advancement of deep sequencing technique, it is now possible to
gather information of human viral microbiota.
▰ Many viruses colonize the human skin, called as skin virome.
▰ Examples - human papillomavirus and bacteriophages that infect the
commensal skin bacteria such as staphylococci.
Essentials of Medical Microbiology

13. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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Essentials of Medical Microbiology
Anatomical site Total
bacteria/ g or
mL
Anaerobic/
aerobic ratio
Anaerobic normal
bacterial flora
(common)
Aerobicnormalbacterialflora,commensal
fungiandparasites
Mouth Predominant Less predominant
Saliva 108 – 109 1:1  Anaerobic cocci
 Actinomyces
 Fusobacterium
 Bifidobacterium
 Prevotella
 Spirochetes
Viridans
streptococci
Commensal parasites in
oral cavity
 Trichomonas tenax
 Entamoeba gingivalis
Tooth surface 1010–1011 1:1
Gingiva 1011–1012 103:1

14. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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Essentials of Medical Microbiology
Anatomical
site
Total
bacteria/ g
or mL
Anaerobic/
aerobic
ratio
Anaerobic normal
bacterial flora
(common)
Aerobicnormalbacterialflora,commensalfungia
ndparasites
Nasopharynx Predominant Less predominant
Saliva  Prevotella species
 Anaerobic cocci
 Fusobacterium
 Streptococci (α
and non-
hemolytic)
 Neisseria (non-
pathogenic
species)
 Diphtheroids
 Staphylococcus
epidermidis
 Haemophilus
 Meningococcus
 Pneumococcus
 Staphylococcus
aureus
 Gram-negative rods
 Yeasts
Tooth surface
Gingiva

15. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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Essentials of Medical Microbiology
Anatomical
site
Total
bacteria/
g or mL
Anaerobic/
aerobic ratio
Anaerobic normal
bacterial flora
(common)
Aerobicnormalbacterialflora,commensalfungiand
parasites
Gastrointestinal tract Predominant Less predominant
Stomach 0–105 1:1 Lactobacillus Helicobacter pylori
Jejunum/ileum 104–107 1:1  Anaerobic cocci
 Bacteroides
fragilis
 Fusobacterium
 Bifidobacterium
 Prevotella
 Clostridium
 Enterobacteriacea
e and other gram-
negative rods
 Enterococci
 Streptococci (α
and non
hemolytic),
 S. agalactiae
Diphtheroids
Candida albicans and other
yeasts
Staphylococcus aureus
Commensal Entamoeba
species
Commensal intestinal
flagellates
Terminal
ileum and
colon
1011–1012 103:1

16. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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Essentials of Medical Microbiology
Anatomical
site
Total
bacteria/
g or mL
Anaerobi
c/
aerobic
ratio
Anaerobic normal
bacterial flora
(common)
Aerobicnormalbacterialflora,commensalfungiandpa
rasites
Female genital tract Predominant Less predominant
Vagina
107–109 10:1
 Anaerobic cocci
 Lactobacillus
 Prevotella
 Bifidobacterium
 Clostridium
 Corynebacterium
species
 Lactobacillus species
 Streptococci (α, non-
hemolytic and
 S. agalactiae)
 Neisseria (non-
pathogenic species
 Enterococci
 Enterobacteriaceae
and other gram-
negative rods
 S. epidermidis
 Candida species

17. MICROBIOLOGY OF NORMAL FLORA (Cont..)
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Essentials of Medical Microbiology
Anatomical
site
Total
bacteria/
g or mL
Anaerobic/
aerobic ratio
Anaerobic normal
bacterial flora
(common)
Aerobicnormalbacterialflora,commensalfungiandpa
rasites
Skin Predominant Less predominant
102–103 3:2
 Propionibacterium
 Anaerobic cocci
 Staphylococcus
epidermidis
 Diphtheroids
 Micrococcus species
 Neisseria (Non-
pathogenic species)
 Streptococci (α and
non hemolytic)
 Staphylococcus aureus
 Candida species
 Acinetobacter species

18. ROLE OF NORMAL FLORA
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Essentials of Medical Microbiology

19. ROLE OF NORMAL FLORA
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Various microorganisms present in the normal flora have different relationship
with the host.
▰ They may have beneficiary effect on the host
▰ They may be harmful to the host
▰ They may exist as commensals
Essentials of Medical Microbiology

