Normal Flora.pptx.........................

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1. Dr. Madiha Maboos Microbiology and Immunology 411-T

2. LEARNING OBJECTIVES: CHAPTER: NORMAL FLORA What is normal flora How important and beneficial it for us What are the factors that can effect normal flora of us Some basic normal flora found on us How normal flora protect us and what relation it forms with us Beneficial and harmful effects normal flora   os LEARNING Objectives

3. Normal Flora Normal flora are the microorganisms that live on another living organism (human or animal) or inanimate object without causing disease. The human body is not sterile; we become colonized by bacteria from the moment we are born. We are covered with, and contain within our intestines, approximately one hundred trillion bacteria that form the normal flora of our bodies. This normal flora helps to prevent us becoming colonized with more dangerous bacteria, which might lead to infection . The normal flora of humans are exceedingly complex and consist of more than 200 species of bacteria.

4. Microbial flora of the healthy human host The reasons for understanding the normal flora of the healthy human body ▶ Normal flora vs. human body ▶ Some normal flora: opportunistic pathogens when injury occurred, when resistance of body decreased, when moved to another site Origin of the normal flora Relationship between normal flora and human host Distribution and occurrence of the normal flora

5. Local Environment (pH, temperature, redox potential, O2, H2O, and nutrient levels…). Diet Age Sex Stress Health condition (immune activity …) Admission to the hospital After Taking Shower Antibiotics ,….. etc Three developmental changes in humans, weaning, the eruption of the teeth, and the onset and cessation of ovarian functions, FACTORS INFLUENCING NORMAL FLORA invariably affect the composition of the normal flora in the intestinal tract, the oral cavity, and the vagina, respectively. However, within the limits of these fluctuations, the bacterial flora of humans is sufficiently constant to a give general description of the situation

6. A human first becomes colonized by a normal flora at the moment of birth and passage through the birth canal . In utero, the fetus is sterile, but when the mother's water breaks and the birth process begins, so does colonization of the body surfaces . Handling and feeding of the infant after birth leads to establishment of a stable normal flora on the skin, oral cavity and intestinal tract in about 48 hours . The composition of a child’s bacterial flora is dependent on the mother’s micro flora, since she is the primary source for the child’s bacteria at the outset WHEN WE GET COLONIZED WITH NORMAL FLORA

7. Significance of Normal Flora Normal flora may aid the host in several ways: Aid in digestion of food Help the development of mucosa immunity Protect the host from colonization with pathogenic microbes. 10 6 pathogenic microbes GI infection w/ normal flora GI infection 8 w/ reduced flora after Streptomycin treatment 10 pathogenic microbes

8. Knowledge of the normal flora of the human body allows: Prediction of the pathogens causing infection as bacteria tend to grow in specific body sites e.g.  Streptococcus pneumoniae from the upper respiratory tract causing pneumonia or Staphylococcus aureus   from the skin causing intravenous  cannula infections. Investigation for underlying abnormalities in specific areas of the body when bacteria are isolated from normally sterile sites e.g. Escherichia coli isolation from blood cultures indicates probable intra- abdominal pathology because Escherichia coli is part of the normal gastrointestinal flora, Isolation of a  Viridans Streptococcus in blood cultures may indicate infective  endocarditis as a result of poor dentition as Viridans Streptococcus   are part of the normal mouth flora

9. It has been calculated that a human adult houses about 10 12 bacteria on the skin, 10 10 in the mouth, and 10 14 in the gastrointestinal tract. DENSITY OF NORMAL FLORA IN HUMANS

10. HUMANS AS HABITATS Colonization (and infection) frequently begin at mucous membranes These are found throughout the body. Consist of single or multiple layers of epithelial cells , tightly packed cells in direct contact with the external

11. Associations between Humans and the Normal Flora In fact, not much is known about the nature of the associations between humans and their normal flora, but they are thought to be dynamic interactions rather than associations of mutual indifference.  Both host and bacteria are thought to derive benefit from each other, and the associations are, for the most part, mutualistic .  The normal flora derives from their host receives: A steady supply of nutrients, A stable environment, And protection and transport. The host obtains from the normal flora: Nutritional and digestive benefits, Stimulation of the development and activity of immune system, And protection against colonization and infection by pathogenic microbes. While most of the activities of the normal flora benefit their host, some of the normal flora is: Parasitic (live at the expense of their host), Pathogenic (capable of producing disease). Commensal relationship (relationship where there is no apparent benefit or harm to either organism during their association is referred) Diseases that are produced by the normal flora in their host may be called endogenous diseases .  Most endogenous bacterial diseases are opportunistic infections , meaning that the organism must be given a special opportunity of weakness or let-down in the host defenses in order to infect. An example of an opportunistic infection is chronic bronchitis in smokers wherein normal flora bacteria are able to invade the weakened lung.

