Module/Chapter 2: Human microbiota

What is the formal definition of the human microbiota?

Commensal(microbes that benefit from the host whereas the host is neither benefited nor harmed) organisms that co-exist with humans without causing harm. Microbes that are frequently found on or in the human body of healthy persons.

The oral cavity is a _________ environment.

Complex

What is the most common member of the GI tract?

Escherichia coli

How did Escherichia coli get its name?

Escherichia coli was identified from the colon hence "coli", from a German soldier in the beginning of the 20th century.

T/F: Skin covers a very large surface area of 2m^2; therefore, it has the largest biomass of microbes.

False; Although the skin contains a large surface area of 2m^2, it does not contain the largest biomass of microbes. The gastrointestinal tract contains the greatest biomass.

T/F: Both regions of the urinary tract are colonized by microbiota.

False; Microbiota only colonize the lower region of the urinary tract, whereas the upper region is considered sterile.

T/F: Bacteria are located far from the air when they are anaerobes.

False; Small amounts of oxygen diffuse into deeper tissue layers and can readily be used by host cells or by actively metabolizing aerobes and facultative anaerobes- therefore, anaerobic conditions can be found a fraction of a millimeter below the surface. Therefore, other bacteria utilize all the oxygen which creates a favorable environment for anaerobes.

T/F: Most members of the human microbiota are virus', fungi, protozoa and worms.

False; bacteria are the majority of the human microbiota, whereas virus' fungi, protozoa and worms are found in low numbers in a healthy individual.

T/F: Normal microbiota colonize the lower respiratory tract.

False; normal microbiota colonize ONLY the upper respiratory tract(nasopharynx, oral cavity, and throat[pharynx]). The lower respiratory tract is considered STERILE.

T/F: Normal microbiota colonize both the upper and lower respiratory tract.

False; normal microbiota colonize ONLY the upper respiratory tract(nasopharynx, oral cavity, and throat[pharynx]).The lower respiratory tract is considered STERILE.

T/F: microbes of the human microbiota are able to colonize any location/tissue/organ of the body(and not cause an infection).

False; there are sterile parts of the body that microbes of the human microbiota are not able to colonize and if they do then an infection will occur.

What types of bacteria of normal microbiota colonize the upper respiratory tract?

G + and G- Examples of G+ bacteria that colonize the respiratory tract include: -Staphylococcus -Streptococcus -Corynebacteria. Examples of G- bacteria colonize the respiratory tract include: -Neisseria -Haemophilus

What kind of conditions do gram + bacteria grow better in?

Gram + bacteria survive better in the dry conditions, like that of the skin.

What bacteria found in the human microbiota, specifically within the STOMACH, is considered to be a carcinogen in some individuals?

Helicobacter pylori

How common is helicobacter pylori in the stomach of healthy individuals?

Helicobacter pylori is found in the stomach of 1 out of every 2 healthy individuals = 50% of healthy individuals.

What is most common term used today to describe the microbes that are found on or in the body that which do not cause an infection?

Human microbiota

What are examples of bacteria in the human microbiota that colonize the GI tract?

-Helicobacter -Escherichia coli

What are the different terms that describes the microbes that are found on or in the body that which do not cause an infection?

-Human microbiota -Normal flora -Microbial flora

What are examples of bacteria of the human microbiota that colonize the genital system/female vagina?

-Lactobacilus -Escherichia -Streptococcus -Yeast candida albicans

What are the sites that in accordance to class that microbiota colonize?

-Skin -upper respiratory tract -oral cavity -gastrointestinal tract -urinary tract -genital system

What are examples of gram + bacteria that colonize the skin and thus, are able to handle dry conditions of the skin?

-Staphylococcus -Streptococcus -corynebacteria

What anatomical structures are found within the gastrointestinal tract?

-Stomach -Small intestine -large intestine

What are examples of bacteria of the human microbiota that colonize the urinary tract?

-Streptococcus -Escherichia

What are some common bacteria that colonize the oral cavity?

-Streptococcus -Actinomyces -Borrelia

What are some examples of anti-colonizing properties of the host?

-Sweeping microbes away by liquid currents -Kill microbes with host phagocytes -Starve microbes for lack of needed nutrients -Inhibit growth by secreting antimicrobial factors

What are examples of substances that are produced by the human microbiota that do not allow the colonization of new comers?

-antibiotics -lethal proteins like bacteriocins

What are the roles of the human microbiota?

-common source of infection(opportunistic pathogens) -immune stimulation (cross reactivity) -Keeping out invaders(bacteriocins) -Role in human nutrition and metabolism -Source of carcinogens

How do bacterial overcome this anti-colonization property of the host: Kill microbes with host phagocytes

-microbes avoid being taken up; for example certain bacteria contain a capsule that contains this function which helps to avoid being lysed. -kill the phagocyte; for example, with various toxins.

What anatomical structures are found in the upper respiratory tract?

-nasopharynx -oral cavity -throat

Where are microbes within the human microbiota largely found within the body?

-skin -upper respiratory tract -digestive tract (gut)[mouth to anus] -urinary tract -genital system(vagina)

How do members of the human microbiota keep out new members?

