The Human Microbiome Flashcards
(T/F) Microbes in the human body are all harmful.
False!
Most are harmless and many are actually beneficial to the human body!
Match the terms to their definitions:
1) Microbiome
2) Microbiota
A) A term used to describe all the microbes in a microhabitat (e.g., skin microbiota).
B) A functional collection of different microbes in a particular environmental system (e.g., the human microbiome).
Microbiome: A functional collection of different microbes in a particular environmental system (e.g., the human microbiome).
Microbiota: A term used to describe all the microbes in a microhabitat (e.g., skin microbiota).
(T/F) Different microhabitats support different microbes, so the skin will have very different microbes than the mouth.
True!
Fill in the blank:
All sites on a human that contain microorganisms are part of a ________.
Microbiome
(T/F) Our bodies carry about twice as many bacterial cells as human cells and about 100 times more non-redundant bacterial genes than human genes.
False!
Our bodies carry about AS MANY bacterial cells as human cells and about 100 times more non-redundant bacterial genes than human genes.
(T/F) There is more bacteria in the skin than the intestine and more in the mouth than the lungs.
False!
There is MORE bacteria in the INTESTINE than the SKIN and more in the mouth than the lungs.
What are the three future benefits of knowing the human microbiome?
1) Development of biomarkers for predicting predisposition to diseases
2) Designing targeted therapies
3) Personalized drug therapies and probiotics
Which one of the statements regarding the human microbiome is false?
1) There is complex interactions between the host and its microbiota.
2) No one species is the most abundant across all individuals (diversity between individuals is high).
3) All microbial groups are present in the same levels in different niches.
4) Similarities between individuals are more evident at higher taxonomic levels (phyla).
3!
Particular microbial groups typically dominate certain niches. This is due to the biochemical attributes (e.g., acidophiles in stomach).
(T/F) The human microbiome changes depending where you live, your age, or if you have pets.
True!
Which microbiota niche is the most studied?
The gastro-intestinal microbiota.
Why is the skin difficult to colonize?
Dry, salty, acidic and has protective oils.
Which factors influence the composition of the bacteria in the skin?
- Environmental factors (weather, pets)
- Host factors (age, personal hygiene)
What are the three main micro-environments in the skin?
1) Dry skin
2) Moist skin
3) Sebaceous skin
What are the two distinct layers of the skin? What do each of the layers compose of?
1) EPIDERMIS: (top layer) keratinocytes & squames
2) DERMIS: (deeper layer) sub-cutaneous tissues, sebaceous and sweat glands, hair follicles and immune cells.
What kind of bacteria are mostly present on the skin? Why?
Gram positive bacteria; they are more resistant to salt and dryness.
(T/F) It is mostly different kinds of bacteria that is found on the skin. If there is fungi on the skin, it is only 1 kind.
True!
(Malassezia spp is the fungi’s name)
How do S. epidermidis inhibit S. aureus biofilm formation and eventually kill them?
S.epidermidis produce a serine protease (Esp) to inhibit S.aureus biofilm formation.
The S.epidermidis that express the Esp induce KERATINOCYTES to produce ANTIMICROBIAL PEPTIDES via IMMUNE CELL SIGNALLING, killing S.aureus.
How do S.hominis decrease S.aureus colonization?
They produce LANTIBIOTICS that synergize with human antimicrobial peptide LL-37.
How do propionibacterium acnes promote S.aureus aggregation and biofilm formation?
They produce a small molecule called COPROPORPHYRIN II.
Which bacteria out of these kill S.aureus and prevent its biofilm formation and which promote S.aureus aggregation and biofilm formation?
1) S. epidermidis
2) S. hominis
3) Propionibacterium acnes
4) S. lugdunensis
1) S. epidermidis (Esp + kill)
2) S. hominis (produce lantibiotic)
4) S. lugdunensis (produce antibiotic)
3) Propionibacterium acnes (coproporphyrin II promotes aggregation and biofilm formation)
(T/F) The human body can secrete different types of antimicrobials; some bacteria are more affected by these than others.
