Transcript 08 Ecology of microorganisms

Microbiology, Virology, and Immunology
Department
Ecology of microorganisms.
The microflora of the human
body. Dysbacteriosis.
What is Microbial Ecology?
What is “Microbial”?
– of or referring to a minute life form; a
microorganism, especially a bacterium that
causes disease. Not in technical use.
What is “Ecology”?
– the study of the interactions between organisms
and their environment
Microbial ecology = The study of interactions between
microorganisms and their environment (chemical, physical, and
biological environment!)
In microbial ecology the main concepts are:
population - an elementary evolutional unit
(structure) of a definite species;
biotope - site, habitation of a population, for
parasites - place of their localization in an
organism;
In microbial ecology the main concepts are:
microbiocenosis - microbial association,
that is collection of populations of different
species of microorganisms, which live in the
defined biotope (for example, in an oral
cavity, skin);
ecosystem - system, in which enters a
biotope and microbiocenosis.
Symbiosis - living together of two dissimilar organisms
Types of symbioses:
Neutralism - the populations, existing in
one biotope do not stimulate and do not
oppress each other.
Mutalism exists when organisms live in an
obligatory but mutually beneficial
relationship.
The mutualistic association between rhizobia
and N-fixing bacteria
E. coli synthesizes vitamin K in the intestine
in exchange the large intestine provides nutrients necessary for
survival of the microorganisms
Types of symbioses:
Commensalism - such relationship, at which
the member called the commensal receives
benefits, while its coinhabitant is neither
harmed nor benefitted.
Bifidobacteria
Types of symbioses:
Antagonism - oppression of one
population another. The microbes –
antagonists
produce
antibiotics,
bacteriocines, fatty acids, which cause
destruction of bacteria or delay their
reproduction.
A
B
Types of symbioses:
Parasitism - such kind of symbiosis, at which one
population (parasite) brings harm to the host, and for
itself has a benefit.
parasitic microorganisms
Microflora of soil
• The soil is the major environment for
a habitation of microorganisms.
• The amount of bacteria in one gram
of soil can be very great - from 200
millions up to 10 billions
• The ground mass of bacteria is on
depth 10-20 cm.
The microflora of soil includes hundreds of
species of bacteria, viruses, protozoa,
actinomyces and fungi. It is various species of
putrefactiving, ammonifying, nitrifying,
denitrifying, nitrogen-fixing bacteria,
numerous iron bacteria and sulphur-bacteria.
The most often inhabitants of soil are the
representatives of genus Azotobacter,
Nocardia, and Clostridium.
producers
consumers
The role of microorganisms ?
decomposers
Help in
- the decomposition of pollutants and toxic wastes
the efficient utilization of limited natural resources
transformations of chemical substances that can
be used by other organisms
• critically important to all form of life
closely linked with the flow of energy
• the ultimate source of all carbon is CO2
- raw material for photosynthesis
- major waste product of respiration and
combustion
Org.cpd.
CO2 fixation
Anaerobic
respiration and
fermentation
(anaerobic m.o.)
(phototrophic
bacteria)
Methanogenic
Anaerobic
procaryotes
CO2
Aerobic
CH4
CO2
Methane-oxidizing
procaryotes
Respiration
(animals, plants,
and m.o.)
Org.cpd.
CO2 fixation
(cyanobacteria, algae,
plants, and
chemoautotrophic
procaryotes)
The carbon cycle
Beggiatoa
sulfate
R-SH
assimilation
(some procaryotes)
So
Thiobacillus
sulfate
assimilation
Aerobic
desulfurylation
R-SH
Thiothrix
SO42-
H2 S
R-SH
Anaerobic
Chromatium
Chlorobium
Dissimilatory
sulfate reduction
Desulfovibrio
So
Chromatium
S2O32-
Chlorobium
Higher
plant
bacteria
phytoplankton
Dissolved
org.ortho-P
Dissolved
org.-P
Sediment
zooplankton
Precipitated
inorg.-P
General microbial number (GNM) – quantity
(amount) of all saprophytic bacteria in 1 g of soil is
examined.
