Brief description of human commensals and pathogens

1. Commensal & Pathogenic Microbiota of Human body
MEHER RIZVI
Associate Professor
Department of Microbiology and Immunology
• Microbiome - collective genomes of all the microorganisms
(bacteria, fungi and viruses) that reside in a person, literally share our
body space

2. Objectives
Describe the distinction between colonization & disease
Illustrate common commensal flora
Discuss factors which regulate microbial colonizing flora
Describe distinction between strict pathogens and opportunist
pathogens

3. Figure 14.2
Normal Microbiota and the Host
• Human body is
built by 10
trillion cells
• 100 trillion non-
pathogenic
bacteria/microorga
nisms that reside
in or on a human
body
• Human body/Commensal microbiota exist as a community
There are millions of microbes per square inch
Of human body.

4. Microbiome and human body environment
• Microbial community vary at different body sites on the same person (different ecosystem)
• Bacteria of a specific body site from different persons have more common characteristic (common
ecosystem).
• The microbiome of a healthy and diseased person looks very different (rearranged ecosystem)

5. The following sites are “hotspots” for microbial life
Some microbes are native,
normally found in the body:
Resident Flora
Some microbes are introduced,
suddenly arriving at a new
residence in the body: Transient
flora
There is a delicate balance
of microbes that are
maintained to keep that
environment healthy.
Weakened immune
systems can throw off that
balance and allow the
wrong microbes to grow
out of control.

6. Microbiome-Our Friend
• Gut microbiome
• Produce hydrolytic enzymes - help our digestive system
• Synthesize vitamins – K, B2, B12 and folic acid
Compete for the nutrients: Competitive inhibition
• Skin and gut microbiome
• Modulates our innate and adaptive immunity
• Prevents growth of pathogens
• Produce antimicrobial substances
• Compete for the nutrients

7. Microbiome
(bacterial
Phenotype)
Individual
genetic
material
What we eat
(diet)
Homeostasis
Health
Perturbation Diseases
What is a healthy Microbiome?
One size does NOT fit all - Each person’s microbiome is unique
-------------------------------------------------------
Low risk of allergies
Infection resistance
Allergies
Metabolic syndrome
Obesity
Infections
Who we are ?

9. Sterile Sites:
Blood
Brain
Bladder
Internal tissues normally sterile
Lung
Liver
Spleen
Media needed:
Enriched:
Blood agar
Chocolate agar

10. Skin
There are several skin
environments: oily, dry, moist.
Some microbes prefer one over
another.
The skin has natural defenses
including slightly acidic sweat and
antimicrobial peptides.
Microbes hide in crevices to
recolonize skin after washing with
soap
Antibiotic washes and oral
antibiotics disturb normal balance
of microbes on the skin
There is a normal balance of microbes on the skin that protect introduced microbes from harming us. Damaged skin gives
opportunities for microbes to invade the bloodstream and cause serious illness.

11. Normal flora – Skin
• Anatomic sites: an ecosystem composed of 1.8 m2 of diverse habitats
Sterile at birth
• Commensals get established within minutes of birth
Commensals:
Staphylococci
Coryneforms
Micrococci
Anaerobes
Pathogens:
Streptococcus pyogenes
Staphylococcus aureus
Media:
Blood agar

12. Upper respiratory tract

13. Nasal cavity
The interior lining of the nose contains mucous secreting glands.
A wide variety of microbes are normally found there.
• Staphylococcus epidermidis bacteria forms a biofilm that coats the mucosal
lining
• Staphylococcus aureus bacteria is kept under control by a protease found in S.
epidermidis.
• If microbiota disturbed, S. aureus can become pathogenic and cause infection
The nose is a primary defender against inhaled pathogens
Cilia and mucous lining trap inhaled microbes

14. Oral Cavity
A wide variety of
microbes regularly
enter the oral
cavity
Saliva, pH, temperature,
immune system prevent
many species from
surviving
Oral antibiotics inhibit growth: Essential before tooth extraction
Brushing and flossing teeth clears some built up biofilm:
Brushing can lead to bacteremia
Dental extraction: Excessive bacteremia which can lead to subacute
bacterial endocarditis in people with congenital heart disease
Bacterial biofilm forms on teeth, gums, buccal cavity.

