C hair of M icrobiology, V irology, and I mmunology

1. Chair of Microbiology, Virology, and Immunology MICROBIAL ECOLOGY Lecturer Prof. S.I. Klymnyuk

2. Ecology (oicos – house, hold, logos - doctrine) - science about legitimacies of creation and functioning of biological systems and their mutual relation with an environment. The microecology is the science about places of invading of microorganisms and their ecological links. At learning a microbial ecology use the same concepts, as well as in a common ecology. Main of them are the following: 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; 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

3. From old times it is known, that the microorganisms are omnipresent, that is ubiquitous organisms. Huge quantities of them meet in soil, water and air. The environment of their habitation is plants, animal, man. Everywhere bacteria are existed as microbiocenoses. The modern microbial biocenoses were generated as a result of durable evolution. Mutual relation (cohabitation) of different species of microbes among themselves and with other forms of life are called symbiosis.

4. Types of symbioses 1. Neutralism - the populations, existing in one biotope do not stimulate and do not oppress each other. 2. Mutalism - mutually advantageous cohabitation; one population synthesizes materials (matter), which are the basis of power supply for another (for example, legume bacteria and bean plants, aerobic and anaerobic bacteria in an organism of the man). 3. Commensalism - such form of symbiosis, at which one of jointly living populations extracts for herself advantage(benefit), but does not put a harm of other population. The commensalism is characteristic for many inhabitants of human body.

5. Types of symbioses 4. Antagonism - oppression of one population another. The microbes – antagonists produce antibiotics, bacteriocines, fatty acids, which cause destruction of bacteria or delay their reproduction. 5. Parasitism - such kind of symbiosis, at which one population (parasite) brings harm to the host, and for itself has a benefit. The causative agents of bacterial, virus and fungic illnesses concern to microbes - parasites.

6. Microflora of the soil The soil is the major environment for a habitation of microorganisms. The first bacteria, as well as all alive ones, have appeared in water. However in more later geological periods, when on a surface of globe the soil was derived, it became main habitation of microorganisms and main arena of their vital activity. The amount of bacteria in one gram of soil can be very great - from 200 millions up to 10 billions. Manured and ploughing ground are stocked with microorganisms most densely. The soil of woods, moor, the sands of desert contain few microbes. The most surface sphere of soil (crust by width of 2-3 mm) is very poor by microorganisms. A desiccation and the solar rays perniciously 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.

7. 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 transformation 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.

8. Carbon cycle in nature

9. Nitrogen cycle in nature

10. Nitrogen fixing bacteria

11. With discharges of the sick people and animals into soil can get and some time such microorganisms as C.tetani, C.perfringens, C.novyi, C.botulinum, S.typhi, Shigella spp. and others will be saved. The important value soil microflora has during wars. At mass wounds the danger of contamination of wounds by ground is considerably enlarged. It contains spores of anaerobic bacteria, which penetrating in a wound can cause such serious wound fevers as a tetanus and anaerobic gas infection. It always should be taken into account in the system of prophylaxis of communicable diseases.

12. Sanitary - indicative bacteria of soil are Escherichia coli, Streptococcus faecalis, Clostridium perfringens and 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 definition coli - 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, Cl.perfringens, B.anthracis and others).

13. 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 collection of all aqueous microorganisms is named as a microbial plankton. The microflora of reservoirs consists of two groups of microbes: autochtonal (or aqueous) microorganisms and allochtonal (brought from the outside). The autochtonal microflora are presented by microorganisms, which 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.

14. 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. It is distinguished polisaprogenic, mesosaprogenic and oligosarpogenic zones of water.

15. Zones of water clearness 1. 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. 2. 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. 3. Oligosaprogenic a zone (zone of pure water). The quantity of bacteria changes from 10 up to 1000 in one ml.

16. 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.

