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Bench to bedside and beyond > 8. Human Microbiome > Flashcards

8. Human Microbiome Flashcards

1
Q

what is a microbiome?

A

all of the living Microorganisms in an environment

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2
Q

Microbiome vs microbiota

A

microbiome
- the entire habitat including the Microorganisms their genomes and the surrounding environmental conditions

microbiota
- the microorganisms present in a defined environment

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3
Q

what is one health?

A

studies looking at the link and interactions between humans, animals and the environment with disease

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4
Q

The importance of environmental biomes

A

without microorganisms we wouldn’t be here
bacteria and fungi are everywhere and are essential to life

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5
Q

what are the 3 host-microbe interactions?

A

Commensalism = one party benefits, the other is neutrally affected
Mutualism = both parties benefit
Parasitism = one party benefits, the other is harmed

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6
Q

what is a core microbiota?

A

a common set of microorganism that are present in a set of host eg all humans
- shared similarities within species but still individualised
- changes over time but many microorganisms present for many years

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7
Q

what can the core microbiota help us identify?

A

dysbiosis - the state of disease
can be used for diagnosis and monitoring can be used for prophylaxis

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8
Q

what do microorganisms acquired from birth develop into?

A

a distinct microbiome through environmental and genetic factors

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9
Q

what does a healthy microbiota look like?

A
  1. attached to the epithelial cells
  2. forms a protective layer on top of the cell
  3. produce antimicrobial peptides as prophylaxis and to keep the microbiota in check
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10
Q

what happens with depleted microbiota?

A
  1. less protection
  2. bacteria can get through the epithelial barrier
  3. cause disease
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11
Q

what can disrupt the normal microbiota?

A
  1. exposure to antibiotics
  2. changes in health or immunity
  3. hormonal changes
  4. local trauma
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12
Q

what microorganisms tend to be in the skin microbiome?

A
  1. Staphylococcus aureus
  2. Pseudomonas
  3. Streptococcus
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13
Q

what microorganisms tend to be in the Ear microbiome?

A
  1. Staphylococcus
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14
Q

what bacteria are mostly in the internal microbiota?

A

gram negatives and anaerobes

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15
Q

what microorganisms tend to be in the Oropharynx microbiome?

A
  1. Staphylococcus
  2. Viridans streptococci
  3. neisseria
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16
Q

what microorganisms tend to be in the stomach microbiome?

A
  1. helicobactor
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17
Q

what microorganisms tend to be in the small intestines microbiome?

A
  1. Lactobacillus
  2. bacteroides
  3. enterobacteriaceae
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18
Q

what microorganisms tend to be in the large intestines microbiome?

A
  1. Bacteroides
  2. fusobacterium
  3. E. coli
  4. Proteus
  5. klebsiella
  6. peptostreptococcus
  7. Enterococcus
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19
Q

what microorganisms tend to be in the vagina microbiome?

A
  1. Lactobacillus
  2. gardnerella vagunalis
  3. candida
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20
Q

Strep. Pneumonia

A
  1. infects the nasopharynx
  2. gram positive diplococci
  3. pneumolysin that breaks down cells
  4. causes meningitis and sepsis
  5. it has a range of effect depending where it is found
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21
Q

Pneumonia

A
  1. bacterial, viral or fungal
  2. viral pneumonia is a big problem
  3. most pneumonia causing microorganisms we can carry as commensals with no problem
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22
Q

what are biofilms?

A

an aggregate of microorganisms attached to a surface and/or each other, often embedded in a self produced matrix consisting of extracellular polymeric substances

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23
Q

why are bioflims a preferred mode of growth for microorganisms?

A
  1. the matrix is a protective physical barrier
  2. micro niches form with anaerobes on the inside of the biofilm and aerobes on the outside
  3. quorum sensing can occur easily
  4. sharing of plasmids and genetic information is easy and efficient
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24
Q

what are the 5 stages of biofilm formation?

A
  1. attachment - van Der Waals or ionic forces
  2. colonisation
  3. production of matrix - recruit proteins and microbes
  4. maturation
  5. dispersion - breakdown of the matrix and leaving the biofilm
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25
Q

Oral microbiota

A
  1. numerous different surfaces so everyone will have a different microbiota
  2. over 1000 microbial species in total
  3. mostly harmless
  4. some help break down food and aid digestion
  5. with out them pathogenic bacteria we inhale or ingest would be able to enter and infect the mouth
26
Q

Parts of a healthy oral microbiome

A
  1. streptococcus
  2. actinomyces
  3. veilonella
27
Q

disease-associated parts of the oral microbiome

A
  1. porphyromonas gingivalis
  2. treponema denticola
  3. tannerella forsythia
28
Q

what is a red complex bacteria?

A

the presence of one these bacteria indicates the beginning of an infectious disease

29
Q

what do primary colonisers bind to in the mouth to establish a community?

A
  1. sialic acid residues
  2. ß 1,4- linked galactose
30
Q

what do secondary colonisers bind to?

A

similar receptors to the primary colonisers just on the primary bacteria not the host cells

31
Q

example of secondary coloniser

A

Fusobacterium nucleatum
- considered a bridging microbe for the maturation of the biofilm and community

32
Q

Oral disease: tooth decay/gum disease

A
  1. biofilm pockets that produce acids and break down enamel
  2. S. mutans
  3. C. albicans
  4. P. Gingivalis
33
Q

Oral diseases: denture associated stomatitis

A
  1. C. albicans
  2. streptococci
  3. P. aeruginosa
34
Q

Oral diseases: cancers

A
  1. C. albicans and other candida
  2. HPV 16 + 18
  3. Fusobacterium
  4. Clostridium
  5. Haemophilus
  6. enterobacteriaceae
35
Q

Oral diseases: candidosis

A
  1. yeast/fungal
  2. caused by a disruption of community balance allowing one or more organism to grow uncontrolled
  3. almost always an underlying host predisposing factor
36
Q

what can effect the amount of growth of disease organisms in the microbiome?

