Microbio exam 4

lecture 14, 15 and 16

what is the normal microbiota?

microorganisms that normally live on and in the human body without usually causing disease. They can be bacteria, fungi, archaea, and viruses

What is the difference between microbiota and microbiome?

Microbiota refers to the microbes themselves. Microbiome often refers to the whole microbial community, and sometimes also their genes and environment. In class, they are often used closely together

what is a virome

The virome is the collection of viruses associated with the body.

What is transient microbiota?

microbes that are present only temporarily. They do not permanently colonize a site

what is colonization

the ability of a microbe to remain attached to a body surface and replicate there

what are adhesins

microbial molecules that help microbes attach to host cells, which helps colonization happen

what is symbiosis

a close relationship between two different organisms, such as a host and its microbiota.

what is mutualism

a relationship where both organisms benefit. Many normal microbiota-host interactions are mutualistic.

what is commensalism

a relationship where one organism benefits and the other is unaffected.

what is parasitism

a relationship where one organism benefits at the expense of the other.

what is bioburden

the number of microorganisms that typically inhabit an environment.

what is dysbiosis

an unhealthy disruption or imbalance in the composition of the microbiome.

What is microbial antagonism?

when normal microbiota interfere with pathogen colonization, helping prevent infection.

What is an opportunistic pathogen?

a microbe that usually does not cause disease in a healthy person but can cause disease if the host is weakened or the microbe enters the wrong body site.

How do microbiota benefit the host?

They help digest food, synthesize compounds such as vitamins, block pathogen colonization, and help train and enhance the immune system.

Why can the microbiome be called a “virtual organ system”?

Because it performs important body-wide functions like metabolism, immune support, protection from pathogens, and signaling to the host, similar to an organ system.

how does the microbiota help the immune system

It trains and enhances immune function, and the immune system constantly samples the microbiota. Some microbes also produce immunomodulatory signals.

How do microbiota communicate with the host?

They communicate through chemical signals, microbial products, and host-microbe interactions. The gut-brain axis is one major example.

What is the gut-brain axis?

It is two-way communication between the gut and brain. Brain activity can alter gut function, and the gut microbiota can influence the nervous system and brain function.

Give examples of microbiota affecting the host

Certain bacteria can change host gene expression and change the production of anti-inflammatory signals.

why can normal microbiota become harmful

Their location matters. If they move to the wrong place, they can cause infection and disease.

Why are immunocompromised hosts at higher risk from the microbiome?

Because microbes that are normally harmless can overgrow or invade tissues more easily when host defenses are weakened.

How can antibiotics harm the microbiome?

Overuse or inappropriate use of antibiotics can disrupt normal microbiota, promote dysbiosis, and contribute to antibiotic resistance.

What factors can cause dysbiosis?

Infections, antibiotics, new foods, emotional stress, and many other environmental or physiological changes

Is the microbiota static over a lifetime?

No. The microbiome changes over time from early life through aging. It is not fixed.

When does microbiome colonization begin?

It may start before birth, though this is still discussed, and colonization definitely continues after birth as the body is exposed to the outside environment.

Where do early microbes come from?

From the mother, caregivers, food, water, skin contact, and the surrounding environment.

Why does microbiota composition change over time?

Because of age, diet, environment, antibiotic use, stress, body site conditions, and exposure to new microbes.

What can dysbiosis lead to?

It can contribute to infection, inflammation, digestive problems, skin disease, vaginal yeast infections, C. difficile disease, and other disorders depending on the body site.

What is the hygiene hypothesis or disappearing microbiota hypothesis?

It is the idea that changes in human behavior have changed our microbiota, with reduced exposure to some ancestral microbes.

What kinds of modern changes may alter microbiota composition

Clean water, cesarean delivery, preterm antibiotics, reduced breastfeeding, smaller family size, widespread antibiotic use, increased bathing and soaps, and some dental practices.

What health problems are associated with the hygiene hypothesis?

It has been linked to increases in allergies, autoimmune disease, and metabolic disease, though some of this remains controversial

What are major body sites populated by microbiota?

Skin, mouth, nose, respiratory tract, stomach, intestines, vagina, urethra, and bladder.

Which body compartments are more likely to be sterile or microbe-free?

Kidneys and ureters should be microbe-free. Many internal tissues are normally sterile because physical and chemical defenses prevent colonization.

