Lecture 5 Flashcards

1
Q

Microbiome

A

Microbiome– total community of microorganisms in an environment or body location

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2
Q

Normal flora

A

Microorganisms that are present either in or on an animal that is “healthy”
Constant change in numbers and species within the body
Relationship between the normal flora and host is described as SYMBIOSIS
Mutualism
Commensalism

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3
Q

Symbiosis

A

An association of two or more different species of organisms
In Microbiology, refers to:
1) Bacterial/virus/yeast
2) Animal/plant
Relationship can be positive or negative

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4
Q

Ectosymbionts

A
  • live on the host
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5
Q

Endosymbionts

A

live in the host

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6
Q

Mutualism

A

Both organisms benefit from the relationship
Eg. rumen bacteria

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7
Q

Commensalism

A

Type of symbiosis where only one of the organisms benefits from the relationship
The other is neither helped nor harmed
“Commensal” is the organism that is helped

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8
Q

Competition between micro-organisms

A

Occurs when 2 or more microorganisms share a space
Compete for the available resources (nutrients, space

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9
Q

Outcomes of competition between microorganisms

A

1 one will out-compete the other

#2 both will exist at lower levels

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10
Q

Roles of normal flora

A

Aids with digestion of food products
- Especially important in ruminant ability to digest insoluble fiber
Provides essential nutrients
- GI flora synthesize vitamins, essential amino acids
Stimulates the immune response
- Maintains a low-level of ongoing immune activity so can respond faster in an infection
Protect against infection by more virulent microbes

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11
Q

How does normal flora fight against infection

A

Through competition for space, nutrients
Bacteria can alter pH of environment to inhibit growth of other microbes
Bacteria produce their own anti-microbial factors (bacteriocins) that prevent colonization by less desirable bacteria
Maintain low levels of immune stimulation
Bind to and block pathogenic bacteria from binding to receptors on cell surfaces

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12
Q

How do you control normal flora

A

Competition
- Each population exists in lower numbers than if only one population was present
The immune system
- Balance between normal flora and the immune system
- Immune system maintains normal flora at acceptable levels

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13
Q

Diseases are caused when by normal flora

A

There is too little normal flora
There is too much normal flora
Normal flora moves to a new location where it is not normally found

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14
Q

Overgrowth of normal flora

A

Most common cause is decreased function of the immune system
Can’t keep levels of normal flora in check
Can also occur if normal flora moves to a new location
When normal flora causes disease, it is now called an opportunistic pathogen
An infection caused by normal flora is called an opportunistic infection

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15
Q

Loss of normal flora

A

Can be decrease in overall numbers of bacteria or decreased number of species
Results in lack of competition, lack of bacteriocins, pathogenic bacteria have space to attach…
Allows for pathogenic species to colonize or allows increase in numbers of one species normally present in low numbers
Eg. Oral antibiotics can cause Clostridial enteritis
Eg. Loss of skin bacteria leads to yeast overgrowth
Animals grown in labs without normal flora have very high risk of infection/disease

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16
Q

Normal flora in nose

A

Staphylococcus aureus and Staphylococcus epidermidis
Found just inside nostrils

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17
Q

Normal flora in oro-pharnyx

A

Combination of aerobic and anerobic bacteria
Common e.g. - Staphylococcus, Streptococcus, Haemophilus
Mostly non-pathogenic bacteria unless they gain access to tissues are that normally sterile (sinuses, middle ear, brain)

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18
Q

Normal flora in trachea

A

“Transiently colonized” by bacteria from the oronasopharynx
Microbes are continually being removed by the mucociliary elevator
Mucus traps microbes and particles
Cilia located on mucosal epithelial cells sweep the mucus upwards into the oral cavity where it can be spit out or swallowed
One of the main mechanisms that keeps microbes out of the lower airways
Damage (virus infection, smoke inhalation, etc.) will increase risk of infection

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19
Q

Normal flora in lower resp tract and how are microbes removed

A

NO normal flora - generally sterile
May transiently colonize with bacteria from the upper respiratory tract, but these bacteria cannot establish
Microbes are continuously removed by:
Mucociliary elevator
Phagocytosis by alveolar macrophages (WBC in alveoli)
Lysozyme in mucus

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20
Q

Risk factors for microbial colonization of the lower respiratory tract are

A

Acute or chronic aspiration
Inhaling infectious materials into the lungs, usually from the oral cavity or esophagus/stomach
Increased risk with megaesophagus, gastroesophageal reflux, chronic vomit, cleft palate
Damage to the mucus-generating cells and cilia of the upper respiratory tract
Traumatic/chemical injury (e.g., smoke inhalation)
Primary viral infection causes damage to cells (seen in kennel cough, shipping fever in cattle)
Inflammation (asthma)