True.
Fill in the blanks:
The oral cavity is a _______, ___________ microbial habitat.
Complex; heterogeneous
What kind of enzymes does the saliva contain?
Antimicrobial
But despite this, high concentration of nutrients near surfaces in the mouth promote localized microbial growth.
(T/F) The oral microbiota are normally harmless, but can cause disease.
True
What is BACTEREMIA? What can it lead to?
Bacteremia is when the oral microbiota enter the bloodstream. This can lead to subacute bacterial ENDOCARDITIS.
Prevented by antibiotic prophylaxis.
Fill in the blanks:
The _______ airways have more bacteria than the _________ airways.
Why?
Higher (upper respiratory tract); lower (lower respiratory tract)
Bacteria continually enter the upper respiratory tract from the air during breathing.
Ciliated mucosal cells move particles (bacteria included) up and out of the lungs.
Fill in the blanks:
Most bacteria from the air that enter the upper respiratory tract are trapped in the _____ of the _____ and _____ passages.
They are expelled with ______ secretions or swallowed and killed in the ______.
Mucus; nasal and oral
Nasal; stomach
(T/F) The lower respiratory tract (lungs + trachea) are sterile.
False! Though they were originally thought to be sterile, the lungs and trachea harbor normal microbiota.
What are the most prominent bacteria found in the lower respiratory tract?
Prevotella, streptococcus, and veillonella
What makes up the “mucociliary elevator”? What is its role?
The ciliated mucous lining of the TRACHEA, BRONCHI and BRONCHIOLES.
Role: sweeps foreign particles up and out of the lung.
Why must an immune response in the lungs be well controlled and almost “surgeon-like” in its precision?
The anatomy of the lungs that allows for gas exchange is VERY DELICATE.
A strong immune response causes tissue damage that could kill.
How do the epithelial cells of the lungs defend themselves (instead of triggering an immune response) ?
1) Secretion of MUCUS
2) Secretion of SURFACTANTS that normally decrease surface tension but can also be microbicides
3) Can DETECT pathogens and secrete MICROBICIDAL POLYPEPTIDES, or CYTOKINES such as IL-25 and IL-33
*2 and 3 usually done by Type II epithelial cells
Fill in the blanks regarding the lungs protecting itself:
A large population of resident alveolar ________ constantly clear debris and intruders by ____________.
Macrophage; phagocytosis
*resident meaning they don’t move
Fill in the blanks regarding the lungs protecting itself:
___________ cells present in the respiratory epitheli also set the tone for the immune response with their ability to present ____ to cells of adaptive immunity.
Dendritic; Ag (antigen)
(T/F) The kidney and the bladder are normally sterile.
True!
*kidney infections r rlly risky
Which bacteria frequently cause urinary tract infections in women?
E.coli
P. mirabilis
(T/F) UTIs are one of the most common infections worldwide, affecting over 100 millions people each year, where 12-15% of biological women affected annually and 50% by their 32nd bday. It is also a top ten common reason for seeing a doctor in Canada.
True!
Which one the statements regarding STIs is false?
1) STIs are sometimes included in UTIs, although UTI is generally referred to as bladder infections.
2) STIs primarily affect the gastro-intestinal system and are an important cause of patient morbidity.
3) There are apprx 20 million new cases of STIs annually in the US; half of which occur in 15-24 year olds.
2 is false!
STIs primarily affect the UROGENITAL system and are an important cause of patient morbidity.
(T/F) The microbiota of the genital tract is the same between males and females.
False! They are different.
Fill in the blanks regarding the microbiota of the genital tract of women:
The vagina of the adult female is weakly ______ and has a lot of ________.
Acidic; glycogen
Answer these questions regarding the genital tract of women:
1) Which resident organism in the vagina ferments the glycogen and produces lactic acid?
2) What kind of environment does the lactic acid maintain?
3) What is the pH before puberty and after menopause of the vagina? Why?