More exact rating is manufactured at definition
coli - index, that is amount of bacteria E.coli in 1 g of
soil.
The soil is considered pure, if its coli-index does not
exceed 2000, and the quantity of termophilic bacteria is
in limits 100 - 1000.
Sanitary - indicative bacteria of soil
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Escherichia coli,
Streptococcus faecalis,
Clostridium perfringens
termophilic bacteria.
A degree of fecal contamination
of soil is determined on presence and
quantity(amount) of first three species.
Soil Pathogens
Clostridium botulinum,
Clostridium tetanus,
Clostridium perfringens,
Bacillus anthracis
Microflora of water
Water is a natural medium of a habitation of
various microorganisms.
In sweet and salty waters representatives of
all groups of bacteria are found Protozoa,
Fungi, Viruses, Water - plant.
The microflora of reservoirs consists of two groups
of microbes:
autochtonal (or aqueous) microorganisms /
permanently live and are multiplied in water/. It is
more often such species: Micrococcus candicans, M.
roseus, Sarcina lutea, Bacterium aquatilis communis,
Pseudomonas fluorescens. The anaerobes represent by
species Clostridium, Bacillus cereus, B. mycoides.
allochtonal (brought from the outside).
The microbial composition of water is in the
large degree mirrors a soil microflora. A major
factor, which determines quantity of microbes in
water is presence in it of necessary nutritious
materials, that are various biological matters.
Main path of microbial contamination of water
is penetration of unpurified waste from sewage of
the populated area. Therefore, the more water is
polluted with similar organic matters, there are
more in it of microorganisms.
Zones of water clearness
Polisaprogenic zone is the zone of strong contamination.
It contains many organic matters and almost there is no
oxygen. The quantity of bacteria in 1 ml of water reaches
one million and more.
Mesosaprogenic zone is the zone of moderate
contamination(pollution)). In it the nitrifying and aerobic
bacteria prevails. The total number of microorganisms
compounds hundreds of thousand in one ml.
Oligosaprogenic zone (zone of pure water). The quantity
of bacteria changes from 10 up to 1000 in one ml.
Sometimes the pathogenic bacteria in water can
get and they will be saved for some time: Salmonella
spp., S. typhi, V. cholerae,
.S. dysentеriae, L. interrogans.
Often various viruses are found: Polioviruses,
Rotaviruses, Enteroviruses, Hepatitis A virus and
others.
The pathogenic microorganism getting in
reservoirs, abundant in a zone of strong
contamination, gradually die in a zone of moderate
contamination. They are almost not found in
oligosaprogenic zones.
Common microbial number of water is examined by
inoculation of 1 ml of water in melted and refrigerated up to 50
C in agar in Petri dishes.
Coli-index is determined by a method of membrane filters or
fermentation tests.
Membrane filters method
Membrane filtration for
determinging the coliform
count in a water sample using
vacuum filtration.
Membrane filters method
Enzymatic assay for coliform
• Colilert system
system(for P-A test)
• β-galactosidase
of of
coliform
-galactosidase
coliform
substrate
→→
nitrophenol
(yellow)+Gal
substrateONPG
ONPG
nitrophenol
• β-glucuronidase
coli
-glucuronidaseofofE.E.
coli
fluorogenic
MUG
fluorogenicsubstrate
substrate
MUG
Microflora of air
Air for microorganisms is less favorable
environment, than soil and water.
There are almost no the nutritious materials
necessary for reproduction of bacteria. Desiccation
and the ultraviolet rays operate perniciously on
microorganisms.
Nevertheless, many microbes in air can be saved
more or less long time.
Main sources of microbial air pollution is the soil,
water and man.
Microflora of air
The composition of a microflora of air is very
various. It depends on cleanness of air, deposits,
temperature, humidity, climate and geographical
conditions. Than it is more in air of a dust, smoke,
soot, the more micro-organisms.
Vice-versa, above mountains, seas, oceans and
woods, where air is pure, it is not enough of
microbes.
In open air spaces there are less of microbes,
than in the closed rooms.
