Week 1 Flashcards
Metagenomics meaning
refers to the application of genomics-based techniques for the direct genetic analysis of the microbial content of a host or environmental site, without the need for the isolation and
laboratory culturing of individual species
Microbiota meaning
refers to the microbial cellular population living in a plant or
animal host
Microbiome meaning
refers to the total genetic material belonging to a specific
microbiome, but it is sometimes used in place of the term microbiota
metagenome meaning
A “metagenome” is the mixture of genetic sequences derived from the genomes of the microbes
present in a host or environmental site
Dysbiosis meaning
A term that denotes an unhealthy state of the microbiota
Symbiotic versus Parasitic Relationships
SYMBIOTIC
Commensalism
State of infection in which the microbe benefits without damaging the host
e.g. Desulfomonas pigra colonises the large intestine.
Mutualism
State of infection in which both host and microbe benefit
e.g. Escherichia coli colonises the large intestine and produces vitamins B, K
PARASITIC
State of infection in which the microbe benefits at the expense of the host
e.g. Mycobacterium tuberculosis and infection of the lung
Normal Microbiota benefit
This can benefit the host by preventing the colonisation of host sites by pathogenic bacteria by
competing for space
competing for nutrients
producing substances harmful to pathogens
changing the physicochemical conditions
Symbiosis to Opportunism
As with any relationship, circumstances can change and bacteria can turn on their
hosts with little warning.
Under normal conditions, E. coli in the large intestine has a mutualistic relationship
with the human host. In its normal site of colonisation and in a healthy host, it does not cause disease. But change one of these factors and disease may ensue if it is given access to other host sites
Factors Affecting Microbiome Composition
Diet
Medication
Stage of Life
Exercise
Stress
Host Genetics
External environment
Pet ownership
Clostridioides difficile what does it cause + risk factors
Clostridioides difficile is the main causative agent of Antibiotic-Associated Diarrhea (AAD) and health care-associated infective diarrhoea.
The clinical manifestations of Clostridioides difficile infection (CDI) range from mild diarrhoea to pseudomembranous colitis, toxic megacolon, and even death.
Risk factors for C. difficile-associated diarrhea (CDAD) include:
- advanced age
- antimicrobial exposure
- previous hospitalization
Phylotyping
Phylotyping involves the use of nucleic acid-based techniques for establishing the evolutionary relatedness between species
For this, genes which have the following characteristics are selected:
Wide distribution
Highly conserved
Contain regions of variation
No Lateral (Horizontal) Gene Transfer
The gene encoding the Small Sub-Unit (SSU) rRNA in all cellular life forms meets these criteria
SSU rRNA gene sequencing and
phylogeny determination steps
- Isolate DNA from cells
- PCR
- DNA sequencing
- Sequence analysis
- Generate phylogenetic tree
The Skin
Thin outer layer (epidermis)
Thick underlying layer (dermis)
Subcutaneous layer (hypodermis)
Epidermis is quite dry and has several layers of dead cells which act as a barrier
Epidermal cells are shed regularly such that the epidermis is renewed every 2 to 4 weeks
The skin secretes substances which have antimicrobial activities
sebaceous glands secrete sebum which contains organic acids
sweat glands secrete salt
Infection versus Colonisation
Infection is the process by which an infectious agent invades and multiplies in body tissue resulting in the host developing clinical signs and symptoms of infection and/or an immune response such as acute inflammation. (inflammation is a sign)
Colonisation refers to when microorganisms grow on body sites of the host without causing disease or without requiring treatment.
contamination
contamination refers to when a microorganism has been introduced into the sample from an external source due to poor specimen collection technique.
Clostridioides difficile colonization vs infection
“C. difficile colonization” as the detection of the organism in the absence of CDI symptoms;
and
“C. difficile infection” as the presence of C. difficile toxin (ideally) or a toxigenic strain type and clinical manifestations of CDI
Probiotics
Use of ‘beneficial’ bacteria
Normal Microbiota
refers to the population of microorganisms that normally inhabit the body of a
“healthy individual”
Sterile vs non sterile sites
Sterile (no bacteria of any kind so all bacteria found there are significant)
-urine, blood, CSF, Bile, fluids, deep tissue samples
non-sterile (these sites are open to the external environment and are normally colonised by bacteria)
-swabs (throat, skin, wound, ear, nasal), sputum samples, nail clippings, faeces
