Microbiology, Virology, and Immunology
Department

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

• 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 CO
2
- raw material for photosynthesis
- major waste product of respiration and combustion

CO
2 fixation
(phototrophic bacteria)
Org.cpd.
Anaerobic respiration and fermentation
(anaerobic m.o.)
Anaerobic
Aerobic
CO
2
Respiration
(animals, plants, and m.o.)
Methanogenic procaryotes
CH
4
CO
2
Methane-oxidizing procaryotes
Org.cpd.
CO
2 fixation
(cyanobacteria, algae, plants, and chemoautotrophic procaryotes)

The carbon cycle

sulfate assimilation
R-SH
(some procaryotes) desulfurylation
R-SH H
2
S
Chromatium
Chlorobium
S o
Beggiatoa
Thiothrix
Thiobacillus
Aerobic
SO
4
2-
Anaerobic
Dissimilatory sulfate reduction
Desulfovibrio
S
2
O
3
2-
S o sulfate assimilation
R-SH
Chromatium
Chlorobium

Higher plant
Dissolved org.-P bacteria phytoplankton zooplankton
Dissolved org.ortho-P
Precipitated inorg.-P
Sediment

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

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

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.

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
-glucuronidase of E. coli

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.

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.

• Skin
• Conjunctiva
• Oral cavity
• Intestinal tract
• Upper respiratory tract
• Urogenital tract
Dental plaque consists of a biofilm of bacteria 300-
500 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
– 10 13 cells
– 10 14 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.

Site
Bacterial Flora of the Body
Total Bacteria Ratio
(per/ml or gm) Anaerobes:Aerobes
Upper Airway
Nasal Washings
Gingival Crevice
10 3 -10 4
Saliva
Tooth Surface 10 10 -10 11
10 8 -10 9
10 11 -10 12
1:1
3-5:1
1:1
1000:1
Gastrointestinal Tract
Stomach
Small Bowel
Ileum
Colon
10 4 -10 7
10 2 -10 5
10 2 -10 4
10 11 -10 12
Female Genital Tract
Endocervix
Vagina
10
10
8
8
-10
-10
9
9
1:1
1:1
1:1
1000:1
3-5:1
3-5:1

• 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
42

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

 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

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

 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

• 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)
52

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.


Lactobacillus

Corynebacterium

B. fragilis, varius streptococci

C. albicans
Internal reprodactive organs are normally sterile .

I
II

Epitelhial cells
 acid-tolerant lactobacilli
(Doderllein`s bacilli)
 many glicogen
 the pH is maintained between 4.4 and 4.6

III
IV

Epitelhial cells
 acid-tolerant lactobacilli
(Doderllein`s bacilli) are absent
 little glicogen
 the pH is maintained between
6.9 and 7.6
 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
• none
Harm

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 .

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
• Compete with pathogens for colonization sites
• Produce substances that inhibit pathogens
• Stimulate local immunity
Harm
• Plaque formation and dental disease


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

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

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

 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

 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 crossreactive (“natural”) antibodies
 Influence immunology of gut-associated lymphatics

Not so beneficial: “side effects”
• Dental plaque
– Biofilm on hard, smooth enamel surface
• 300-500 bacterial cells thick
Streptococcus sanguis,
Streptococcus mutans

• Dental caries : destruction of enamel, dentin or cementum of teeth
– bacteria in plaque produce lactic acid
Streptococcus mutans
– Lactic acid demineralizes enamel

• Periodontal disease
– Gingiva, cementum, periodontal membrane, alveolar bone
– Rich in anaerobes






Some normal flora become opportunistic pathogens
Staphylococcus aureus,
Streptococcus mutans,
Enterococcus faecalis,
Streptococcus pneumoniae,
Pseudomonas aeruginosa, etc.

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

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.

–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
(tropism)

–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