Profiling and micro biome study Flashcards
reasons to study the microbiome
eradicate harmful components - h.pylori, ulcers
treat diseases more naturally
prevent disease formation - lack of natural protection and dysbiosis
diseases now considered affected by the micro biome
psoriasis, BV, Chrons, obesity and acne
16S RNA sequencing
all bacteria have this as a part of their 30s subunit of prokaryotic ribosome
- highly conserved and variable regions
- identify and distinguish between taxonomic groups
organisms which are very closely related
same (hyper)variable region - newly synthesised
METAGENOME SEQUENCING
- whole genome sequencing
- functions and pathways
- essential for defining the microbiome
what does a profiling technique need to be
- able to deal with huge amounts of data generated
- culture independent sequence analysis - small amount able to be cultured
- reproducible and representative
how many genomes currently sequenced from gut microbiota
178 - 2phyla
Enterobactericae
gram -ve
e.coli - opportunistic
salmonella - obligate
WGS
genome characteristics, outbreak analysis, antibiotic susceptibility testing and virulence investigations
WGS was used to investigate
transmission in hospitals of vancomycin resistant E.faecilbacterium
WGS can provide
a map of the virulome
MALDI-TOF MS
matrix assisted laser desorption/ionisation tim of flight mass spectrometry
- gold standard for microbial identification
- fast cheap and reliable
MALDI TOF MS can identify
bacteria and fungi cultivated on agar plates or in liquid medias
- antibiotic/myotic resistance testing
what does MALDI TOF rely on
RIA and ELISA
radio immune assay and enzyme linked immunosorbent assay
MALDI TOF overview
- antibody + mass spec]
- can see small proteins and peptide in forces - calibration curve tabled
- stable isotopes
toxin quantification is easy