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Microbiology, Virology, and ImmunologyDepartment
Ecology of microorganisms.
The microflora of the human body. Dysbacteriosis.
What is Microbial Ecology?
What is “Microbial”?
What is “Ecology”? – the study of the interactions between organisms and their environment
– of or referring to a minute life form; a microorganism, especially a bacterium that causes disease. Not in technical use.
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.
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.
Symbiosis - living together of two dissimilar organisms
The mutualistic association between rhizobia and N-fixing bacteria
E. coliE. coli synthesizes vitamin K in the intestine synthesizes vitamin K in the intestinein exchange the large intestine provides nutrients necessary for in exchange the large intestine provides nutrients necessary for survival of the microorganismssurvival 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.
Microflora of soil
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.
The role of microorganisms ?
producers consumers
decomposers
- 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
Help in
• 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 CH4 CO2
Anaerobic
Aerobic
CO2 fixation
CO2 fixation
Respiration
Anaerobic respiration and fermentation
Org.cpd.
Methanogenic
procaryotes
Methane-oxidizing
procaryotes
(phototrophic bacteria) (anaerobic m.o.)
(cyanobacteria, algae, plants, and chemoautotrophic procaryotes)
(animals, plants, and m.o.)
The carbon cycle
R-SH H2S SO42- R-SH
So
Dissimilatory sulfate reduction
SoS2O3
2-
R-SH
sulfateassimilation
sulfateassimilation
desulfurylation
Anaerobic
Aerobic
Chromatium
Chlorobium Chromatium
Chlorobium
Beggiatoa
Thiothrix
Thiobacillus(some procaryotes)
Desulfovibrio
Higher plant
Precipitated inorg.-P
Dissolved org.-P
zooplanktonphytoplankton
bacteria
Dissolved org.ortho-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.
Escherichia coli, Streptococcus faecalis, Clostridium perfringens termophilic bacteria.
Sanitary - indicative bacteria of soil
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.
Microflora of water
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 clearnessPolisaprogenic 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 filtration for determinging the coliform count in a water sample using vacuum filtration.
Membrane filters method
Membrane filters method
Enzymatic assay for coliform• Colilert system
• β-galactosidase of coliform
substrate ONPG → nitrophenol• β-glucuronidase of E. coli
fluorogenic substrate MUG
• Colilert system (for P-A test)
• β-galactosidase of coliform
substrate ONPG → nitrophenol (yellow)+Gal• β-glucuronidase of E. coli
fluorogenic substrate MUG
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.
Microflora of air
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 n
ormal 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
• Skin
• Conjunctiva
• Oral cavity
• Intestinal tract
• Upper respiratorytract
• Urogenital tractDental 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
• 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.
Numbers of bacteria that colonize different parts of the body
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 BodySite Total Bacteria Ratio
(per/ml or gm) Anaerobes:Aerobes
Upper AirwayNasal Washings 103-104 3-5:1Saliva 108-109 1:1Tooth Surface 1010-1011 1:1Gingival Crevice 1011-1012 1000:1
Gastrointestinal Tract
Stomach 102-105 1:1Small Bowel 102-104 1:1Ileum 104-107 1:1Colon 1011-1012 1000:1
Female Genital Tract
Endocervix 108-109 3-5:1Vagina 108-109 3-5:1
42
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
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: CorynebacteriumNeisseriaStaphylococcus MycoplasmaAdenovirusHerpervirus
Normal flora of the respiratory tract:
Staphylococcus aureus Staphylococcus epidermidis Corynebacterium varius Streptococci Neisseria species Haemophilus influenzaeMoraxella 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
52
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)
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
Epitelhial cells
acid-tolerant lactobacilli (Doderllein`s bacilli)
many glicogen
the pH is maintained between 4.4 and 4.6
I
II
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
III
IV
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.
Streptococci Lactobacterium Veilonella NeisseriaCorynebacteriumBacteroidesH. InfluenzaeTreponemaLeptospiraC. 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
Helicobacter pylori
Yeast
Sarcina
Fungi
Lactobacterium
Staphylococcus
Campylobacter
(all up to 30 species).
Normal flora of GI tract - stomach
Harm
• Causes gastric ulcers
• Probable association with duodenal ulcers
Helicbacter pylori
Microflora of the small intestine
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.
Bacteria: Bacteroides Bifidobacterium Eubacterium Fusobacterium Lactobacillus coliforms (Escherichia
coli, Enterobacter) fecal Steptococci Clostridium
Fungi: Candida
Protozoa: Entamoeba coli, Trichomonas hominis
Normal flora of the colon:
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 - BenefitsSynthesize 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 acidStreptococcus mutans
– Lactic acid demineralizes enamel
Normal flora - Risks
• Periodontal disease
– Gingiva, cementum, periodontal membrane, alveolar bone
– Rich in anaerobes
Opportunistic flora Some normal flora become
opportunistic pathogensStaphylococcus 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 (tropism)
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