12. Sometimes the relationship between a member of the normal flora an its host cannot be deciphered. Such a relationship where there is no apparent benefit or harm to either organism during their association is referred to as a commensal relationship. Many of the normal flora that are not predominant in their habitat, even though always present in low numbers, are thought of as commensal bacteria. However, if a presumed commensal relationship is studied in detail, parasitic or mutualistic characteristics often emerge. COMMENSAL RELATIONSHIP . NORMAL FLORA ARE MUTUALISTIC Much is not known about the nature of the associations between humans and their normal flora, but they are thought to be dynamic interactions rather than associations of mutual indifference. Both host and bacteria are thought to derive benefit from each other, and the associations are, for the most part, mutualistic. The normal flora derive from their host a steady supply of nutrients, a stable environment, and protection and transport. The host obtains from the normal flora certain nutritional and digestive benefits, stimulation of the development and activity of immune system, and protection against colonization and infection by pathogenic microbes.

13. Normal Flora of The Skin The adult human is covered with approximately 2 square meters of skin. The density and composition of the normal flora of the skin varies with anatomical locale. The skin microbes found in the most superficial layers of the epidermis and the upper parts of the hair follicles are: Gram-positive cocci ( Staphylococcus epidermidis and Micrococcus sp.) And Corynebacteria such as Propionibacterium sp. These are generally nonpathogenic and considered to be commensal , although mutualistic and parasitic roles have been assigned to them. For example, staphylococci and propionibacteria produce fatty acids that inhibit the growth of fungi and yeast on the skin. But , The most important sites are: ` 1.Axilla 2 . G r oi n 3.Areas between the toes

14. COMMON SKIN BACTERIUM MAY BE NEW OPPORTUNISTIC PATHOGEN if Propionibacterium acnes, a normal inhabitant of the skin , become trapped in hair follicle, it may grow rapidly and cause inflammation and acne. Helococcus kunzii is a recently identified bacterium that is thought to be a nonpathogenic member of normal human skin flora and is rarely associated with skin infections . In the study though, the researchers report the isolation of the organism from an infected cyst on the breast of a 57-year-old immunocompromised woman . Finding provides further support for the opportunistic role of H. kunzii in causing infection in both immunosuppre ssed and immunocompetent patients," say the researchers .

15. A) The nares (nostrils) Staphylococcus epidermidis Corynebacterium Staphylococcus aureus Neisseria sp. Haemophilus sp Streptococcus pneumoniae B) The upper respiratory tract (nasopharynx). Non-hemolytic streptococci Alpha-hemolytic streptococci Neisseria sp. Streptococcus pneumoniae Streptococcus pyogenes Hemophilus influenzae Neisseria meningitidis C) The lower respiratory tract (trachea, bronchi, and pulmonary tissues): Usually sterile. The individual may become susceptible to infection by pathogens descending from the nasopharynx e.g. H. influenzae S. pneumoniae ). Normal Flora of the Respiratory Tract/ Nose

16. Normal Flora of The Oral Cavity Oral bacteria include: Viridans streptococci Lactobacilli Staphylococci ( S. aureus and S. epidermidis ) Corynebacterium sp. Bacteroides sp. Streptococcus sanguis (dental plaque) Streptococcus mutans (dental plaque) Actinomyces sp.