Why are some body sites sterile?

Because barriers such as low pH, flow of fluids, cilia, tears, lysozyme, mucus, and immune defenses prevent microbes from establishing there.

What is the environment of the skin epidermis?

Acidic pH about 4 to 6, high salt, low moisture, and can contain lysozyme in skin

What kinds of microbes are common on skin?

Mostly Gram-positive microbes that resist drying and salt. (Ex. Staphylococcus epidermidis, Bacillus spp., and Candida spp.)

What barriers must skin microbes overcome?

Dryness, salt, acidity, and antimicrobial substances like lysozyme

Are skin barriers physical or chemical innate defenses?

Both. Skin itself is a physical barrier, while acidity, salt, and lysozyme are chemical defenses.

What are examples of skin dysbiosis?

Acne, rashes, dermatitis, and other skin diseases. Cutibacterium acnes is associated with acne.

Why does the eye have low bioburden?

Tears continually wash the surface, tears contain lysozyme, and many microbes there are only transient.

What type of innate defenses protect the eye?

Physical washing by tears and chemical defense from lysozyme

What is a common dysbiosis or infection of the eye?

conjunctivitis

What defenses are important in the mouth?

Saliva washes microbes away and contains lysozyme, so microbes that live there must be able to adhere well.

Which early microbes colonize an infant’s mouth?

Nonpathogenic Neisseria, Streptococcus, Actinomyces, Lactobacillus, and some yeasts.

What changes after teeth emerge

Anaerobes begin colonizing more, including Prevotella and Fusobacterium

Why is adhesion important in the mouth?

Because saliva constantly washes surfaces, so microbes must stick to teeth and oral tissues to remain there.

How do Streptococcus mutans and Streptococcus salivarius persist in the mouth?

They form a glycocalyx that helps them adhere strongly to oral surfaces and to each other. (biofilm)

How do oral microbes contribute to cavities?

Fermentation by microbes on teeth produces acid, which dissolves tooth enamel and causes dental caries

Where are most aerobes found in the mouth?

On tooth surfaces and other oral surfaces.

Where are more anaerobes found in the mouth?

Below the gums and in the crypts of the tonsils.

What are important oral dysbiosis outcomes?

cavities, periodontal disease, and bacteremia after dental procedures

Which part of the respiratory tract has the highest bioburden?

The upper respiratory tract, including nasal passages, oral cavity, and pharynx.

What is the mucociliary escalator?

It is the ciliated mucus lining of the trachea, bronchi, and bronchioles that sweeps foreign particles and microbes upward and out of the lungs.

Why are respiratory microbes similar to oral and nasal microbes?

Because the upper respiratory tract connects to those sites, and cilia and mucus move microbes through these connected regions

Which bacteria are listed as common in the respiratory tract?

Streptococcus, Prevotella, and Veillonella.

What respiratory conditions are linked to dysbiosis?

Respiratory infections, worse disease severity in COPD, and altered microbiota in diseases such as cystic fibrosis

Why does the stomach usually have low bioburden?

Because the stomach is very acidic, usually below pH 4, which kills most bacteria.

Which bacteria can be found in the stomach?

Low numbers of organisms such as Streptococcus and Veillonella.

Why can Helicobacter pylori survive in the stomach?

Because the mucus lining of the stomach has a higher pH, around 5 to 6, which allows H. pylori to grow there.

What stomach problems are associated with dysbiosis?

Increased survival of microbes when stomach pH rises, and H. pylori overgrowth causing gastritis and gastric ulcers

Which major bacterial phyla dominate the human intestine?

Bacteroidetes and Firmicutes.

What is the environment of the duodenum and jejunum?

About pH 8, alkaline, with bile salts present, which limits growth. It tends to contain mostly Gram-positive bacteria such as lactococci, enterococci, and Actinobacteria.

What is the environment of the ileum and colon?

pH about 5 to 7, lower bile salt levels, very diverse microbial ecosystem, and large numbers of anaerobes.

Are there more aerobes or anaerobes in the intestine?

Far more anaerobes. The intestine has about a 1000:1 ratio of anaerobes to aerobes.

What are key functions of GI microbiota

Ferment unused energy substrates, train the immune system, prevent pathogen growth, regulate gut development, produce vitamins, and produce signals that influence host fat storage.

How do intestinal microbes communicate with the host?

