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C hair of Medical Biology, M icrobiology, V irology, and I mmunology. MICROBIOLOGY OF ENVIRONMENTS. MICROBIOLOGY OF HUMAN BODY. Lecturer Prof. S. Klymnyuk. Ecology (oicos – house, hold, logos - doctrine) is the study of relationships among organisms and their environment.

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Chair of Medical Biology, Microbiology,

Virology, and Immunology


Lecturer Prof. S. Klymnyuk

Ecology (oicos – house, hold, logos - doctrine) is the study of relationships among organisms and their environment.

The microecologyis the science about places of invading of microorganisms and their ecological links.

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 assemblage, association, that is collection of populations of different species of microorganisms, which dwell (live) in the defined biotope (for example, in an oral cavity, reservoir);

ecosystem - system, in which enters a biotope and microbiocenosis.

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.

Types of symbioses:

Commensalism - such relationship, at which the member called the commensal receives benefits, when its coinhabitant is neither harmed nor benefitted.

The structural interactions of the bacteria probably are a reflection of the complex metabolic interactions that are known to occur between different teeth plaque microorganisms.

For example: the production of succinic acid from Campylobacter species that is known to be used as a growth factor by Porphyromonas gingivalis. Streptococcus and Actinomyces species produce formate, which may then be used by Campylobacter species. Fusobacterium species produce both thiamine and isobutyrate that may be used by spirochetes to support their growth.

Types of symbioses:

Antagonism - oppression of one popula-tion another. The microbes – antagonists produce antibiotics, bacteriocines, fatty acids, which cause destruction of bacteria or delay their reproduction.

Types of symbioses:

Parasitism - such kind of symbiosis, at which one population (parasite) brings harm to the host, and for itself has a benefit.

Ricketsia – intracellular


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 most surface sphere of soil (crust by width of 2-3 mm) is very poor by microorga-nisms. A desiccation and the solar rays pernici-ously influence them. The ground mass of bacteria is on depth 10-20 cm. On depth of 1,5-2 m of untouched ground the microbes do not meet almost.

The microflora of soil includes hundreds of species of bacteria, viruses, protozoa, actinomyces and fungi. It is various species of putrefactiving, nitrifying, denitrifying, nitrogen-fixing bacteria. The most often inhabitants of soil are the representatives of genus Azotobacter, Nocardia, and Clostridium. Many bacteria of genus Rhisobium, Nitrosomonas, Nitrosospira, Nitrobacter, Pseudomonas are very often found. Almost always there are denitrifying bacteria (B.denitrificans), ammonifying microbes (Urobacillus pasteurii, Urobacillus leybii), numerous iron bacteria and sulphur-bacteria.
All of them play the great role in a turnover of materials in a nature, improve productivity of our fields, provide life on the Earth. The microorganisms of soil take an active part in all processes of transfor-mation of materials and energy: synthesis of a biomass, biological nitrogen fixation, fermentation, corruption, denitrification of the cycle sulfur, iron lactas, phosphorum, carboneum and other elements.
Sanitary - indicative bacteria of soil are:
  • 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.

More exact rating is manufactured at definitioncoli - index,that is amount of bacteria E.coli in 1 g of soil.

Also general microbial number (GNM) – quantity (amount) of all saprophytic bacteria in 1 g of soil is examined.

The soil is considered pure, if its coli-index does not exceed 2000, and the quantity of termophilic bacteria is in limits 100 - 1000.

Under the epidemic indications soil also is inspected on presence in it pathogenic bacteria (Salmonella, Shigella, C. tetani, C. botulinum, C. perfringens, B. anthracis and others).

Water is a natural medium of a habitation of various microorganisms. In sweet and salty waters representa-tives 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
  • Polisaprogeniczone 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.
  • Mesosaprogeniczone 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.
  • Oligosaprogenica 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: S. typhi, V. cholerae, S. dysentеriae. Often various viruses are found: Polioviruses, Hepadnaviruses,Enteroviruses 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 oligosaprogeniczones.


Water plays very important role in epidemiology of many contagious diseases(typhoid, dysentery, cholera, poliomyelitis, virus hepatites and others). The causative agents of these illnesses are discharged with feces of the patients and carriers. Together with sewage they enter in water of open reservoirs. In summer time some bacteria, including Vibrio cholerae, can even multiply. To catch it is possible through ice, in which the pathogenic bacteria can be saved during several weeks and even of months.