17. Normal Flora of The GIT   In the upper GI tract of adult humans, ( mainly acid-tolerant lactobacilli) can be cultured from the normal stomach. The proximal small intestine has a relatively sparse Gram-positive flora, consisting mainly of lactobacilli and Enterococcus faecalis .   The distal part of the small intestine contains, includes coliforms ( E. coli and relatives) and Bacteroides , in addition to lactobacilli and enterococci . The flora of the large intestine (colon) is qualitatively similar to that found in feces. Coliforms become more prominent, and enterococci , clostridia and lactobacilli can be regularly found, but the predominant species are anaerobic Bacteroides and anaerobic lactic acid may reside in the colon of humans. In bottle-fed infants Bifidobacteria are not predominant. When breast-fed infants are switched to a diet of cow's milk or solid food, bifidobacteria are progressively joined by: Enterics Bacteroides Enterococci Lactobacilli Clostridia

18. Functions and Products of Intestinal Flora Intestinal microbes carry out a variety of essential metabolic reactions that produce various compounds The type and amount produced is influenced by the composition of the intestinal flora and the diet Compounds produced include vitamins B 12 and K gas

19. SITES OF HUMAN BODY THAT THE NORMAL FLORA MICROBES COLONIZE Respiratory tract and head outer ear, eye, mouth, oropharynx, nasopharynx Sterile sites: sinuses, middle ear, brain, lower respiratory tract (trachea, bronchiole, lung) Gastrointestinal tract esophagus, stomach, small intestine, large intestine Genitourinary system anterior urethra, vagina Sterile sites: bladder, cervix, uterus Skin

20. Especially in hosts rendered susceptible by: 1. Immuno-suppression (AIDS & SCID ) 2. Radiation therapy & Chemotherapy 3. Perforated mucous membranes 4. Rheumatic heart disease…etc . NORMAL FLORA MAY ACT AS OPPORTUNISTIC PATHOGENS

21. Sterile tissues In a healthy human , the internal tissues such as: blood brain muscle cerbrospinal fluid (csf.) are normally free of microorganisms. Norm a l Flora abse n t i n …

22. Beneficial Effects of the Normal Flora The effects of the normal flora are inferred by microbiologists from experimental comparisons between "germ-free" animals (which are not colonized by any microbes) and conventional animals (which are colonized with a typical normal flora). Briefly, some of the characteristics of a germ-free animals that are thought to be due to lack of exposure to a normal flora are: 1. The normal flora synthesize and excrete vitamins in excess of their own needs, which can be absorbed as nutrients by their host. For example, in humans, enteric bacteria secrete Vitamin K and Vitamin B12, and lactic acid bacteria produce certain B-vitamins. Germ-free animals may be deficient in Vitamin K to the extent that it is necessary to supplement their diets. 2. The normal flora prevents colonization by pathogens by competing for attachment sites or for essential nutrients.   This is thought to be their most important beneficial effect, which has been demonstrated in the oral cavity, the intestine, the skin, and the vaginal epithelium.   3. The normal flora may antagonize other bacteria through the production of substances which inhibit or kill nonindigenous species. The intestinal bacteria produce a variety of substances ranging from relatively nonspecific fatty acids and peroxides to highly specific bacteriocins , which inhibit or kill other bacteria. 4. The normal flora stimulate the development of certain tissues , i.e., the caecum and certain lymphatic tissues ( Peyer's patches) in the GI tract. 5. The normal flora stimulates the production of natural antibodies. Since the normal flora behaves as antigens in an animal, they induce an immunological response, in particular, an antibody- mediated immune (AMI) response.   Low levels of antibodies produced against components of the normal flora are known to cross react with certain related pathogens, and thereby prevent infection or invasion.   Antibodies produced against antigenic components of the normal flora are sometimes referred to as "natural" antibodies.

23. FECAL BACTERIOTHERAPY DR.T.V.RAO MD 27 Fecal bacteriotherapy , which is now officially and scientifically known as fecal micro biota transplantation and is also referred to as fecal micro biota therapy, fecal transfusion, fecal transplant, stool transplant, fecal enema or human probiotic infusion ( HPI ), is a medical treatment for patients with pseudomembranous colitis (caused by Clostridium difficile ), or ulcerative colitis that involves restoration of colon homeostasis by reintroducing normal bacterial flora from stool obtained from a healthy donor.