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21
Q

Normal flora skin

A

Few normal flora due to hostile environment
Dry
Oils, pH of sweat is anti-bacterial
Sloughing of skin cells - adhered bacteria also fall off
Normal flora tends to be transient

22
Q

Common flora on skin

A

Staphylococcus intermedius
Staphylococcus aureus
Fungi (Malasezzia) in moist areas, such as armpits, groin, flank folds
Less often: Corynebacterium, Clostridium perfringens,Streptococcus, Micrococcus

23
Q

Abnormal skin flora

A

If skin becomes warm/moist, there will be increased bacteria and yeast -can cause pathology
Breach of intact skin allows bacteria to adhere to underlying subcutis and proliferate
If bacterial population is disrupted, yeast population may go into “overgrowth” and cause disease

24
Q

Normal hair flora

A

Contaminated by anything in the environment
Always considered a contaminant
Different flora with external hair versus hair follicle
Bacteria, mites (demodex)
Can support its own biofilm under certain environmental conditions

25
Normal eye flora
From birth throughout life, there are small numbers of bacteria present on the conjunctiva Includes Staphylococcus and Streptococcus Numbers held in check by lysozyme in tears
26
Normal external ear flora
Similar bacteria and yeast as found on skin Most common:Staphylococcus Also Streptococcus, Pseudomonas, Enterobacteriacae (Gram negative intestinal bacteria), Malasezzia (yeast)
27
Normal mouth flora
Contains hundreds to thousands of different species of microbes Divided into 2 populations: Aerobic – associated with teeth Facultative anaerobes, anaerobes – periodontium Bacterial plaque = mat of microbes (biofilm) solidly attached to teeth Increased colonization if enamel wear/scratches, malocclusion, diet high in fermentable carbohydrates, poor hygiene If plaque is extensive, will extend subgingivally where it changes from aerobic to anaerobic populations
28
Normal monogastric stomach flora
Limited number of normal flora Most common are Lactobacillus, Enterococcus, Helicobacter felis
29
Rumen flora
Distinct and complex normal flora Allows animal to digest and extract nutrients from cellulose (e.g. hay, grass) Microbes themselves are also digested by the animal to provide macronutrients Ability to derive nutrition from cellulose and normal flora enable ruminants to survive under very harsh nutritional/environmental conditions (deserts, arctic tundra, rocky mountains) 10^12 microbes/ml rumen fluid Composed of bacteria, protozoa, fungi, archaea and viruses Gram negative bacteria predominate Most common bacteria are E. coli, Lactobacilli, Streptococcus bovis, Bacteroides Fibrolytic microbes break down cellulose Mostly strict (some facultative) anaerobes Anaerobic bacteria ferment sugars to alcohols and acids that are absorbed through the rumen wall Lactobacilli produce building blocks for milk sugar production
30
Archaea
Archaea are evolutionarily “old” prokaryotic organisms Make-up ~3% of microbial mass Convert hydrogen gas and CO2 (by-products of cellulose fermentation) to methane: H2+ CO2 → CH4 Methane is belched out during rumination
31
Viruses in rumen flora
Bacteriophage are viruses that infect and kill bacteria Causes cells to lyse Contents are then used as nutrients by the animal
32
Normal flora in small intestine
Bacteria, fungi, protozoa Very few microbes in the duodenum Microbe numbers increase moving distally towards cecum Mixed anaerobes Strict anaerobes > facultative anaerobes Enterococcus, E. coli, Enterobacteriacae, Clostridium, Lactobacillus Some pathogenic bacteria may be present in very small numbers in healthy animals ( Salmonella, Campylobacter– both associated with food poisoning)
33
Function of small intestine flora
Vitamin synthesis Vitamin K production Vitamin B9 (folate), B12 (cobalamin) Contribute to digestion, especially fiber Enhance segmental contractions, peristalsis Inhibit colonization by pathogenic bacteria Competition Production of bacteriocins Stimulate immune tissues in the small intestine Take part in drug metabolism pathways
34
Normla flora in large intestine
Largest microbial population in body 10^11 bacteria / gram feces Mostly anerobic bacteria (strict and facultative) Dominant species is E. coli in cats, dogs, bovids Also fecal Streptococcus ,Enterococcus ,Klebsiella, Bacteroides, Clostridium, Lactobacillus, Bifidobacterium, Enterobacteriaceae Also Candida (yeast), enterovirus, adenovirus Strains of E. coli that are pathogenic to humans found in 30% of dog feces sampled in one study Also present in cattle feces Colonization starts at birth with ingestion of birth canal secretions and feces Also acquired through nursing Profile of flora changes with diet Will also change with GI inflammation Rapidly affected by oral antibiotics Oral antibiotics will ALWAYS affect the normal GI flora If enough of the normal flora is eliminated, tend to see Clostridial overgrowth, which can lead to diarrhea and/or colitis Lack of balance between normal flora and the immune system can contribute to Irritable Bowel Disorder