20. Beneficial Effects
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▰ Prevent colonization of pathogen:
▰ Synthesize vitamin
▰ Waste produced antagonize other bacteria
▰ Immune stimulation
▰ Prevent allergic diseases (Hygiene hypothesis)
▰ Complement activation
Essentials of Medical Microbiology

21. Beneficial Effects (Cont..)
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Essentials of Medical Microbiology

22. Disturbed Normal Flora Promote Infection
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▰ Injudicious use of broad spectrum antimicrobial agent
▰ Host factors such as immune suppression, reduced peristalsis may promote
the pathogen to grow.
▰ Physical destruction of the normal flora: by irradiations, chemicals, burns, etc.
▰ If the inoculum size of the entering pathogen is high then it can dominate over
the normal flora.
▰ Minor trauma
Essentials of Medical Microbiology

23. Harmful Effects
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May be agents of disease:
▰ Members of the normal flora may cause various endogenous disease.
▰ When the host immunity is lowered, the transient flora may invade and
produce disease, e.g. gram -negative organisms (E. coli) colonizing the
respiratory tract can cause pneumonia.
Essentials of Medical Microbiology

24. Harmful Effects (Cont..)
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May be agents of disease (Cont..):
▰ If they enter a wrong site or tissue (e.g. blood, sterile body cavities)—then
even the resident flora can produce disease.
Essentials of Medical Microbiology

25. Harmful Effects (Cont..)
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▰ Transfer to susceptible hosts: Some pathogens of humans that are members
of the normal flora for one host can produce disease if transferred to the
other host.
▰ Bacterial synergism
▰ Contribute to the drug resistance of pathogens
▰ Competition for host nutrients
Essentials of Medical Microbiology

26. Diseases produced by normal flora
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Essentials of Medical Microbiology
Diseases produced by normal flora Anatomicalsitefromwhichthe flora
istransferred
Urogenital infections including UTI Intestinal flora such as Escherichia
coli, Klebsiella, Proteus
Endocarditis Oral flora (Viridans streptococci)
Dental caries and periodontal disease Oral flora (Streptococcus
mutans)
Peritonitis, abdominal infection Intestinal flora
Pneumonia Transient respiratory flora
Septicemia From any site

27. Probiotics
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▰ Probiotics” is defined as the live microorganisms (part of normal flora) which,
when administered in adequate amounts, confer a health benefit to the host.
▰ They are extremely useful in the conditions where the normal intestinal flora is
suppressed.
Essentials of Medical Microbiology

28. Probiotics (Cont..)
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▰ Probiotics are commercially available in the form of capsule or sachet,
consisting of mixture of some important beneficiary bacteria and yeast of
human intestinal flora such as Bifidobacterium, Lactobacillus, Saccharomyces,
etc.
Essentials of Medical Microbiology

29. Beneficiary effects of probiotics
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▰ To treat various forms of GIT conditions like:
 Gastroenteritis due to any cause
 Antibiotic-associated diarrhea
 Lactose intolerance
 Irritable bowel syndrome and colitis
 Necrotizing enterocolitis
 Helicobacter pylori infection
Essentials of Medical Microbiology

30. Beneficiary effects of probiotics (Cont..)
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▰ Reducing serum cholesterol level by breaking down bile in the gut - inhibiting
its reabsorption.
▰ Reducing blood pressure (by producing ACE inhibitorlike peptides during
fermentation).
▰ Immune function restoration and preventing infections.
▰ Bacterial vaginosis (restoring the acid pH of vagina by lactic acid producing
bacteria). Essentials of Medical Microbiology

31. Prebiotics
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▰ Prebiotics are the dietary nondigestible fibers which when administered,
stimulate the growth and activity of commensal microorganisms and thereby
exert beneficiary effect to the host indirectly.
Essentials of Medical Microbiology

32. Questions:
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▰ Q1. The most common commensal in human intestine is:
a. Bacteroides fragilis
b. Escherichia coli
c. Klebsiella pneumoniae
d. Lactobacillus
Essentials of Medical Microbiology

33. Questions:
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▰ Q2. Which of the following is not a component of commercially available as
probiotics:
a. Bifidobacterium
b. Lactobacillus
c. Bacteroides fragilis
d. Saccharomyces
Essentials of Medical Microbiology

34. Questions:
34
▰ Q3. Which of the following is not a commensal in human female genital tract:
a. Lactobacillus
b. Streptococcus agalectiae
c. Neisseria
d. Trichomonas vaginalis
Essentials of Medical Microbiology