our microbiome

Question 1

what does microbiome mean?

Answer 1

its a functional collection of all microbes in a particular enviroment

Question 2

what is the human microbiome?

Answer 2

its all of the microbes living on/in human tissues and biofluids including bacteria, archea, viruses, fungi and protists

Question 3

what is the holobiont concept?

Answer 3

its the concept that the host species living on and in that form a discrete ecological unit

Question 4

what is the Hologenome?

Answer 4

its the collection of all genomes of all the members of the holobiont for example in the human body there are more bacterial cells than human cells

Question 5

what is the importance of our microbiome?

Answer 5

• microbes provide a key protective barrier/ defence against pathogens
• gut microbes help to digest food, synthesise vitamins and also influence the development + efficiency of our immune system

Question 6

what are 2 types of bacteria in the human microbiome?

Answer 6

akkermansia muciniphila

• gram negative anaerobic bacterium
• promotes host tissue differentiation by causing continuous regeneration of the protective mucin layer

bacteroirdes thetaiotaamicron

• gram-negative, anaerobic bacterium
• breaks down complex carbohydrates into products that can be absorbed by the body

Question 7

the immune system and the microbiome

Answer 7

• initial protection against microbes is provided by a set of barriers, when breached, invading microbes trigger the innate immune system and adaptive immune system
  factors which affect microbial growth are things like temperature, pH and salt

Question 8

pathogen-associated molecular patterns (PAMPs)

Answer 8

• evolutionary conserved germline-encoded receptors are structurally different but share a common feature of PAMPs
  these are highly conserved structures that microbes would have trouble doing without or changing
  example - peptidoglycan a key component of bacterial cell walls
  PAMPs are recognised by pattern-recognition receptors (PRRs)

Question 9

what microbes grow on our skin?

Answer 9

10 to the power 11 microbes in moist areas
the skin is difficult to colonise because of how dry, salty and acidic it is, protective oils and sweat also affect microbe growth
microbes mostly grow on the ears, scalp, genitals and armpits
they’re mostly gram-positive bacterial species which are more resistant to salt and dryness such as staphylococcus epidermis

Question 10

what is involved in our oral and nasal microbiome?

Answer 10

at first, an infants mouth is colonised with:

• Non-pathogenic Neisseria (gram-negative)
• Streptococcus, lactobacillus, actinomyces (gram-positive)
• As teeth start emerging, other bacteria start growing: Prevoltella; fusobacterium: between gums and teeth; Streptococcus mutans: tooth enamel
• Nasopharynx and oropharynx- staphylococcus aureus and S. epidermis
• Some bacteria (e.g. prevotella fusobacterium) can be associated with periodontal disease)

Question 11

what is involved in our respiratory tract microbiome?

Answer 11

it was originally thought to be sterile but the lungs and trachea harbour normal bacteria
the ciliated mucous membrane lining of the trachea, bronchi and bronchioles make up the mucociliary escalator which sweeps foreign particles up and out of the lung
many microbes present only transiently

Question 12

what is involved in the genitoyrurinary tract?

Question 13

what is involved in the genitourinary tract?

Answer 13

• much of it is free of microbes
• the urethra contains staphylococcus epidermis, enterococcus species and some members of Enterobacteriaceae
• composition of the vaginal microbiota changes over the cycle and lifetime
• lactobacillus species is very common
• there is also interplay between human hormones and the microbiome

Question 14

what is involved in the gastrointestinal tract?

Answer 14

the stomach has a low pH and so few microbes survive
- cut microbes can produce metabolites like tryptamine

lower GI tract

• mostly anaerobic 10to the power 11- 10 to the power 13 bacteria/gm of faeces
• 1000 anaerobes: 1 facultive organism
• ~1500 different bacterial species found overall
• the GI microbiome varies between individuals and it helps to protect you against pathogens

Question 15

what happens when accidental penetration of certain organisms beyond a site of colonisation occurs?

Answer 15

this can cause infections

pertubingg the homeostasis of out microbiome can lead to inflammation and disease

Question 16

what is the hygine hypothesis?

Answer 16

its the idea that our microbiome is less healthy than it should be as its smaller
this is because of how clean we are, so our microbiome is less diverse than it used to be which makes it easier for pathogens to infect us
- a possible example of this is allergies, our immune system is too ready to attack anything that gets in its way

Question 17

what are some diseases associated with microbes normally present in our microbiome?

Answer 17

caries and periodontis - cutubacterium acne
inflammatory bowel disease (IBD)
vaginitis ; oral thrush - candida species

Question 18

what is the link between obesity and our microbiome?

Answer 18

complex interactions among genes, diet and a long term imbalance between energy intake and expenditure
Jeffrey Gordon’s studies showed there’s a link between obesity in humans and their microbiome [ transplantation of microbiomes from monozygotic human twins into germ-free mice]
observational studies show correlations between different gut microbiome compositions and obesity and lean weight
- intestinal microbes can also digest many foods that we can’t, in this process, they produce short-chain fatty acids (SCFAs) that our cells can then use in many ways - the amounts of these may influence the development obesity

Question 19

what did the observational stdies which linked your body’s microbiome to obesity look at?
and how can microbiota influence obesity?

Answer 19

bacterioroids - firmicutes balance or the presence of certain species e.g. pervotella
microbiota can influence obesity by:
- harvesting energy from ingested foods
- triggering intestinal inflammation

Question 20

how can inflammation induced by microbes influence the development of obesity?

Answer 20

lipopolysaccharides (LPS or endotoxin) produced gram-negative species which promote inflammation
a high fat diet can promote absorption across the epithelium

Question 21

how can we modulate our microbiome?

Answer 21

• probiotics
• prebiotics
• fecal transplants 💩
• personalised medicine