15. Normal flora – Upper Respiratory Tract
• Anatomic sites: Mouth, oropharynx and nasopharynx:
Sterile at birth
• Commensals get established within 4-12 hrs
Commensals:
Streptococcus viridans
Coag. neg Staphylococcus
Commensal Neisseria spp
Coryneforms
Anaerobes
Streptococcus pneumoniae
Pathogens
Throat
Streptococcus pyogenes:
pharyngitis
C. diphtheriae: Diphtheria
Bordetella pertussis: Whooping
cough
Nasal cavity:
Staphylococcus aureus
Streptococcus pneumoniae
Media:
Blood agar
Selective media:
Potassium tellurite BA
Crystal violet BA

16. Normal flora – Eye (Conjunctiva)
• Protective mechanisms:
• Blinking mechanically removes bacteria
• Lachrymal secretions include lysozyme
Commensals
Coagulase negative
Staphylococci
Coryneforms
Pathogens
Chlamydia trachomatis
S. aureus
P. aeruginosa

17. Normal flora – Ear
Protective mechanisms: Ear wax- traps and throws out bacteria
Commensals
Staphylococci
Coryneforms
alpha hemolytic
Streptococci
Pathogens: Middle ear
Streptococcus pneumoniae
Haemophilus influenzae
Moraxella catarrhalis
Pathogen: Outer ear
Pseudomonas spp

18. Normal flora – Lower Respiratory Tract
Anatomic sites: Trachea, bronchi, alveoli:
Sterile
Defence mechanism:
Efficient cleansing action of the ciliated epithelium-Bacteria reaching the lower
respiratory tract swept upward by the action of the mucociliary blanket.Removed
by coughing, sneezing, swallowing, etc.
Pathogens
Streptococcus pneumoniae
Haemophilus influenzae
Media
Enriched media:
Chocolate agar
Blood agar

19. Human Gut
Major barriers for microbes entering the gut:
• low pH
• Saliva and Bile
• Immune system
• Finding a place to attach to intestinal wall
• Surviving a widely varied diet
For those microbes that manage to colonize the gut:
• gut flora perform regular tasks of digestion, vitamin production, many others
• Gene transfer between the myriad of species in the gut can generate new combinations of drug
resistant “superbugs”

20. Normal flora –Gastro-intestinal Tract
Anatomic sites: Oesophagus, stomach, jejunum, ileum, colon, rectum:
Sterile at birth. Commensals get established within 4-12 hrs
Commensals:
Anaerobes
Enterobacteriaceae
Pseudomonas spp
Pathogens:
Vibrio cholera
Salmonella spp
Shigella spp
Media:
Selective media
XLD

21. Urogenital Tract
Urinary system almost
sterile due to urea and other
chemicals
Urine often flushes out
microbes that find their
way in
Introducing a catheter into the
urethra can introduce microbes
directly into the bladder, where a
biofilm can grow and cause bladder
infection
The vagina has a low pH due to Lactobacillus secreting lactic acid and hydrogen peroxide.

22. Normal flora – Urinary tract
Upper urinary tract (kidneys, ureters, bladder) : sterile
Distal urethra harbours commensals
Commensals: Urethra
• Enterobacteriaceae
• coagulase negative Staphylococci
• Streptococci
• Anaerobes Bladder (Cystitis)
Pathogens:
Escherichia coli
Klebsiella pneumonia
Staphylococcus saprophyticus
Pseudomonas aeruginosa
Urethritis
Pathogen:
N. gonorrhoeae
Media:
Differential medium
CLED

23. Normal flora - Genital tract
• All parts of genital tract are sterile except vagina
Vagina: Commensals
Lactobacilli
Pathogens
Neisseria gonorrhoeae
Chlamydia trachomatis
Treponema pallidum
Media
Selective media:
NY city media for N.
gonorrhoeae

24. Urogenital
Lactobacillus and vaginal epithelial cell
Lactobacillus normally
maintain low pH while
other species are kept in
small numbers in the
vagina
If Lactobacillus
decreases from
antibiotics…
Candida albicans can
take over and cause a
yeast infection
G. vaginalis and vaginal epithelial cell
Gardnerella vaginalis can grow
too much and cause bacterial
vaginosis.

25. Interplay Between Medicine and
Microbes
Antibiotics
Kills infectious bacteria but also disrupts natural flora.
Can result in yeast infections, digestive problems, etc.
Chemotherapy drugs
Gut flora has been shown to modify some drugs during
metabolism. This causes many side effects, including
upset stomach.

26. Use of Antimicrobial Products
How many do we really need?
Products kill germs to
reduce infection
But do we need some natural
exposure to germs to keep our
normal flora around?
Will this allow “superbugs” to grow
and become more prevalent…causing
problems for the future?

27. How to take care of our “second genome”
• We are what we eat
• Probiotics – application of life microbial culture
• Typically lactic acid producing bacteria ingested to
aid digestion and protect intestine from pathogens
• Prebiotics - refer to chemicals that induce the
growth and/or activity of commensal
microorganisms