24. Harmful Effects of the Normal Flora Harmful effects of the normal flora, some of which are observed in studies with germ-free animals, can be put in the following categories. All but the last two are fairly insignificant. 1. Bacterial synergism between a member of the normal flora and a potential pathogen. This means that one organism is helping another to grow or survive. There are examples of a member of the normal flora supplying a vitamin or some other growth factor that a pathogen needs in order to grow. This is called cross-feeding between microbes. Another example of synergism occurs during treatment of "staph-protected infections" when a penicillin-resistant staphylococcus that is a component of the normal flora shares its drug resistance with pathogens that are otherwise susceptible to the drug. 2. Competition for nutrients Bacteria in the gastrointestinal tract must absorb some of the host's nutrients for their own needs. However, in general, they transform them into other metabolisable compounds, but some nutrient(s) may be lost to the host. 3. Induction of a low grade toxemia Minute amounts of bacterial toxins (e.g. endotoxin ) may be found in the circulation. Of course, it is these small amounts of bacterial antigen that stimulate the formation of natural antibodies. 4. The normal flora may be agents of disease . Members of the normal flora may cause endogenous disease if they reach a site or tissue where they cannot be restricted or tolerated by the host defenses. Many of the normal flora are potential pathogens, and if they gain access to a compromised tissue from which they can invade, disease may result.

25. Microbiology of Air, Soil and water Air Microbiology : Air microbiology is a scientific discipline that concerns the microorganisms, including bacteria, archaea , fungi and viruses, in the atmospheric air. It is a sub discipline of environmental microbiology. Airborne microorganisms: Airborne particles are a major cause of respiratory ailments of humans, causing allergies, asthma, and pathogenic infections of the respiratory tract. Some important diseases of humans transmitted from person to person by inhaled airborne particles Virus diseases : Cold, flu, influenza. Bacterial diseases : Chickenpox ( Varicella ) Whooping cough ( Bordetella pertussis ) Flu (Influenza) Meningitis ( Neisseria species) Measles ( Rubeola ) Diphtheria ( Corynebacterium diphtheriae ) German measles (Rubella) Pneumonia ( Mycoplasma pneumoniae , Streptococcus species) Mumps (Mumps) Tuberculosis (Mycobacterium tuberculosis) Smallpox ( Variola ) Several other diseases, below, are acquired by inhaling particles from environmental sources, not directly from an infected person. Psittacosis (Chlamydia psittaci ) Dried, powdery droppings from infected birds (parrots, pigeons, etc.) Legionnaire's disease ( Legionella pneumophila ) Droplets from air-conditioning systems, water storage tanks, etc., where the bacterium grows. Acute allergic alveolitis (various fungal & actinomycete spores) Fungal or actinomycete spores from decomposing organic matter (composts, grain stores, hay, etc.)

26. Air Borne Human Diseases

27. Water Microbiology Importance of water : Water is the medium of life. All organisms are composed primarily of water. Liquid water is the medium in which all cellular chemical reactions occur. It is essential for survival and growth of organism. Microbiology of Water: Study of microorganisms and their communities inwater environment is called Aquatic microbiology. The scope of Aquatic Microbiology is wide and includes the habitats like planktons, benthos, microbial mats and bio-film which may be found in lakes, rivers, streams, seas, groundwater, rain, snow and hail. Water Microbiology Water born diseases H 2 O can act as a vector for the transmission of bacterial, viral and protozoan agents which cause a variety of diseases (mainly intestinal). It can also be linked to worm invasions and viral/protozoan diseases transmitted by insects (aquatic hosts or insect breeding in H 2 O - indirect). Water is responsible for, by some estimates , approximately 80% of all infectious disease not just waterborne diseases, but any disease where water plays a role. Water contains a variety of microbes including: Viruses Bacteria Protozoa Helminthes Fungi

28. Water Microbiology Importance of water : Water is the medium of life. All organisms are composed primarily of water. Liquid water is the medium in which all cellular chemical reactions occur. It is essential for survival and growth of organism. Microbiology of Water: Study of microorganisms and their communities inwater environment is called Aquatic microbiology. The scope of Aquatic Microbiology is wide and includes the habitats like planktons, benthos, microbial mats and bio-film which may be found in lakes, rivers, streams, seas, groundwater, rain, snow and hail. Water Microbiology Water born diseases H 2 O can act as a vector for the transmission of bacterial, viral and protozoan agents which cause a variety of diseases (mainly intestinal). It can also be linked to worm invasions and viral/protozoan diseases transmitted by insects (aquatic hosts or insect breeding in H 2 O - indirect). Water is responsible for, by some estimates , approximately 80% of all infectious disease not just waterborne diseases, but any disease where water plays a role. Water contains a variety of microbes including: Viruses Bacteria Protozoa Helminthes Fungi