17. The most important metrics of fecal contamination of water all over the world is examination of bacteria of an intestinal rod group. Under this common concept combine bacteria of the family Enterobacteriaceae (Citrobacter, Escherichia, Enterobacter, Klebsiella). It is gram-negative rods fermenting lactose and a glucose up to an acid and gas within 24 hours. These bacteria are discharges in an environment only with feces of the man and hematothermal animals. Among them are coliform rods, which ferment lactose at 37 C to an acid and gas. From this group fecal intestinal rods are selected, which ferment lactose at 44,5C. These bacteria determine fresh fecal contamination. The index of fecal contamination is definded also by means of S. faecalis, C. perfringens, Proteus and coliphages.

18. 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. • Quantity coli-phages (number of colony-forming units) in 1000 ml of water - absence. • Besides in 25 litters of potable water pathogenic Protozoa (cyst of lamblia, dysenteric amebas, balantidia) and ovum of helmints there should be absent.

19. 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.

21. 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. 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. Main sources of microbial air pollution is the soil, water and man.

23. In natural conditions in air there are hundreds saprophytic microorganisms. A microflora of air is divided on resident (it is more often) and temporary, less resistant (it is found out is sporadic). The greatest quantity of microbes stocky layers of an atmosphere contains. 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. In open air spaces there are less of microbes, than in the closed rooms.

24. The contamination of air by the pathogenic microorganism descends by a trickling way in composition of aerosol. It is derived during talk, cough, sneeze. The microbes get in air also with particles of an epithelium of dermal integuments. They are durably saved in air and up to a sedimentation is evaporated. The dust phase has large drops, which fast settle and are evaporated. The bacteria in such phase can are transferred on the large distances. This is very dangerous. They can penetrating into lungs. The patient may discharges pathogenic bacteria and viruses together with a sputum, spit and salive. Even the healthy man at one sneeze discharges in air 10000-20000 microbial bodies, and the patient - in many times more.

25. The quantity of microbes in air varies in the large ranges - from several bacteria up to tens and hundreds thousand in 1 м3. In one gram of a dust can be up to 1 million of bacteria. Total number of bacteria in 1 м3 of air is accepted for expressing by general microbial number. A sanitary - hygienic rating of air is made not only according to general microbial number. More important value has revealing sanitary - indicative microorganisms. Such bacteria are the representatives of a microflora of upper respiratory tract: Streptococci haеmolyticus, S.viridans, Staphylococcus aureus.

26. 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. Examination of air microflora is made according to Koch’s sedimentation method or Krotov’s aspiration method.

27. Microflora of foodstuff In foodstuff there is a specific microflora, which adds them the defined gustatory qualities and consistence (curdled milk, yogurt). The microflora can penetrate into many products from the outside - nonspecific microflora. The intensive reproduction of separate species of bacteria makes products unsuitable for the use. Often foodstuff contaminate with bacteria of such genus as Salmonella, Shigella, Staphylococcus, Escherichia, Clostridium botulinum, C.perfringens, C. difficile. They can cause typhoid, dysentery, cholera, gastroenteritis, botulism and other illnesses.

28. Milk contaminate with such microbial genus as Staphylococcus, Streptococcus, Mycobacterium, Salmonella, Brucella, Enterovirus. It happens at milking, transportation and processing of milk and lactic products. Meat is contaminated during disease of animals and poultry, during their killing, cutting, incorrect storage and transportation. Often in meat it is found the representatives of genus Salmonella, Proteus, Staphylococcus, Streptococcus, Clostridium. The fish is contaminated by many species of microorganisms. They get in it from water, flakes, intestine, hands of staff, which handles fish production. The most dangerous bacteria are C.botulinum, V.parahaemolyticus. There may be also causative agents of a typhoid, dysentery, cholera, hepatites.

29. Vegetables and fruit are contaminated by species of Salmonella, Shigella, Vibrio, Enterovirus. They get from hands of the people, which gather, transport and sell these products. The incorrect preservation of vegetables (tomatoes, mushrooms and others) can cause botulism. Eggs often are infected by Salmonella, Fungi, Actinomycetes, and egg powder by Staphylococcus. Especially dangerous are the eggs of gooses and ducks. Bread product are poorly favourable environment for reproduction of the pathogenic microorganism. Only products from the overwintered grain cause sometimes toxic agranulocytosis. It is caused by the representatives of species of Fusarium.