A
  1. the presence of other organisms
  2. presence of a specific organism
  3. metabolites
  4. chemicals
37
Q

what can reduce pathogenicity of a C. albicans infection?

A

adding a specific bacteria like P. Gingivalis

38
Q

what are the benefits of the oral microbiomes?

A
  1. produce amylase and protease to break down foods
  2. reduce colonisation of opportunistic pathogens
  3. contribute to oral health and overal health through metabolic by products
39
Q

Respiratory tract microbiota

A
  1. host tolerance and clearance
  2. microbiome exclusion
  3. 1000s of fungal spores inhaled everyday but the microbiota prevents infection
40
Q

Healthy components of the respiratory microbiome

A
  1. S. epidermidis
  2. viridans group streptococci
  3. Corynebacterium spp
  4. propionibacterium spp
  5. haemophilus spp
41
Q

disease associated components of the respiratory microbiome

A
  1. S. pneumoniae
  2. S. pyogenes
  3. H. influenzae
  4. M. catarrhalis
42
Q

link between the oral and respiratory microbiota

A

some opportunistic pathogens colonise the oral cavity as a means to get into the respiratory tract. things like intubation can the cause infection
need to monitor transmission between the 2 sites

43
Q

GI tract mircobiome

A
  1. intestines = most colonised
  2. density gradient increasing from gut to large bowel
  3. gut = transient colonisation due to pH barrier
  4. 90-95% of the large bowel are anaerobes
44
Q

Microorganism components of the stomach

A
  1. lactobacilli
45
Q

Microorganism components of the small bowel - duodenum

A
  1. lactobacilli
  2. streptococci
46
Q

Microorganism components of the small bowel - ileum

A
  1. enterbacteria
  2. bacteroides spp
47
Q

Microorganism components of the large bowel

A
  1. bacteroides spp
  2. fusobacterium spp
  3. strep. faecalis
  4. E. coli
  5. Lactobacillus
  6. staph. aureus
48
Q

Microorganism components of the rectum

A
  1. bacteroides spp
  2. bifidobacteria
  3. coliforms
49
Q

host-microbe interactions - C.diff

A
  1. can be carried asymptomatically for long periods
  2. life threatening infections in the absence of other microbes
  3. treatment with broad spectrum antibiotics reduces microbiome diversity and colonisation
  4. C. diff thrives and takes over causing infection with toxins causing tissue damage
  5. spore forming so very resistant to treatment
  6. treat with antibiotics or faecal transplants
50
Q

faecal transplants

A

spray the inside of the colon with extra bacteria
this can help reduce symptoms but doesn’t get rid of the spores

51
Q

microbiome monitoring

A
  1. commercial companies offering at home analysis
  2. core microbiome profiling and looking for specific pathogens and normal ranges
  3. still in its infancy and screening for specifics
52
Q

Microbiome and influence on drug efficacy

A

Positive:
form of a drug that is converted to its active form by Microorganisms in the gut

Negative:
Eggerthella lenta (in 40% of the population) can break down and inactivate digoxin that is used for heart failure
- increase the dose
- treat with antibiotics as well to reduce the bacteria?

53
Q

Microbiome and drugs: multi-layer antimicrobial administration

A
  1. several layers of liposome coating with different antimicrobials in different layers
  2. targeted disruption of the membrane releases the next layer
  3. put certain drugs in the hydrophobic and hydrophilic areas
  4. good at tackling resistance and biofilms
54
Q

the microbiome and the brain

A

the gut’s Microorganisms are known to impact neurological conditions such as:
1. Alzheimer’s
2. Parkinsons - E. coli curl protein causing protein misfolding
3. motor neurone disease - akkermansia muciniphila make vit B, aiding symptoms
4. Autism- possible infection during pregnancy
5. Anxiety

55
Q

what are keystone microorganisms?

A

the microorganisms that even at low abundances can remodel a healthy benign community/microbiome into a disease causing microbiome through dysbiosis
OR those that are missing from a community can result in dysbiosis

generally reserved for pathogenic microorganisms

56
Q

Example of a keystone pathogen

A

P. gingervalis
remodelling effects on the microbiome and the host
indirectly using the host immune system
OR
directly

57
Q

how do we determine the microbiome?

A
  1. community profiling - taxonomical
  2. functional profiling - the role of microorganisms
  3. Ecological profiling - abundance, interactions, patterns
  4. Stability and variability
  5. NGS of 16S rRNA for bacteria and 18S rRNA for fungi (these have bias)
58
Q

Next Gen Sequencing problems

A

if you don’t have the sequence you cannot determine if the sequence is present and 70% of the microbiota cannot be cultured to be sequenced

59
Q

what are the unknowns about the microbiota?

A
  1. there is so much we don’t know about species/genera/phyla are present as not all can be cultured
  2. most may rely on other microbes to grow or have specific environmental conditions/supplementation
60
Q

Probiotics vs prebiotics

A

Probiotics = microbes for healthy guts?
- not much scientific benefit
Prebiotics = foods for healthy guts?
- yes very good for you

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