1) Lactobacillus acidophilus
2) Acidic environment (pH~5.0)
3) pH is neutral; L. acidophilus only colonizes the vagina at puberty and disappears during menopause.
What are candida yeasts?
Commensals (reside on the body without harming human health) that can cause OPPORTUNISTIC INFECTIONS.
For example, when L.acidophilus is displaced and can’t protect the mucosa anymore.
When is the L.acidophilus displaced from the mucosa?
1) After Abx treatment
2) Douching (washing)
3) Sexual intercourse (semen is alkaline)
(T/F) The male genitalia microbiota is understudied.
True!
Which one of the statements regarding the male genitalia microbiota is false?
1) Circumcision is the only influence on the composition of the penis microbiome (fewer anaerobic bacteria within six months after men were circumcised).
2) The species found resemble that of the gut.
3) Female and male partners seem to share genital microbiota. The anaerobes associated with bacterial vaginosis is also found on uncircumcised penises.
1!
Circumcision is the LARGEST influence on the composition of the penis microbiome (fewer anaerobic bacteria within six months after men were circumcised).
AGE and SEXUAL ACTIVITY are other factors affecting microbiota composition.
(T/F) Anal receptive intercourse in homo and heterosexuals can contribute to the spread of anorectal STIs and other microbial infections.
True!
Which one of the statements regarding the gastro-intestinal microbiota true?
1) Humans are digastric and omnivorous.
2) Microbes in gut affect EARLY DEVELOPMENT, HEALTH, and PREDISPOSITION to disease.
3) Colonization of gut begins at puberty.
4) The GI tract consists of the small and the large intestine only.
2!
1) Humans are MONOGASTRIC (stomach with only one compartment) and omnivorous.
3) Colonization of gut begins at BIRTH.
4) The GI tract consists of the STOMACH, THE SMALL and LARGE intestine.
What is the GI tract microbiota responsible for?
1) Digestion of food
2) Absorption of nutrients
3) Production of nutrients by the indigenous microbial flora (in symbiosis with us)
Out of the three components of the GI tract (stomach, small + large intestine), which one has the least amount of bacteria and which one has the most?
Least amount - STOMACH
Most amount - LARGE INTESTINE
The small intestine has more than the stomach but less than the large intestine.
(T/F) It takes about 1-4 hours for transit from stomach to the large intestine and 24 hours from mouth to the anus.
True!
What are the three major bacterial phyla that the vast majority (~98%) of all human gut phylotypes fall into?
What do individuals consist of?
1) Firmicutes
2) Bacteroidetes
3) Proteobacteria
Individuals may mostly have firmicutes or bacteroidetes or a mix of the two.
(T/F) In contrast to the limited phylum-level diversity, the species diversity of the mammalin gut is ENORMOUS (3,500 to 35,000 species but no more than ~200 in one individual).
True!
(T/F) There is also an abundant amount of archaea, yeasts, fungi and protists in the gut of the humans.
False!
The archaea, yeasts, fungi and protists are either absent or present in very little amounts.
What characteristic of the GI tract prevents many organisms from colonizing it?
The acidity of the stomach and of the small intestine (~pH 2).
Which bacteria is the most prevalent in the GI tract mucous lining?
Helicobacter pylori
It survives stomach at pH 1. It is found in the MUCOUS LINING and occasionally may cause GASTRIC ULCERS.
What is hypochlorydia? How is it caused? What does it lead to?
Hypochlorydia = decreased stomach acidity.
It is caused by malnourishment.
It leads to V. Cholerae to survive the stomach passage and establish infection in the less acidic intestine.
What is the ratio of the anaerobes to a facultative organism in the large intestine?
1,000 anaerobes: 1 facultative organism
*the small amount of oxygen that diffuses from the intestinal wall into the lumen is immediately consumed by facultative bacteria such as E. coli.
What are the various essential metabolic reactions that intestinal microorganisms carry out?