The constant microflora of air is shaped at the
expense of soil microorganisms. In its composition
many species of Actinomyces, Penicillinum,
Aspergillus, Mucor and others go into. There are
many Micrococcous roseus, M. candicans, M.
luteus, Sarcina lutea, S. alba, S. rosea, Bacillus
subtilis, B. mycoides, B. mesentericus.
Many microbial diseases are transmitted
through the air during sneezing, coughing, or
even normal breathing:
bacterial - tuberculosis, diphtheria,
legionellosis, wooping cough, acute angine,
epidemic meningitidis,
viral - influenza, measles, mumps, adenoviral
infection
A sanitary - hygienic rating of air include
 general microbial number
 sanitary - indicative microorganisms:
Streptococci haеmolyticus,
S. viridans,
Staphylococcus aureus.
Examination of air microflora is made
according to
 Koch’s sedimentation method
 Krotov’s aspiration method.
Where the Normal Flora Are Found
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Skin
Conjunctiva
Oral cavity
Intestinal tract
Upper respiratory
tract
• Urogenital tract
Dental plaque consists of a biofilm of bacteria 300500 cells in thickness.
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.
Normal flora
Numbers of bacteria that colonize different
parts of the body
• Human body
– 1013 cells
– 1014 bacteria
• Normal microbial
flora
– Relatively stable
Numbers represent the number of organisms per
gram of homogenized tissue or fluid or per square
centimeter of skin surface.
Normal microflora of the human body:
Constant (obligate, resident, indigenous,
autochthonous) microflora is native, no imported
one of different biotopes.
Microbes become established.
Transient (temporary, facultative,
allochthonous) microflora is not aboriginal, it is
acquired one.
Microbes occupy the body for only short periods.
Bacterial Flora of the Body
Site
Total Bacteria
(per/ml or gm)
Upper Airway
Nasal Washings
103-104
Saliva
108-109
Tooth Surface 1010-1011
Gingival Crevice
1011-1012
Gastrointestinal Tract
Stomach
102-105
Small Bowel
102-104
Ileum
104-107
Colon
1011-1012
Female Genital Tract
Endocervix
Vagina
108-109
108-109
Ratio
Anaerobes:Aerobes
3-5:1
1:1
1:1
1000:1
1:1
1:1
1:1
1000:1
3-5:1
3-5:1
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
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
• Inhibit fungal
growth (athlete’s
foot)
• Body odor
Harm
• Body odor
• Acne
• Opportunistic
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
• Competition with
pathogens for
colonization sites
Harm
•Main carrier site for
pathogenic Staph.
aureus
Normal flora of respiratory tract –
pharynx (throat):
Benefit
• Competition with
pathogens for
colonization sites
• Production of
substances that
inhibit pathogens
Harm
•Main carrier site
for pathogens
transmitted primarily
by respiratory contact
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)
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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 reprodactive organs are normally
sterile.
Degrees of vaginal secret cleanness
of health woman
I
Epitelhial cells
acid-tolerant lactobacilli
(Doderllein`s bacilli)
many glicogen
II
the pH is maintained
between 4.4 and 4.6
Degrees of vaginal secret cleanness
of sick women
Epitelhial cells
III
 acid-tolerant lactobacilli
(Doderllein`s bacilli) are absent
little glicogen
the pH is maintained between
6.9 and 7.6
IV
many proteins, leucosytes
 staphylococci and streptococci
Normal flora of the vagina Benefit
• Competition with
pathogens for
colonization sites
• Production of lactic
acid that inhibits
pathogenic bacteria
and yeasts
Harm
• none
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.
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Streptococci
Lactobacterium
Veilonella
Neisseria
Corynebacterium
Bacteroides
H. Influenzae
Treponema
Leptospira
C. albicans
Actinimycetes
Mycoplasma
Protozoa.
Normal flora of the oral cavity:
Benefit
• Compete with
pathogens for
colonization sites
• Produce substances
that inhibit pathogens
• Stimulate local
immunity
Harm
• Plaque formation and
dental disease
Microflora of the stomach
Yeast
Sarcina
Fungi
Lactobacterium
Staphylococcus
Campylobacter
Helicobacter pylori
(all up to 30 species).