30. The bacteriological research of foodstuff is spent in the scheduled order for a control, at doubt concerning quality of products and at originating alimentary toxinfections. The main task of microbiologic research of foodstuff is the definition of total of bacteria and detection sanitary - exponential species. For the majority of foodstuff such bacteria is E.coli and other representatives of group of intestinal rods. In some foodstuff the presence of anaerobic microorganisms and their toxins, and also representatives of genus Salmonella and Proteus are examined.

31. The prophylaxis of diseases, which are transferred through foodstuff, consists in keeping sanitary - hygienic rules of their manufacture, saving, transportation and implementation. Very important also is keeping the correct technology of preparation of foodstuff, especially canning production. Especially dangerous are the canned food of domestic manufacture. The large value has sanitary knowing of the workers of public catering.

32. Rhizopys, common bread mold

33. Molds

34. Normal microflora of humans The microflora of the human is a complex of microbiocenoses, which meet in an organism of the healthy people. They were generated during evolution, and are characterized by surprising persistence. The quantity and species composition of a normal microflora are influenced age, sex, climate, feeding habits, bacteria of an environment, individual sanitary and hygienic habits etc. Special role in change of a microflora play antibiotics, chemotherapeutic and immunological drugs. They render the large selective influence on a population of some bacteria. These medicines delay sensitive individuals and promote development of resistance species. The struggle with these resistant bacteria is one of difficult and urgent problems of practical medicine.

35. 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. The total number of microorganisms on a skin and in cavities of the man makes 1014. It is in 10 times more, than all cells of the macroorganism. However internal environment (blood, lymph, tissues and organs, which are not connected with an external environment) are sterile.

37. The normal microflora of the man is compounded with two groups of bacteria: 1. A resident or constant microflora. It is often named indigenous or autochthonous microflora. 2. Transitory, Temporary, facultative or allochthonous microflora. Normal microflora is represented mainly by anaerobic microorganisms. It consists mainly of representatives of three genus: Bifidobacterium, Bacteroides, Clostridium. On their part there is 95-97 % of all microflora. This legitimacy is characteristic for a skin, mucous, in cavities and in an intestinal path. Namely it makes a resident microflora. The aerobic bacteria compound 3-5 % of all microorganisms and fall into transitional part of a microflora. However, its separate representatives can be the evident residents (Staphylococcus, Corynebacterium, Escherichia and others).

38. The very important feature of a normal microflora of the man is that it is strictly individual and anatomically is stable. How many people exist so many individual microbial assemblages are. The bacteria from the neighbour to the neighbour can be transferred, but the transmit bacteria, as a rule, do not get accustomed. The individual stability of a microflora is so expressed, that in America the patent for definition of a criminal on his microflora detected on a place of a crime is registered. The anatomical stability means, that the microflora of an oral cavity and nose does not get accustomed on a skin and other. Any time the microflora, which has got on the given biotope, can be, but permanently is not saved.

39. The fetus during pregnancy is sterile. During genus the child is contaminated by a microflora of patrimonial paths of the mother. It is representatives of genus Lactobacterium, Streptococcus, Escherichia more often. Further in an organism the neonatal microbes enter from hands, mammas both respiratory paths of the mother and serving staff. They also enter from an environment. The constant (stationary) microflora starts to form since the tenth day. On mucous in the beginning there are filamentous microorganisms. They will form a continuous grid, which covers a surface. On these filamentous bacteria start to be adsorbed microorganisms, which will derivate solid layer or biofilm. Since 20-25 days after birth a skin and mucous become covered by a most thin biofilm, which consists of a mucin and polysaccharides of a microbial origin. In thickness of this biofilm there is a plenty of microorganisms. They are allocated not single, and as original colonies. The thickness of a biofilm in different places (biotopes) is various. It is very thin on a skin and mucous of nose, but reaches the large thickness on a mucous colon.