29. Water Microbiology Importance of water : Water is the medium of life. All organisms are composed primarily of water. Liquid water is the medium in which all cellular chemical reactions occur. It is essential for survival and growth of organism. Microbiology of Water: Study of microorganisms and their communities inwater environment is called Aquatic microbiology. The scope of Aquatic Microbiology is wide and includes the habitats like planktons, benthos, microbial mats and bio-film which may be found in lakes, rivers, streams, seas, groundwater, rain, snow and hail. Water Microbiology Water born diseases H 2 O can act as a vector for the transmission of bacterial, viral and protozoan agents which cause a variety of diseases (mainly intestinal). It can also be linked to worm invasions and viral/protozoan diseases transmitted by insects (aquatic hosts or insect breeding in H 2 O - indirect). Water is responsible for, by some estimates , approximately 80% of all infectious disease not just waterborne diseases, but any disease where water plays a role. Water contains a variety of microbes including: Viruses Bacteria Protozoa Helminthes Fungi

30. Disease Caused by Water Water-Associated diseases Water-washed diseases: Water-associated diseases can be classified under 4 different categories: Water-borne diseases: They are produce by ingestion of contaminated water. They are mainly enteric diseases. Classical H2O -borne diseases are mostly: Protozoal infection ; Amoebiasis , Giardia and Cryptosporidium etc. Bacterial infection; cholera and typhoid fever (rare),  Campylobacteriosis , bacillary dysentery, leptospirosis (rare), dysentry , E.coli infections. Viral infections; infectious hepatitis, poliomyelitis, SARS (Severe Acute Respiratory Syndrome). Two basic patterns of polio infection are: A) A minor illness which does not involve the CNS, sometimes called abortive poliomyelitis, B) Major illness involving the CNS, which may be paralytic or non-paralytic. • Helminthes infection: Ringworm or Tinea is a typically mild disease of the skin, scalp or nails caused by a fungus. • It’s link with water is via poor personal domestic hygiene and shortage of water for cleaning and washing. Diseases caused by poor personal hygiene. Obviously more common in tropical, 3rd world countries where maybe water scarcity is present. Intestinal: Shigella (dysentery); typhoid; cholera; scabies, Yaws (Yaws is caused by T. Pallidum subspecies pertenue , affects skin, bone and cartilage), l eprosy , conjunctivitis, and non-intestinal infections (Eye & skin diseases); other skin infections and ulcers. Campylobacter; Giardia ; Cryptosporidium; viruses.

31. Disease Caused by Water Water-based diseases: Water-related diseases Diseases caused by pathogens that have a complex life- cycle which involves an intermediate aquatic host. All of these diseases are caused by worms, Schistosomiasis : caused by the Schistosoma worm which uses aquatic snails as an .intermediate host, also known as Bilharzia / bilharziosis or snail fever is a parasitic disease caused by several species of platyhelminths . Dracunculiasis : cause by Guinea worm which uses a small crustacean as an intermediate host Diseases caused by pathogens carried by insects that live near H2O and act as mechanical vectors. Difficult to control and diseases are severe Examples: Yellow fever (viral disease) is transmitted by the mosquito Aedes spp. Dengue (viral) transmitted by the mosquito Aedesaegypti (breeds in water); Malaria is caused by a protozoan (Plasmodium spp.) and is transmittedby a mosquito (Anopheles spp.) Trypanosomiasis (Gambian sleeping sickness) is also caused by a protozoan transmitted by the riverine Tsetse fly ( Glossina spp .)