35
Coliforms
Rod-shaped Gram negative Motile Non-spore-forming bacteria Can ferment lactose Normally found in feces Also can be found in water, soil, on vegetation when found in the environment, it is an indicator that there was fecal contamination
36
Fecal coliforms include
Escherichia, Enterobacter, Klebsiella
37
SIBO stands for and is caused by
Small Intestinal Bacteria Overgrowth When the normal flora of the small intestine starts to resemble the colon Occurs when there is decreased peristalsis and/or damage to the cecum --> allows normal large intestinal flora to migrate into small intestine
38
Colon bacteria affects of coliforms
Create gas → cause gas distension Interfere with digestion/absorption Compete for nutrients
39
Contamination by coliforms results in
Inflammation, diarrhea, colic
40
Normal flora of liver
The liver is sterile (no normal flora) If there is biliary cholestasis (lack of proper bile acid flow through the bilary ducts), bacteria that was in the gallbladder could potentially enter the liver After death there is rapid contamination of the liver from intestinal bacteria
41
Normal flora of perpuce
Contaminated Normal flora: Staphylococcus aureus, Mycoplasma spp.; also bacteria normally found on skin and fur Can habor chronic asymptomatic pathogens that are NOT considered normal flora
42
Normal flora of vulva
Mix of bacteria found on skin and vagina
43
Normal flora in vagina and cervix
Flora changes with cycling estrogen levels Lactobacillus, Streptococcus canis, Staphylococcus aureus
44
Normal flora in urethra
Distal urethra -Normal flora consistent with skin microbes -Colonization with normal flora from the intestinal tract tends to cause disease Proximal urethra and bladder in males -sterile Proximal urethra and bladder in females -Supposedly sterile, in reality is transiently colonized by flora from the distal urethra -numbers are very, very low
45
Colonization of the urethra and bladder are caused by and prevented by
Colonization in the proximal urethra and bladder is with microbes from the skin, fur, external genitalia and feces Colonization is usually prevented by: Flushing during urination Distance from the outside Urine pH inhibits growth of microbes Normal urine pH is 6.2-6.5 Some bacteria can produce urease, which cleaves urea to increase the pH of the urine so it is more hospitable to colonization Epithelial cells produce antimicrobial substances that inhibit bacteria from attaching and replicating
46
Flora in ureters, prostate, uterus, and kidneys
Always sterile - any microbes present are always considered pathogenic Prostate secretes its own prostatic anti-bacterial factor Uterus is protected by the cervix Production of acid by Lactobacillus in the vaginal mucosa also prevents colonization by other bacteria Changes to the cervix and vagina during estrus increase risk that bacteria can enter uterus Many persistent pathogens can potentially colonize the genital tract (i.e., STDs) May be present in otherwise healthy animals but are never considered normal flora
47
Normal flora in dry cow mammary glands
Bacillus spp. and Staphylococcus hominis most important Prevent colonization of teats with pathogenic bacteria
48
Normal flora in milking cows mammary glands
Mammary glands at constant risk of infection, Milk is an ideal culture medium Trauma to the teat ends during milking allow bacteria to enter readily
49
Microbe free tissues
Internal tissues Brain, spinal cord Bone, muscle, joints Heart, blood Inside of the eyeball Kidneys, liver, spleen Peritoneum, pleural space Lower respiratory tract Bronchi, bronchioles, lung parenchyma Upper urogenital tract (Proximal urethra and bladder), ureters, kidneys, uterus, prostate
50
Axenic animals are and used for
AKA germ-free animals Used to describe an animal that is totally free of microorganisms NO infection NO normal flora Animal is born by cesarean under complete asepsis → transferred to sterile environment (sterile air, food, bedding, water) Used for research Very high risk of infection if exposed to the normal environment
51
Gnotobiotic animals are and used for
Used for research These are axenic animals, to which known, specific microbes are introduced Result is an animal with known identities of all normal flora and other microbes Must be maintained in otherwise sterile environments to prevent introduction of unknown microbes
52
SPF is and used for
Specific Pathogen Free Used for research Animals that definitely do not have a specific microbe/pathogen If that microbe/pathogen is introduced to the animal, any change that occurs is specifically attributed to the introduction of the new microbe/pathogen