Normal flora of GI tract - stomach
Helicbacter pylori
Harm
• Causes gastric
ulcers
• Probable
association with
duodenal ulcers
Microflora
of the small intestine
 Bifidobacterium
 Lactobacillus
Bifidobacterium bifidum
 Enterococcus
 E. coli
Lactobacillus
Normal flora of GI tract:
small intestine
Benefit
• Production of
vitamins and
nutrients
• Competition with
pathogens for
colonization sites
• Production of
substances that
inhibit pathogens
Harm
• Possible
relationship with
inflammatory
conditions
• Transfer antibiotic
resistance to
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:
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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
• Competition with
pathogens for
colonization sites
• Production of
substances that inhibit
pathogens
• Stimulate development
and activity of immune
system
Harm
• Relationship with
inflammatory bowel
diseases
• Production of
carcinogens and
relationship with colon
cancer
• Methanogenesis
Importence of normal flora:
1. Colonization resistance
2. Antagonistic role
3. Stimulate immunity
4. Take part in all kinds of metabolism
5. Produce vitamines, enzymes, hormons
6. Digestive role
Normal flora - Benefits
Prevent colonization by competing for
attachment sites
Prevent colonization by competing for
essential nutrients
Antagonize bacterial growth: Fatty acids,
peroxides, bacteriocins kill or inhibit
nonindigenous species
Normal flora - Benefits
Synthesize and excrete vitamins: vitamin K,
vitamin B12
Stimulate development of certain tissues:
Caecum and lymphatic tissues (Peyer’s patches) in
GI tract
Production of cross-reactive (“natural”) antibodies
Influence immunology of gut-associated
lymphatics
Normal flora - Risks
Not so beneficial: “side effects”
• Dental plaque
– Biofilm on hard, smooth enamel
surface
• 300-500 bacterial cells thick
Streptococcus sanguis,
Streptococcus mutans
Normal flora - Risks
• Dental caries: destruction of enamel,
dentin or cementum of teeth
– bacteria in plaque produce lactic acid
Streptococcus mutans
– Lactic acid demineralizes enamel
Normal flora - Risks
• Periodontal disease
– Gingiva, cementum, periodontal
membrane, alveolar bone
– Rich in anaerobes
Opportunistic flora
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Some normal flora become
opportunistic pathogens
Staphylococcus aureus,
Streptococcus mutans,
Enterococcus faecalis,
Streptococcus pneumoniae,
Pseudomonas aeruginosa,
etc.
Opportunistic flora
Breach of skin/mucosal barrier:
trauma, surgery, burns
•Surgery to mouth leads to abscesses of bone,
lung, brain
•Dental manipulation: wounds seed with oral
streptococci might invade via blood and adhere
to heart valve previously damaged due to
rheumatic fever
•Intra-abdominal abscesses: anaerobes from
intestinal tract
Opportunistic flora
Bacterium at one site may be commensal,
but might be pathogenic at another site
– Commensal in gastrointestinal tract
(E. coli) might be pathogenic in lung or
urinary tract
The dysbacteriosis is change of a quantitative
relation and composition of a normal microflora
of an organism, mainly of it intestine.
Thus there is a decrease or disappearance of
some bacteria and sharp increase others,
especially infrequent or not characteristic for the
given biotope of microorganisms. As a rule, the
quantity of an facultative- anaerobic microflora is
enlarged. It can be the Gram-negative rods,
staphylococci, Candida albicans and species
Clostridium.
Candidosis
Probiotics
–Oral administration of living organisms to
promote health
–They contain the dried up clouds of alive
bacteria having strong antagonistic
properties
–Mechanism speculative: competition with
other bacteria; stimulation of nonspecific
immunity
–Species specific: adherence and growth
Prebiotics
–Non-digestible food that stimulates
growth or activity of GI microbiota,
especially bifidobacteria and
lactobacillus bacteria (both of which
are noninflammatory)
–Typically a carbohydrate: soluble
fiber