In many countries for a rating of quality of potable water the normative documents or state standards are taken. Microbiologic index of safety of potable water are the following:

1. Common microbial number in one ml of water - no more than 100.

2. Number of bacteria of intestinal rod group (coli-index) in 1000 ml of water - no more than 3.

3. Index of fresh fecal contamination, that is quantity(amount) E.coli in 1000 ml of water - absence.

4. Quantity coli-phages (number of colony-forming units) in 1000 ml of water - absence.

5. Besides in 25 litters of potable water pathogenic Protozoa (cyst of lamblia, dysenteric amebas, balantidia) and ovum of helmints there should be absent.

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.

Microflora of air

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.

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 microorganisms. 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.
Examination of air microflora is made according to Koch’s sedimentation method or Krotov’s aspiration method.
A sanitary - hygienic rating of air


general microbial number

sanitary - indicative microorganisms:

Streptococci haеmolyticus,

S. viridans,

Staphylococcus aureus.

The large value there is a cleanness of air in operation rooms, reanimation department, dressing rooms, maternity halls and chambers for neonatal.

Total number of microbes in operation hall before the operation should not exceed 500 in 1 м3, and after operation - 1000 in 1 м3. The quantity of haemolytic and viridans streptococci should not be at all.



of humans

The organism of the man is occupied
  • more than500 species of bacteria,
  • about 50 species of viruses,
  • more than 20 species of protozoa.

It is a huge zoological garden.

normal microflora of the human body
Normalmicroflora of the human body:

Constant (obligate, resident, indigenous, autochthonous) microflora is native, no imported one of different biotopes.

Transient (temporary, facultative, allochthonous) microflora is not aboriginal, it is acquired one.

normal flora of skin
Normal flora of skin:

Staphylococcus epidermidis

Staphylococcus aureus

varius streptococci


Pseudomonas aeruginosa



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:







normal flora of the respiratory tract
Normal flora of the respiratory tract:

Staphylococcus aureus

Staphylococcus epidermidis


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 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
Degrees of vaginal secret cleanness of health woman
  • Epitelhial cells
  • acid-tolerant lactobacilli (Doderllein`s bacilli)
  • many glicogen
  • the pH is maintained between4.4 and 4.6



degrees of vaginal secret cleanness of sick women
Degrees of vaginal secret cleanness of sick women
  • 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



microflora of the intestinal tract
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. They are a main microflora of the child at nursing. At artificial feeding or at transition to the mixed feeding there is an increase of the putrifactive microorganisms. 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 microorga-nisms. 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.

In the oral cavity bacteria are foundon the tooth surface (above all in subgingival plaque); in the saliva; on the tongue surface; in the tonsillar crypts.

The main mass of microbes (70 %) is in a debris. In 1 mg of dry mass of scurf can be about 250 million of bacteria.

  • Lactobacterium
  • Veilonella
  • Neisseria
  • Corynebacterium
  • Bacteroides
  • H. Influenzae
  • Treponema
  • Leptospira
  • C. albicans
  • Actinimycetes
  • Mycoplasma
  • Protozoa.
microflora of the stomach
Microflora of the stomach
  • Yeast
  • Sarcina
  • Fungi
  • Lactobacterium
  • Staphylococcus
  • Campylobacter

(all up to 30 species).

Helicobacter pylori

microflora of the small intestine
Microflora of the small intestine




E. coli

Bifidobacterium bifidum


Normal flora of the colon:


  • Bacteroides
  • Bifidobacterium
  • Eubacterium
  • Fusobacterium
  • Lactobacillus
  • coliforms (Escherichia coli, Enterobacter)
  • fecal Streptococci
  • Clostridium


  • Candida


  • Entamoeba coli,
  • Trichomonas hominis
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.

Peridontal disease:

A – normal gingiva;

B - disease

Importence of normal flora:

Colonization resistance

Antagonistic role

Stimulate immunity

Take part in all kinds of metabolism

Produce vitamines, enzymes, hormons

Digestive role

The dysbacteriosisis 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.

To treat dysbacteriosesof an intestine and colitises we apply special bacteritic preparatrions: colibacterin, bifidobacterin, lactobacterin, bificol, bactisubtil. They contain the dried up clouds of alive bacteria having strong antagonistic properties. These eubiotics reduce a normal microflora of an intestine.
The gnotobiotes allow more precisely to study a role of a normal microflora in synthesis of vitamins and amino acids, in creation inherent and artificial immunity. The large value has gnotobiology in learning space, conditions of life of the man and animals in space, in conditions of durable flight of missiles on other planets.
The animals without microbes (gnotobiotes/germ-free animals) are divided into some groups:

1. Monobiotes - completely deprived of microbes;

2. Dibiotes - animals infected by one species of bacteria;

3. Polybiotes – having two and more microbial species in organism.