40. Microflora of a skin The quantity of microorganisms on a skin can vary in the large limits: from 100 microbial bodies on 1 см2 in the field of a forearm up to 2,5 million/см2 in axillary fosses. From a surface of a skin of the man is washed off about 1,5 billion of bacteria. Density of microbial populations on a skin is subjected daily, monthly and seasonal fluctuations. It also depends on a status of health, trade, age, sex etc. Most typical the representatives of the inhabitants of a skin are Propionibacteria, Corynebacterium species (C.acnes, C.xerosis, C.pseudodiphtheriticum, C.minutissimum, C.lipоphylicum) and species Staphylococcus (S. epidermidis, S.saprophyticus, S.hominis, S.haemolyticus, S.capitis – total 29 species) are. Approximately for 10 % of the people on a skin as found S.aureus.

41. Skin bacteria

42. There are representatives of a species Micrococcus (M.luteus, M.varians, M.roseus, M.sedentarius and others), fungi of genus Pityrosporum (P.ovale, P.orbiculare) less often. Find species of Mycobacterium (M.fortuitum) and Clostridium (C.perfringens, C.cereus), Bacillus and C.albicans are less often. Each anatomical isolated zone (biotope) has the specific features concerning quantity and species composition. American microbiologists Bibel and Lovel have made skin flora maps. From the epidemiological point of view important biotopes are the perineum, skin in a place of operational cuts, mammas of the puerperas and feeding mothers skin of the face, axillary recesses. Very often microflora of mammas can cause purulent - septic diseases for the mother and child.

43. The surgeons have offered many ways of processing of hands before the operation. However not any of them does yields an absolute sterility. Durable washing of hands (3-5 minutes) water with soap and brush results in decrease of bacteria in 10 times. In 10 minutes of continuous washing the quantity of bacteria is again enlarged, and in 15 minutes their quantity becomes more, than before washing. It happens because the microbes begin to come out of depths of a skin (bag of hair, ducts of sweat glands). The surgeons began to handle hands by alcohol, by iodine or to dress gloves.

44. The healthy pure skin has well-marked bactericidal properties. It is stipulated by presence on a skin of unsaturated fatty acids, immunoglobulins of sweat etc. However, at violation sanitary - hygienic mode, standard conditions of work and life, at operation of various chemical materials (colour, varnishes, the oils) can arise purulent disease of a skin and its appendages.

45. 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 0С), humidity, the oddments of food, alkaline reaction of a spit and wide aeration promote reproduction of microbes. The basic group of bacteria of an oral cavity is compounded by streptococci (S.salivarius, S.mitis, S.mutans, S.haemolyticus, S.viridans). Here permanently dwell Lactobacterium, Veilonella, Neisseria, Corynebacterium, Bacteroides. Besides in an oral cavity we meet H.influenzae, T.oralis, T.denticola, T.pseudopallida, C.albicans, Leptospira, Actinimycetes, Mycoplasma, Protozoa.

46. Among the transitional inhabitants of an oral cavity are described Enterobacteriaceae (Escherichia, Enterobacter, Citrobacter, Klebsiella, Proteus). We meet P.aeruginosa, Bacillus, Clostridium less often. The presence E.coli in composition of a stomatic microflora (especially at presence of tooth prostheses) testifies to a unsuccessful status of an oral cavity. 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. The main part in maintenance of constant(stationary) quantitative and quality composition play lysozim (muramidase), lactoferrin, peroxidase, nuclease, secretory IgA.

47. The opportunistic pathogenic bacteria of an oral cavity can cause an endogenic infection. This is promoted by traumas, change of pH spit, application of antibiotics. The large value there is also sensibilization of an organism to microbial allergens. Main causative agents of a caries are S.mutans and S.sanguis.

49. Microflora of a stomach and intestine At birth a gastrointestinal path and feces of the child are sterile. In three - four 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.

50. This microflora has strong antagonistic properties. It is very useful to the child, oppresses development of putrefacient bacteria, depresses and removes from an organism pathogenic and conditional - pathogenic microorganism. After the ending of nursing in the child constant biozenose of an intestinal path is gradually formed. The quality and quantitative composition of a microflora of different departments of an intestine becomes unequal. But a prevailing position in a gastrointestinal path Bifidobacterium, Bacteroides, Clostridium occupy.