Commensal Flora Flashcards
All [] in/on a human that contain [] are part of the microbiome
- sites
- microorganisms
Can microbes in the gut affect early development, health, and predisposition to diseases?
yes
Why do most microbes on human pose direct threats to our health?
- Physche!
- Few contribute to health and fewer pose direct threats to health
- Most are benign
Why is it termed, “commensal” flora?
- We actually aren’t sure if they are commensal - but we know they are there for a reason - probably mutualistic
Will all the sites on the body be colonized by the same organism?
- Not normally (there are “generalist” cases but don’t worry about them)
- Microbes won’t live in multiple sites in human biome
Why is the Human Microbiome Project useful?
- Once we know what is normally found, we will know what is unusual and may be causing diseases
What were the goals of the Human Microbiome Project?
- Establish what organisms live at certain sites on the human body
- generate genome sequences for 3000 new reference strains
- Develop new analytical and bioinformatic tools
- Create a resource repository
- Study the ethical implications of this knowledge
How do we assess the human microbiome?
- Culture-independent with next gen sequencing
- 16s (or 18s) rDNA libraries and Illumina sequencing
- Variable regions 1-3
- Variable regions 3-5
- variable regions 7-9
- Shit doesnt always agree because of a lot of factors
Why do set of hypervariable regions on 16s/18s rDNA not agree phylogenetically?
- Regions mutate at different rates
- Researchets error during sample processing
- Our databases do not contain enough sequences tom compare to
- Differences in PCR specificity of these regions
- All of the above
All of the above.
What is sampling bias?
- 1 sample you pull may not represent the entire microbiome
- Take the mouth for example…different microbes on tongue than on the gums
- Restricted by
- age, weight, race, point of time
- Use universal primer that is not always universal
- Classified by current databases which are….bias
What are “normally” the only bacteria that can stik to the enamel surfae? Why?
Streptococci
They have the sticky capsule
What is the thick layer of bacterial growth on teeth?
Dental plaque - usually made of streptococci
How does streptococcus mutans differ from normal streptococci bacterial on the teeth?
- It ferment gluose….acidifying its environment –> leads to dental carries
What types of microbes grow after extensive dental plaque grows?
- Anaerobic bacterial
- Veillonella
- Porphyomonas gingivalis - gingivitis
A [] group of organisms colonizes the upper respiratory tract
- restricted
- Examples
- staphylococci, streptococci, diptheroid bacilli
- G- cocci
- SImilar to some mouth and throat bacteria….
Why is the upper respiratory tract thought to lack microflora?
- Physche
- Its the lower respiratory tract that was though to lack microflora.
- This has changed recently though as we have discovered some microbes live there, at least temporarily.
- We do not have evidence that things live there long term
The microflora of the throat - [] []
What does it depend on?
- Extremely variable
- Depends on oral and nasal microbiome
How do microbes from the mouth and throat get to the lungs?
Micro aspiration
Do lungs have a microbiome?
YES
Why isn’t the stomach the largest microbiome?
Acidity levels are too low - pH = 2ish
Is the large intestine the largest microbiome?
Is it aerobic/anaerobic?
What kind of nutrients do the microbes get?
- Yes, 10^14 microbes
- Anaerobic
- Crappy carbon and plant parts. This is the hard part of food digestion. So microbes really help out here.
What types of compounds are produced by the intestinal microflora that we, as humans, cannot produce without them?
- B12, vitamins, gas, odors
- Organic Acids, enzymes
What are some of the abiotic factors microbes deal with in the intestines?
- Competition
- Immune cells can target microbes in the gut
- Medicines, antibiotics
What part of the digestive tract contains the greatest species richness?
Large Intestine
Are methanogens more prevalent in a lean mouse or obese mouse?
Are bacteriodetes more prevalent in a lean mouse or obese mouse?
- Methanogens - more are found in obese mice
- Bacteriodetes - more found in lean mice
Low H2 in obese mice promotes []
High H2 in lean mice [] fermentation
fermentation
Inhibits
What disorders are linked with the microflora of the GI tract?
- Type I Diabetes - improved glucose sensitivity
- Lupus - segmented filamentous bacteria are linked
- IBS
- Osteomyelitis
- Juvenile Arthritis
The adults vagina is [] acidic and contains significant amounts of [].
What is the main genus of bacteria found in the vagina?
- weakly, glycogen
- Lactobacillus
How to fungi and bacteria even each other out in the vagina?
- The fungi compete for carbon which limits the growth of bacteria
- The bacteria ferment glycogen (sugars) to keep aciditiy levels slightly higher to control fungi levels.
Which tract of the male reproductive tract is frequently colonized?
- The lower tract (up until the bladderish)
- Upper tract is rarely colonized
What “main” bacteria colonizes the vag and the penis?
lactobacilli
Is the bladder sterile in both males and females?
No
What places on the skin are microbe havens?
- Wet/hairy - need the oil and water to help them live.
- normally skin is dry and acidic.
Sweat glands/Hair glands of the skin are normally colonized by what type of bacteria?
- Gram +
- Other normal flora of the skin
What is the #1 barrier against infection?
the skin
Skin bacteria vary [] person-to-person and []-to-[]
- greatly
- site-to-site
Mycobiome stands for what kind of biome?
Fungi microbiome
Are there any known archaeal pathogens?
No
Prokaryotic viruses [] to cause disease directly in humans…
Eukaryotic thought to be primarily [] ….
Unlikely
Pathogens
Is there a microbiome in the brain or blood?
There are studies that suggest it….but nothing directly showing that an active microbiome exists in the brain or blood
How does a baby develop their microbiome in utero?
- Amniotic fluid contains bacteria from mom….some way microbiome from mom is passed to the baby.
- Depends on birth
- Vagina microbiome on skin
- C section - skin of mother is the microbiome from when she first holds it
- Breastfeeding/not breast feeding
So we have all this bacteria but how does it become pathogenic?
- Disease Occurs when….
- bacteria occupy a space not normally colonized with bacteria
- Bacteria turn on expression of virulence factors
- Microbes get out of balance - think yeast infection
