A3: Microbiome Flashcards
What is the diffeence between phages and viruses
Phages infect bacteria and archaea
Viruses infect eukaryotes
What is the viral genomes like
Never the same, eifferent genome sizes, genes
For sequencing what is needed for viral sequencing
Sample manipulation
What are rhe most common viruses in gut
Plant viruses from diet
Can viruses be mutualistic in host or just parhofenic
Xan be mutualists too
Other than human euks what do viruses infect
Microbial eukaryotes like trichomonas
What gene is commonly used for sequencing to study microbiota
Ss rrna (small subunit rrna)16s in pro, 18s in euk, 12 s in mitochondria
Why cant 16s rrna sequencinf be used for viruses
They have no ribosomes
What is pangenome
After looking at wgs of one organism you can look st diff strains of the same species to see if you notice any differences in accesoru genes eg virulence factors
What is the word gicen to studyinf genomes of a whole community from a sample eg faecal
Metagenomics
Why is sequencing more widely used now
Cheaper and much wuicker with new tech like illumina sequencing
How is sequencing usually done if not via 16s rrna
Frafmentstion of dna or rna in the sample of faeces for example
Complete seuwnece of genome and aligned using computers to run 100s of bacteria eg via illumina
What is shot gun sequencing
Selecting random dna to sequence and its large scale
Why is it better to study through metagenomics form samples tather than individual
Hard to culture some microorganisms eg due to being anaerobic
What is environmental metagenomics
Looking at microbiota characterisation in areas like soul, humans, oceans
Is metagenomics only dna
No can be rna cia transcriptomics eg seuqnecing using microarrays
Other than to look st ciruses why is rna sequwncing done
Measure fene expression of populstion
What is 16a rrna seuwnecing
Uaing pcr to amplift that gene, do comparative sequencing and use things like genbank databases (cox et al 2013)
When was wgs important looking at pangenomes
Ecoli outbreak in 2011 found strain was shigotoxigenic ecoli strain (cox et al 2013)
Guve an example pf diseased vs healthy in metabenomics
Found in type 2 lower butyrate producing bacteria like roseburia (cox et al 2013)
How is metagenomics diff to other sequencing
Finds the actual functionality of the microbiota cia sequence and functional analysis via bioinformatics
What other types of metagenomics is ther
Proteomics, metabolomica eg looking at levels of butyrate
What are cross sectional studies used in investifating human microbiome
Observing all members of the sample at a speicfic time
What are longitudinal studies
Where therr are repeated eg sakpling after periods of time with the same variables
What type of study is used to suggest causes of chenges in microbiome
Case- control eg comparint smokers to non smokers
Where in the gi tract has lowest amount of microbitos
Stomach due to hastric acid and other barriers. Only 10^1 cels/g
Where in the gi tract has largest microbiota amount
Colon at 10^12 cells/g
Give an example of how iveryime there are changes in composition (clemente et al 2012)
After eating solid food you get bacteroidetes and firmicutes mostly in colon for digestion
Can the way you are burthed affect microbiota? (Clemete et al)
Yes, if c cestion you get things like staph vs in caginal delivery prevotella are present
Whats an example of why functional analysis of microbiome is so importnst
Cazymes whoch digest carbohydrates / ingestible glycans via fermentation
What are the 2 main cazymes
Glycoside hydrolases GH
Polysaccharide lyases
Which cazymes induce glycoside hydrolyases and poly lyases
Carb esterases
Which cazymes dont degrade
Glycosyltransferases
Why are bacteria importent for cazymes
Human genome has 17gh genes and 0 pl genes cs around 9120 gh genes in microbes
Which ohylum encode most cazymes
Bacteroidetes and firmicutes
What types of things do they divest
Plant glycans, animal glycans, starch, glycogen
What is the most abundant glycoside hydrolase and what foes it breakdown
Gh13 breaksdown starch
What is an organism with 97% complete homology in 16a rrna called (weinstock 2012)
Operational taxonomic unit OTU
How many body sites did yhe hmp study over 10k microbes in via 16a rrna (weinstock 2012)
18
How is sequence alignment done wkth shotgun data (weinstock 2012)
On blast for functional analysis