-they occupy space that cannot be filled -they produce substances that don't allow the colonization of new comers -they may take up nutrients that the new member may need to grow/survive

What anatomical structures are found in the lower respiratory tract?

-trachea -bronchi -lungs

What factors effect the distribution/diversity of Human microbiota that colonize the skin?

-weather -age -personal hygiene

How much bacteria is found in the GI tract?

10^14 bacteria = largest microbiota biomass

What type of cells/surface do microbes of the human microbiota reside?

A lot of members of the human microbiota colonize mucous membranes/mucus; furthermore, epithelial cells typically contain mucus membranes.

What are antigenic stimulations?

Antigenic stimulations are substances that stimulate the immune system.

What is cross reactivity?

Bacterial antigens from the human microbiota trigger antibodies that other antigens( with the same properties) is able to do as well.

Why is the skin a unique site for human microbiota colonization?

Because it is in direct contact with the outside environment.

Why do gram + bacteria grow best in dry conditions found on the skin?

Because they have a thick cell wall.

________ ___________ helps to control the number of microbes on the skin.

Personal hygiene

How can compounds become carcinogenic?

Some compounds become carcinogens only after being modified, which can occur through the action of microbes in the large intestine.

Because microbe numbers are low in sterile sites, what does this effect?

Sterile sites and those that are prone to infection(no microbial competition), typically contain host defenses that are more intense.

T/F: Physicians see more patients with diseases resulting from the human microbiota than from agents acquired outside the body.

TRUE; thus, endogenous infections are more common then exogenous.

What is the "diet effect" associated with microbes of the human microbiota that colonize the oral cavity?

The "diet effect" is an important factor in determining what kind of microbial species we have in the microbiota of the oral cavity. When we eat there is a lot of nutrients and fluids and water present, whereas between meals the environment of the oral cavity changes. Therefore, microbes must be able to adapt and go from extreme situations where there are not alot of nutrients and water and times when there is plenty and thus, utilizing those resources to grow in large numbers.

What are other defenses does the body contain other than the immune system that are put in place to prevent normal flora from entering sterile sites of the body?

The body has MANY different types of barrier defenses. -lysozymes in tears/gut -mucous membranes/mucus -saliva -proteolytic enzymes -diarrhea -vomiting

What is the microbiome?

The collective genomes of the microbiota.

What region where human microbiota are found contains the largest biomass?

The gastrointestinal tract; large intestine In the gut alone, the number of species in an individual is certainly in the hundreds and perhaps thousands.

How does the human microbiota help the immune system?

The human microbiota helps train the immune system because antigens from microbes(in the normal flora) can be similar to other pathogens that are a threat to the body. Furthermore, this helps to activate immune cells so they can react faster when they do encounter pathogens; for example, IgA and IgG found on mucosal surfaces.

What type of microbes are found in the human microbiota?

The human microbiota not only contains bacteria but viruses, fungi, protozoa, and a limited number of archaea.

What are the sterile sites of the body that microbes of the human microbiota should NOT colonize?

The sterile sites of the body include those not mentioned in the five sites that they are commonly found; therefore, they are NOT found in MOST parts of the body.

Microbes that enter sterile parts of the body possess what typical characteristic?

They are transit and do not usually colonize; furthermore, if they do it can result in an infection.

What is an important role of human microbiota in the large intestine?

They play are large role in the uptake of nutrients; meaning they help break down things into usable forms for our bodies to digest

What type of microbes are the MOST common cause of infections/diseases?

Those apart of the normal microbiota that get into sterile sites that they should not be. For example, staphylococcus, and streptococcus are found in the human microbiota but are also known to cause human infections/diseases. They act as opportunists.

How do microbes persist in the body?

To colonize the human body, invading microorganisms must be able to resist host mechanisms that could dislodge or kill them as well as compete successfully with other microbial species.

What are "transient" members of the human microbiota?

Transient = lasting only a short time Pathogenic microbes found in the normal flora of some individuals.

Who and where is trouble unlikely in the human body?

Trouble is unlikely from the human microbiota and therefore in sites that the human microbiota reside like the upper respiratory tract, the digestive tract, urogenital tract and the skin.

T/F: Gingival pocket or in feces, strict anaerobes outnumber the others by 100 to 1 or more.

True

T/F: In the early days, it was thought that most bacteria of the body were aerobes or facultative anaerobes.

True

T/F: Most bacteria members of the human microbiota are strict anaerobes.

True

T/F: Research has indicated that the normal microbiota as a risk factor for some cancers.

True

T/F: Research has shown that some microbiota de-toxify some potential carcinogens by degrading them.

True

T/F: strict anaerobic bacteria are found in the large intestine.

True

T/F: the urinary tract contains a lower and upper region.

True

T/F: It has been found that the normal microbiota of the intestine plays a role in human nutrition and metabolism.

True; Although research is still going to prove this. for example, some microbes in the large intestine are able to digest complex polysaccharides as well as we intestinal bacteria such as E. coli can produce vitamin K.

