L11- Fungi Flashcards
What does heterotrophs mean
They acquire nutrients from other organisms
How much bigger are fungi than bscteria making them difficult to study
10-100 x larger
How mant fungi species seen during sequencing mycobiome
50+ (less than bacteria)
Whoch is more diverse, mucosa or skin
Mucosa
What encironmental fungi can be seen in the lung
Aspergillus and cryptococcus
Give 2 examples of how diet affrct mycobiome
Penecillium found in animal diets and agaricus is white mushroom
What increases during breastfeeding
Increase in candida
What fungi incrrase furing solid food intake
Saccharomyces cerevisiae
What increases during a veg diet vs animal
Veg- increase in candida vs mest and cheese has penecillium
What alternativr sequencing method is there to shotgun fir mycobiome
Amplicon - not random as you need to amplify single gene and design primers to compare eith reference databwses
What is teh issue with amplicon
Need to know the sequence to design primers but for fungi there are leas reference genomes available
Instwad of 16srrna what gene is used in amplicon gor mycobikme
Its1 and its2- can capture the diversity of fungi
What does efficiency of shot gun metagenomics depend on
How easy it is to break and lyse cells for sample extraction
WhT sort of detail can you get from metagenomics bias asidr
Strain level detail, functional analysis, relative abundance
What is extraction bias
Fact bacteria are easier to lyse due to universal peptidoglycan so lysozyme methods. Fungi have different glucans and chitin much harder to break. Csnnot extract sample easy
A
Why does larger crll biomwss affect mycibiome studying
Harder to rxtraft dna if there is more biomass to remove etc
What is culture bias and give example lf why this is issue
Some fungi sre mich easierto culture like xandida vs malassezia wuich is harder
Means more reference data on more candida strains than malassezia, makes identification harder
How many reference genetic databases in 2019 of fungi bs bacteria rougkly
Around 4000 for fungi and 180 k for bacteria
Why is metagenomics harder with fungal dna
Both exons and introns
Why is metatranscriptomics better gor fungi
Rna has no introns, and also eliminates dead fungi as need to be metabolically active and live to form rna
What 2 specieis of fungi were most abundant according to hmp
Candida and malassezia
Give an example where the its1 and its2 sequencing amplicon was incosistant
Malassezia cia its1 was not picked up compared to its2
What % of aequenfes from hmp were fungi
0.01% (but the biases werent considered)
Whcih article discusses diet chnages to fungi and bacteria
Lawrence et al 2013