32. HOW TO PREVENT….? Always wash your hand before handling food especially  and after using toilet Wash your fruits and vegetable before use as it contain  harmful chemicals and microbes. Don’t drink water from river, lakes and ponds.  Try to adopt healthy and good hygiene as possible   

33. Soil Microbiology: A study of the microorganisms in soil, their functions, and the effect of their activities on the character of the soil and the growth and health of plant life. Microorganisms in soil are important because they affect the structure and fertility of different soils by showing phenomenon of mutualism and symbiosis. Classification of Soil Microorganism : Soil microorganisms can be classified as: Bacteria. Actinomycetes Fungi. Algae. Protozoa. Bacteria Bacteria are the smallest organisms in the soil and are the only soil microorganisms that are prokaryotic. Bacteria are the most abundant microorganisms in the soil, and serve many important purposes, one of those being nitrogen fixation among other biochemical processes. Bacteria dot the surface of strands of fungal hyphae . Bacterial genera, Pseudomonas can metabolize a wide range of chemicals and fertilizers. Another genera known as Nitrobacter can only derive its energy by turning nitrite into nitrate, which results in a gain of oxygen and is known also as oxidation.

34. Soil-related bacterial infections: • Tetanus • Botulism • Wound infections • Gastroenteritis • Anthrax Actinomycetes : Actinomycetes ( actinobacteria ) are soil µ-organisms. Actinobacteria are a group of Gram-positive bacteria. Actinobacteria include some of the most common soil life, playing an important role in decomposition of organic materials, such as cellulose and chitin, and thereby playing a vital part in organic matter turnover. This replenishes the supply of nutrients in the soil and is important part of humus formation.

35. Fungi : Next to bacteria, fungi are abundant in soil population compared to other microorganisms. Fungi are important in the soil as: Food sources for other Beneficial symbiotic relationships with plants or other organisms. Help to reduce crop residues. Biochemically process nutrients to improve the soil. Pathogenic fungi: • Coccidioides , • Progressive Coccidioidomycosis respiratory failure, chronic pneumonia, and dissemination to other organs, including skin, bones/joints, and the central nervous system. Many infections are inapparent . • Blastomycesdermatitidis • Pulmonary blastomycosis Other infections due to fungi residing in soil related environment include; • Penicilliummarneffei , may cause a fatal systemic mycosis in patients infected with HIV. • Sporotrichosis is a rare, subacute to chronic mycosis caused by the dimorphic fungus Sporothrixschenckii . • Infections caused by Aspergillus species: pulmonary or sinus fungus balls; chronic pulmonary aspergillosis ( cavitary , fibrosing , subacute ).

36. Summary What is normal flora How important and beneficial it for us What are the factors that can effect normal flora of us Some basic normal flora found on us How normal flora protect us and what relation it forms with us Beneficial and harmful effects normal flora

37. Further Reading Brooks G, Carroll KC, Butel J, Morse S, Mietzner T.  Jawetz , Melnick & Adelberg's Medical Microbiology and Immunology. 24 th  Ed. Churchill Livingstone; 2010. Collins CH, Lynes PM, Grange JM, Falkinham JO. Collins & Lyne’s  Microbiological Methods. 8 th  Ed. Vutterworth Heineman ; 2004. Fraise A, Lambert PA, Maillard JY. Russell, Hugo & Ayliffe's Principles and Practice of Disinfection, Preservation & Sterilization. 4 th  Ed. Wiley Blackwell; 2004. Harvey RA, Champe PC, Fisher BD. Microbiology: Lippincott's Illustrated Reviews Series. 4 th  Ed. William & Willkins ; 2004. Hugo WB, Russell AD. Pharmaceutical Microbiology. 7 th  Ed. Black Well Science Ltd; 1998.   Hugo WB, Denyer SP, Hodges NA, Gorman SP. Hugo and Russell's pharmaceutical microbiology. 7 th  Ed. Wiley Blackwell; 2004. McKane L, Kandel J. Microbiology: Essentials and Application. 2 nd  Ed. McGraw Hill Inc; 1995. Pelczar MJ. Microbiology. 7 th  Ed. McGraw Hill Inc; 2007. Pommerville JC. Alcamo’s Funtamentals of Microbiology. 9 th  Ed. John Bartlett Publishers; 2010. Singleton P, Sainsbury D. Dictionary of Microbiology and Molecular Biology. 3 rd  Ed. John Willey & Sons; 2006. Willey J, Sherwood L, Woolverton C. Prescott's Microbiology. 8 th  Ed. C Brown Publishers; 2010. courses.lumenlearning.com/microbiology/chapter/viruses https://www.vaccines.gov/basics/types