T/F: A 15 year old would have a different population of microbes in their human microbiota vs a 60 year old.

True; As we age, the physiology of the skin changes which creates different environments for different microbial species.

T/F: Normal microbiota constituents can find themselves in unaccustomed sites of the body possibly causing disease.

True; For example, when a trauma or surgical wounds occurs near the large intestine, microbiota in the large intestine can cause abscess.

T/F: People who live in different climates will have different normal flora on their skin.

True; Weather/climate is a factor that influences the skin human microbiota.

T/F: bacteria of the normal microbiota that colonize the skin can be found in the urinary tract.

True; because they can pass into the urinary tract. Examples of these bacteria are Streptococcus

T/F: Infectious diseases can occur if microbes of the human microbiota are given the opportunity to colonize somewhere new.

True; for example E. coli from the large intestine find its way into the urinary tract can cause a UTI or if E. coli from the large intestine find its way into the blood causing bacteremia. This is an example stating that a member of the human microbiota can not only cause an infection/disease when they entire sterile sites but also if they enter a NEW location they are not normally found. Of course, the environment must be able to promote growth.

T/F: Most parts of the body are sterile and you would not find members of the human microbiota there.

True; human microbiota are only found in the upper respiratory tract, digestive tract, urogenital tract and the skin.

T/F: The microbiota of someone who doesn't have access to a shower would be different from someone who does have access to a shower.

True; personal hygiene is a factor that influences the skin human microbiota.

Where do UTI infections typically occur?

UTI infections typically occur in the bladder; furthermore this makes sense because the bladder is apart of the upper urinary tract and is sterile. So when bacteria enter the bladder it causes an infection.

Although not alot of bacteria are able to withstand an acidic environment such as that of the stomach.....

different microbial species have adapted to be able to survive in different pH.

Recall, is the mouth apart of the respiratory system or the digestive system?

digestive system

The human microbiota plays a critical role in _________ and _________.

health and disease

The lower respiratory tract is a sterile environment in a __________ individual.

healthy

Although the stomach is very acidic, what bacteria is able to survive this environment and thus, colonizes this area?

helicobacter pylori Note; not a lot of bacteria are able to withstand the acidic environment.

How do bacterial overcome this anti-colonization property of the host: Starve microbes for lack of needed nutrients

microbes derive the needed nutrients from the host cells; for example containing certain hemolysins or proteins like siderophores that help bacteria derive need nutrients from RBC's.

How do bacterial overcome this anti-colonization property of the host: Sweep microbes away by liquid currents

microbes have factors(adhesions) that allow them to adhere to epithelial cells.

How do bacterial overcome this anti-colonization property of the host: Inhibit growth by secreting antimicrobial factors

microbes modify their peptidoglycan layer by adding surface molecules to avoid binding of antimicrobial factors. In addition, microbes can contain capsules that can inhibit the binding of antimicrobial factors.

Bacteria of the human microbiota that colonize the skin cause ________________.

odor; for example underarm odor

Some members of the human microbiota are not pathogenic while others are considered to be ________________ ______________.

opportunistic pathogens

What also effects a microbes pathogenic potential = virulence?

the immune system

What anatomical structure is found in the lower urinary system?

urethra

The female vagina contains a ____________ of species?

variety/number

What is the pH of the female vagina?

weakly acidic pH

What is the pH of the stomach?

~2 = very acidic

What is the pH of the small intestine?

~4-5 = acidic

What is the pH of the large intestine?

~7 = neutral

NIH

National Institutes of Health

Other than helicobacter pylori, what other members of the human microbiota are known to cause certain types of cancer?

No other microbes of the human microbiota have been known to cause cancer and research to find microbes that cause cancer is ongoing in the field of microbiology right now.

What can occur when antibiotics are administered?

Normal microbiota is wiped out and encounters with endogenous and exogenous microbes increases their chances of causing disease. Thus, antibiotics can cause minor members of the human microbiota to grow in large numbers when its members are suppressed.

What type of microbe makes up a large portion of the human microbiota?

bacteria

What anatomical structure is found in the upper urinary system?

bladder

Why are infections more prone to occur in sterile sites of the body?

Infections are more prone to occur in sterile sites of the body because there are typically a sparse load of microbes and therefore, there is not any microbial competition. Of course, the environment must be favorable for the microbe to grow.

Why is the oral cavity considered a complex environment?

It contains mucosal epithelial, contains a teeth surface, and contains anti-microbials (found in saliva). Teeth permit a surface that allows unique microbes to colonize; for example, plaques, biofilms

What has research of the microbiome revealed?

The microbiome has coding capacity for many more metabolic pathways than our own genomes have.

What is a secretion commonly found in the oral cavity? what does this secretion contain and what is its funciton?

The oral cavity secretes saliva which contains anti-microbials like lysozymes, which damage/lyse certain bacteria to limit number of microbes present.

What do virulence properties permit?

Virulence properties permit a microbe's pathogenic potential. This is displayed in how more readily a microbe can cause an infection/disease.

What is the human microbiome project?

a five year(2008-2013) research project by the National Institute of Health(NIH) that studied the microbiota of individuals.