1) Vitamin production
2) Modification of steroids
3) Amino acid biosynthesis
Fill in the blanks regarding the large intestine:
The colon is an in vivo ________ vessel, with the microbiota using nutrients derived from the _________ of food.
Most organisms are restricted to the ______ of the large intestine, while others are in the ________ layers.
Fermentation; digestion
lumen; mucosal
What are the six effects of gut microbiota on its human host?
1) Development of innate and adaptive immunity
2) Microbial barrier
3) Maintain epithelial integrity
4) Source of energy
5) Vitamin biosynthesis, transformation of bile salts, catabolism of complex plant sugars + mucins
6) Metabolism of xenobiotics
What are gut-associated lymphoid tissues (GALT)?
Lamina propria under the lumen (with loosely packed immune cells). These cause the first response to a break in epithelium.
Match the following terms with their definition regrading GALT:
1) M cells
2) Intraepithelial lymphocyte
3) IgA (inoglobulin A)
4) Lymph vessels
A) Antibodies produced by B cells that neutralize various viruses/bacteria.
B) Bring bacteria from the lumen in the lamina propria through TRANSCYTOSIS to cross the mucosal epithelium (not immune cells).
C) Drain debris through lymph nodes that are part of the immune system. Located underneath the lamina propria.
D) Resident and responsive cells that produce cytokines when they recognize antigens at a certain threshold to dampen other immune cells, inducing TOLERANCE.
M cells: Bring bacteria from the lumen in the lamina propria through TRANSCYTOSIS to cross the mucosal epithelium (not immune cells).
Intraepithelial lymphocyte: Resident and responsive cells that produce cytokines when they recognize antigens at a certain threshold to dampen other immune cells, inducing TOLERANCE. (When threshold too high, they release cytokines to stimulate the immune cells.)
IgA: Antibodies produced by B cells that neutralize various viruses/bacteria.
Lymph vessels: Drain debris through lymph nodes that are part of the immune system. Located underneath the lamina propria.
(T/F) Bacteria can be found in the highest concentration in the intestinal epithelium, compared to the lumen or the mucus layer of the large intestine.
False! There is very little bacteria nearby the epithelial cells. They are mostly in the mucus layer or the lumen.
(T/F) Commensal bacteria do not have the virulence factors to break the intestinal epithelium.
True!
(T/F) By constantly monitoring intestinal antigens, the immune cells of the gastric mucosa are always on the alert and eliminate threats locally, without our knowledge.
True!
What are the conditions that must be present to have an immune response?
Stimulation of the innate cells:
Physical barrier is broken by the invading bacteria. The balance between pathogenic and commensal is broken (more pathogens) or a deregulation of the innate system favourable to pathogens.
How is the severity of the pathology a consequence of the host/pathogen relationship?
1) Virulence of microorganisms influence immune response
2) Quality and number of commensals
3) Presence of immune deficiency (over/under activation)
4) Break in tolerance (overreactive immune response)
Defne dysbiosis:
A disruption to the microbiome resulting in an imbalance in the microbiota, leading to PATHOGENESIS.
For E.coli, curly fiber means ______, while no curly fiber means ________.
Disease; no disease
*curly fiber help bacteria adhere to surfaces and form biofilms.
(T/F) Low-fat diet, antibiotics and other environmental factors are pro dysbiosis.
False!
HIGH-fat diet, antibiotics (by getting rid of commensal bacteria) and other environmental factors are pro dysbiosis.
Which one of the statements regarding clostridium difficile is false?
1) The prevalence of this bacteria is on the rise due to nosocomial, old age, immunosuppression, exposure to abx, and serious underlying disease.
2) The symptoms include strong diarrhea, fever, loss of appetite, nausea, and abdominal pain.
3) Mortality and severity of this infection has remained the same over time.
3!
Mortality and severity of this infection has increased.
Development of antibiotic resistance can perpetuate _______.
Dysbiosis
Match the steps regarding clostridium difficile infection:
1) Step 1
2) Step 2
3) Step 3
4) Step 4
A) Antibiotics kill many of these commensal bacteria.