Through microbial products such as butyrate and indole, cross-species signaling, and interactions with host products such as hormones

How might the microbiome influence obesity?

Gut microbes can alter fermentation and production of end products such as acetate and butyrate, which may affect energy harvest and weight gain.

What intestinal problems are linked to dysbiosis?

Bloating, flatulence, more severe infections such as Clostridioides difficile, and inflammatory bowel disease

Which genitourinary organs should be microbe-free?

The kidneys and ureters

What is the microbiota situation in the urinary bladder?

The bladder has a small number of microbes, mainly anaerobes.

Why does the urethra not usually become heavily colonized?

Because the outward flow of urine helps force microbes out

Which microbe is an example of urethral microbiota?

Staphylococcus epidermidis

What is the normal environment of the vagina?

It is acidic, about pH 4.5, and commonly dominated by Lactobacillus species.

What dysbiosis can happen in the genitourinary tract?

UTIs of the bladder or kidneys, vaginal yeast infections, and microbiome changes linked with susceptibility to STDs.

What is a prebiotic?

something that feeds or supports beneficial microbes already living in the body

What is a probiotic?

a live beneficial microbe that is introduced to help maintain or restore a healthy microbiome

What is the difference between a prebiotic and a probiotic?

Prebiotics feed beneficial microbes already present. Probiotics are beneficial microbes themselves

What is a fecal microbiota transplant (FMT)

the transfer of stool microbes from a healthy donor to a patient to restore gut microbiota balance.

When might a doctor do a fecal microbiota transplant?

It is most classically used for recurrent or severe C. difficile infection when normal microbiota need to be restored. This matches the chapter’s discussion of microbiome transplants and C. difficile-associated dysbiosis.

What is phage therapy?

Phage therapy uses bacteriophages, which are viruses that infect bacteria, to target bacterial infections.

Why is phage therapy promising?

It may help control infectious diseases by specifically targeting bacteria, which is especially interesting when antibiotic resistance is a problem

Why are there more anaerobes than aerobes overall in the human microbiota

Many body sites, especially deeper or less oxygen-rich environments such as the intestine, favor anaerobic growth.

What determines which microbes live at a body site?

Local conditions such as pH, oxygen level, moisture, salt, fluid flow, mucus, bile, lysozyme, cilia, and how well microbes can adhere.

What is the big chapter idea of normal human microbiota?

Human health depends on a balanced relationship between the host and its microbiota. Microbes can protect and support us, but if the balance changes or microbes move to the wrong place, they can also contribute to disease.

What is the immune system?

The immune system is a collection of organs, tissues, cells, and cell products that can distinguish self from non-self and help rid the body of non-self.

What is the difference between immunity and susceptibility?

Immunity is the ability to resist infection or disease, while susceptibility is being vulnerable to infection or disease.

What are the two branches of immunity?

Innate immunity and adaptive immunity.

What are the key features of innate immunity?

Innate immunity is present before birth, responds immediately, is nonspecific, is always on, has no memory response, and includes the first and second lines of defense.

What are the key features of adaptive immunity?

Adaptive immunity is acquired, slower to activate, specific to microbes, must first encounter the intruder, has memory, and is the third line of defense.

How are innate and adaptive immunity related?

They are highly interactive and cooperative rather than totally separate systems.

What are the first, second, and third lines of defense?

• First line: skin, mucous membranes, antimicrobial substances.

• Second line: inflammation, fever, phagocytes, innate recognition, interferons, NK cells, complement.

• Third line: adaptive humoral and cellular immunity.

What is hematopoiesis?

Hematopoiesis is the formation of new blood cells.

What are erythrocytes?

Erythrocytes are red blood cells. They are not white blood cells and are not immune effector cells. Their general job is oxygen transport.

What are platelets?

Platelets are blood components derived during hematopoiesis. Their main general role is clotting rather than direct immune defense

What are leukocytes?

Leukocytes are white blood cells. They include lymphoid and myeloid immune cells.

Which cells are lymphoid cells?

B cells, T cells, and natural killer cells.

Which cells are myeloid cells?

Mast cells, eosinophils, basophils, neutrophils, monocytes, macrophages, and dendritic cells

What is a phagocyte?

a cell that can perform phagocytosis, meaning it can ingest microbes or other substances.

What is an antigen?

a compound recognized as foreign by the body or cell and it elicits an adaptive immune response