Joel Manyahi

Microbial ecology
Microbial ecology = The study of interactions
between microorganisms and their environment
(chemical, physical, and biological environment!)
Normal Flora
Community of microbes
that live in and on
individual; can vary
substantially between
environmental sites and
host niches in health and
diseases
Bacterial cell: human, 10:1
Bacterial 300 fold more
protein genes
The Three Types of Symbiotic
Relationships

Table 14.1
Normal Microbial Flora
1. Resident Flora
Microbes that are always present

2. Transient Flora

Microbes that live in or on your body for a period of time
(hours, days, weeks, months) then move on or die off
Transient Microbiota
Remain in the body for only hours to
months before disappearing

Found in the same regions as resident

microbiota

Cannot persist in the body…because…

Competition from other microorganisms
Elimination by the body’s defenses cells
Chemical or physical changes in the body
 Normal Flora
Sterile tissues
In a healthy human, the
internal tissues such as:
 blood
 brain
 muscle
 cerbrospinal fluid (csf.)
are normally free of
microorganisms.
Non

sterile site
Skin
 Eyes (i.e.Cunjunctiva)
 Nose (i.e. Respiratory
tract)
 Mouth (i.e Human Oral
Cavity)
 Ears
 Urogenetal tract
 Elementry tract
 The organism
of the man is
occupied
•more than
500 species of
bacteria,
•about 50
species of
viruses,
•more than
20 species of
protozoa.

It is a huge zoological garden.

Host-microbes
Host
Provide place to colonize
Nutrients
Protection from immune system
Microbes
Provides needed metabolic functions
Stimulate innate and regulatory immunity
Prevent colonization
Normal flora
Composition of microbiota influenced by:
Personal hygiene
Diet
Water source
Medicines
Exposure to environment toxins
Initial Colonization of the Newborn
Uterus and contents are normally sterile
and remain so until just before birth
Breaking of fetal membrane exposes the
infant; all subsequent handling and feeding
continue to introduce what will be normal
flora

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Initial Colonization of the Newborn
 Importance of The Normal
Flora (Advantages)

1. They constitute a
protective host
defense mechanism
by occupying
ecological niches.
(Advantages)

2. They produce vitamin B

and vitamin K in
intestine.
Importance of The Normal Flora
(Advantages)

3. The oral flora

contribute to
immunity by inducing
low levels of
circulating and
secretory antibodies
that may cross react
with pathogens.
Importance of The Normal Flora
(Advantages)
4. The normal flora may
antagonize other
bacteria through the
production of
substances which inhibit
or kill nonindigenous
species.
Importance of The Normal Flora
(Disadvantages)
1. They can cause disease in
the following:
a) When individuals
become
immunocompromised.
b) When they change their
usual anatomic location.
Importance of The Normal Flora

2. The oral flora of humans

may harm their host since
some of these bacteria are
pathogens or
opportunistic pathogens
Role microbiome disease
Disruption of normal microflora-dysbiosis
Exposure to antibiotics – C. difficile ulcerative colitis
Obesity predisposing type 2 diabetes
Shift in skin microbiome – chronic wound infections
Therapeutic
Stool transplant-ulcerative colitis

Probiotics – mixture of bacteria and fungi

Rebalancing microbiomes and its functions
Promote and maintain regular bowel function
Improve tolerance to lactose
Flora of the Human Skin
Skin is the largest and most accessible organ
Two cutaneous populations
Transients: influenced by hygiene
Resident: stable, predictable, less influenced by
hygiene
Normal flora of skin:
Staphylococcus epidermidis
 Staphylococcus aureus
 varius streptococci
 Corynebacterium
 Pseudomonas aeruginosa
 Propionibacterium
 Yeasts
Normal flora of the skin:
Benefit Harm
Inhibit fungal Body odor
growth (athlete’s Acne
foot) Opportunistic
Body odor infections
 Microflora of an eye
The tears perniciously affect on microbes. In 47 % of
people the microflora here is completely absent.
Only few species have adapted to existence on a
conjunctiva:
Corynebacterium
Neisseria
Staphylococcus
 Mycoplasma
Adenovirus
Herpervirus
Normal flora
of the respiratory tract:
 Staphylococcus aureus
 Staphylococcus epidermidis
 Corynebacterium
 varius Streptococci
 Neisseria species
 Haemophilus influenzae
Moraxella lacunata
In a larynx, the trachea and large bronchuses there are few
of microbes.
Smaller bronchi and alveoli are normally sterile.
Normal flora of respiratory tract –
nasal membranes:

Benefit Harm
Competition with Main carrier site
pathogens for for pathogenic
colonization sites Staph. aureus
Normal flora of respiratory tract –
pharynx (throat):
Benefit Harm
Competition with Main carrier site
pathogens for for pathogens
colonization sites transmitted primarily
Production of by respiratory contact
substances that
inhibit pathogens
Flora of the Genitourinary Tract
Sites that harbor microflora
Females – Vagina and outer opening of urethra
Males – Anterior urethra
Changes in physiology influence the
composition of the normal flora
Vagina (estrogen, glycogen, pH)

30
 Normal flora
of the genitourinary tract
In an outside part of a urethra
 Peptococcus
 Corynebacterium
 Mycobacterium smaegme
 Fusobacterium
 Staphylococcus
 Mycoplasma are found.
The kidney, the ureter, the bladder and upper
urethra are sterile.
 Normal flora of vagina:
Lactobacillus
Corynebacterium
 B. fragilis, varius streptococci
 C. albicans

Internal reproductive organs are normally

sterile.
Normal flora of the vagina -
Benefit Harm
Competition with none
pathogens for
colonization sites
Production of lactic
acid that inhibits
pathogenic bacteria
and yeasts
 Microflora
of the intestinal tract
At birth a gastrointestinal path and feces of the child are
sterile. In 3 - 4 days there is an intensive invading them by
bacteria of genus Escherichia, Proteus, Veilonella,
Lactobacterium, Enterococcus, Staphylococcus. However, by
the end of the first week putrefacient bacteria are superseded
by a lactate microflora. It mainly Bifidobacterium bifidum, B.
longum, B. infantis, Lactobacillus acidophilus are.
Bifidobacterium and Lactobacterium play the large role in
decomposition of mammary milk, help the process of
digestion.
 Microflora of an oral cavity
In an oral cavity there is a plenty of
microorganisms. More than 100 species of
aerobic and anaerobic bacteria are described. In 1
ml of a spit can be found about 100 million of
microbial cells.
Constant (stationary) temperature (37 ºС),
humidity, the oddments of food, alkaline reaction
of a spit and wide aeration promote reproduction
of microbes.
Streptococci
Lactobacterium
 Veilonella
 Neisseria
Corynebacterium
Bacteroides
H. Influenzae
Treponema
Leptospira
C. albicans
Actinimycetes
 Mycoplasma
 Protozoa.
Normal flora of the oral cavity:
Benefit Harm
Compete with Plaque formation and
pathogens for dental disease
colonization sites
Produce substances
that inhibit pathogens
Stimulate local
immunity
Microflora of the stomach
Yeast
Sarcina
Fungi
Lactobacterium
Staphylococcus
Campylobacter
Helicobacter pylori (all up to 30 species).
 Normal flora of GI tract - stomach
Harm
Causes gastric
ulcers
Probable
Helicbacter pylori
association with
duodenal ulcers
Microflora
of the small intestine

 Bifidobacterium
Bifidobacterium bifidum
 Lactobacillus
 Enterococcus
 E. coli

Lactobacillus
Normal flora of GI tract:
small intestine
Benefit Harm
Production of Possible
vitamins and relationship with
nutrients inflammatory
Competition with conditions
pathogens for Transfer antibiotic
colonization sites resistance to
Production of
pathogens
substances that
inhibit pathogens
 The microflora of a large intestine is
most abundant and is diverse. Here there
are most favourable conditions for
reproduction of many microorganisms.
Now microbiologists have detected and
have described more than 270 species of
bacteria. Their common biomass
compounds about 1,5 kg. During day the
man with feces discharges of 17-18 billions
microbes.
 Normal flora of the colon:
Bacteria:
 Bacteroides
 Bifidobacterium
 Eubacterium
 Fusobacterium
 Lactobacillus
 coliforms (Escherichia
coli, Enterobacter)
 fecal Steptococci
 Clostridium
Fungi:
 Candida
Protozoa:
 Entamoeba coli,
 Trichomonas hominis
Normal flora of GI tract :
large intestine
Benefit Harm
Competition with Relationship with
pathogens for inflammatory bowel
colonization sites diseases
Production of Production of
substances that inhibit carcinogens and
pathogens relationship with colon
Stimulate development cancer
and activity of immune Methanogenesis
system