B) Neutrophils and red blood cells leak into gut between injured epithelial cells.
C) The colon is colonized by large numbers of commensal bacteria.
D) Clostridium difficile gains a foothold and produces toxins that cause mucosal injury.
Step 1: The colon is colonized by large numbers of commensal bacteria.
Step 2: Antibiotics kill many of these commensal bacteria.
Step 3: Clostridium difficile gains a foothold and produces toxins that cause mucosal injury.
Step 4: Neutrophils and red blood cells leak into gut between injured epithelial cells.
What are some causes of Dysbiosis (dysbacteriosis)?
1) Unbalanced diet (lots of simple carbs + proteins, artificial colours, preservatives, nitrates + pesticides)
2) Inflammatory process in the intestine
3) Chronic and acute infections (HIV, hep C + B, herpes)
4) Diabetes mellitus, cancer, disease of liver + pancreas
5) Treatment with antibiotics
6) The use of chemotherapy, antiviral drugs, radioactive isotopes, hormone therapy
7) Uncontrolled rectal cleaning with enemas
8) Presence of intestinal helminths
*obs studies not mechanistic
What are some consequences of gut dysbiosis?
1) Localized gut inflammation
2) Systemic inflammation
3) Increased oxidative stress
4) Increased production of endotoxins and other biotoxins
5) Intestinal permeability
6) Impaired energy metabolism
7) Impaired nutrient synthesis
8) Impaired enzymatic activity
9) Autoimmunity
(T/F) It is not only pathogenic bacteria, but also yeasts, parasites and viruses that can overpopulate the gut, resulting in gut dysbiosis.
True!
Microbiome begins to develop before birth and their source may be the _______ (which has its own microbiome)
Placenta
Fill in the blanks:
1) Baby is exposed to lots of microbes that reside in the ______ ____ and the ______ _____ once it breaks out of the embryonic membrane.
2) Early colonizing microbes are a source of ________ and tend to be ________ rather than strict anaerobes.
3) Young babies have microbiomes ______ diverse than of adults.
4) By the time the baby is ___ years old, the microbiome diversity is similar to adult composition.
1) birth canal; outside world
2) vitamins; facultative
3) more
4) three
Which statement regarding vaginal vs C-section birth is true?
1) Both vaginally born and C-section infants have a microbiome like their mothers.
2) At 4 months, vaginally born infants are colonized by lactose digesting bacteria.
3) At 12 months, the difference between the two of the gut microbiota is still drastically important.
Statement 2 is true!
1) Vaginally born infants have a microbiome more like their mothers than the ones born via C-section (72% vs 41%).
3) At 12 months, the difference between the two of the gut microbiota is NOT as important but there are still differences.
Breastfed infants have more commensal bacteria because breast milk has a variety of complex __________ that promote their colonization.
At 4 months, there is still clear differences between breast-fed vs bottle-fed. The breast-fed microbiota are associated with __________, _________ protection, and ______ _______ education.
OLIGOSACCHARIDES
probiotics; gut lining; immune system
(T/F) The breast-fed infants have more of C. difficile and citro/enterobacter while bottle-fed infants have more of Bifidobacterium longum.
False!
The breast-fed infants have more of Bifidobacterium longum while bottle-fed infants have more of C. difficile and citro/enterobacter.
*we do not know if the diff between bottle vs breast fed and vaginal birth vs c-section birth has long-term health impacts.
(T/F) Adult microbiota seems to be stable, while Firmicutes and Proteobacteria seem to be less stable.
True!
Which one of these statements is false?
1) Early experiences seem to determine gut microbiome but more research is needed.
2) Aging and frailty are associated with increased microbial diversity.
3) There is an increased proportion of Bacteroidetes in elderly.
4) Individuals living at home rather than in residential facilities have a more diverse microbiota.
2! Aging and frailty are associated with a DECREASED microbial diversity, leaving space for pathogenic bateria.
Why is the human microbiota less diverse than those of our long-ago ancestors? What can this lead to?
Ancestors had an intimate contact with env composed of animals, caves, dirt, poop + bugs. Now, we are indoor species and make use of soaps, antibiotics and disinfectants, restricting our access to microbes.
This can lead/contribute to inflammatory and autoimmune diseases.
For the first few days to week when we die, bacteria and fungi participate in ___________ and act as _______.
Putrefaction (tissue breakdown); decomposers
What happens to the microbiota when we die?
The microbiota stays relatively stable during the 24-48 hours.
Past 48 hours, the microbial ecology start to alter to a point that is no longer recognizable as a human microbiota (unless frozen).
Alpha diversity is diversity _____ sample and beta diversity is diversity _____ samples.
Within; between
What are the two disorders attributed to the gut microbiota?
- Inflammatory bowel disease (IBD)
- Obesity
Match the following IBDs to their definitions:
1) Crohn’s disease
2) Ulcerative colitis
A) Occurs in the large intestine (colon) and the rectum.
B) Can affect any part of the GI tract (from mouth to anus); mostly the portion of the small intestine before the large intestine.
1) Crohn’s disease: Can affect any part of the GI tract (from mouth to anus); mostly the portion of the small intestine before the large intestine.
2) Ulcerative colitis: Occurs in the large intestine (colon) and the rectum.
IBDs are chronic _________ of the gut and disruption of homeostasis (_______).
Inflammation; dysbiosis
(T/F) IBDs are 4X more frequent than in the 50’s and genetic risk cannot explain this. It can be diagnosed at anytime during life and the incidences are high in Canada.
True.
What are the potential causes of IBDs?
1) Failure to develop a tolerance to commensal bacteria in the gut early in life (breastfeeding, vaginal birth, hygiene)
2) Antibiotic use
3) Western diet (rich in animal proteins)
*high fiber diet is beneficial
Which one of the following statements regarding IBDs is false?
1) Transmissible between family members is not possible.
2) Presence of adaptive T cell response against commensal gut bacteria is detected when it should not (break in tolerance).
3) Individuals with IBDs have lower gut microbiome diversity.
Statement 1 is false!
IBD may be transmissible between family members once developed.
Mice that are genetically obese have a different microbiota than normal mice, they have more __________.
Firmicutes (obese humans too).
In lean mice, there is an abundance of H2 which slows fermentation that produces VFAs (short chain fatty acids) and nutrients for the host.
In obese mice, there is less H2 because it is used by the many methanogens to produce methane. These promote fermentation, leading to lots of VFAs and nutrients for the host.
Mice that are genetically obese have a different microbiota than normal mice, they have more __________.
Firmicutes (obese humans too).
In lean mice, there is an abundance of H2 which SLOWS fermentation that produces VFAs (short chain fatty acids) and nutrients for the host.
In obese mice, there is less H2 because it is used by the many methanogens to produce methane. This leads to fermentation and there is more VFAs and nutrients for the host!
Obese mice: more methanogens and firmicutes, less bacteroidetes
Lean mice: less methanogens and firmicutes, more bacteroidetes
(T/F) Obesity in humans is linked to their microbiomes.
True! Obese humans have more firmicutes than non-obese.
The nature + transferability of gut microbiota is dependent on diet + genetics.
What are the two major ways that microbiota influence obesity?
1) harvesting of energy from ingested foods
2) triggering of intestinal inflammation
The metabolic dexterity of intestinal microbes allow them to digest many foods that we cannot.
In the process, these microbes produce _____ _____ _____ _____ that our cells use in many ways.
Short-chain fatty acids (SCFAs).
Amounts and ratios of these influence obesity!
(T/F) Only bacteria tilt the metabolic balance of the gut towards obesity.
False! Archaea do as well.
____________ produced by gram-negative species promotes inflammation and a ______ diet can promote absorption of these across the intestinal epithelium.
Lipopolysaccharide (LPS, or endotoxin) ; high fat
