Lecture 36: Gut microbiome I Flashcards
What proportion of the cells in the human body are of microbial origin?
Around half.
How does the human genome compare in size to the microbiome genome?
The human genome is around 25000 genes, while the gut microbiome is around 23 million genes.
How does the human body weight compare to the weight of the microbiota in it?
The human body weighs 70 kg, but of that, microbiota weigh only 0.2 kg.
What is the difference between microbiota and microbiome?
Microbiota are the cells, while microbiome is the genes.
What are the 3 forms of microbial symbiosis with humans? Explain the difference between them.
Commensalism: one organism benefits while the other is unaffected.
Mutualism: both organisms benefit
Parasitism: one organism benefits at the expense of the other.
What is the holobiome?
The human genome + the microbiome.
Name 3 key functions of the microbiome.
- Metabolizes >50 xenobiotics
- Produce essential vitamins and nutrients that we lack the ability to synthesize ourselves
- Change animal behaviour and mating preferences.
How do microbiomes compare between different people?
They can vary a lot.
What is the older, more traditional method of studying the microbiome?
Culture-based methods.
What does the Great Plate Count Anomaly refer to?
It refers to the notion that most bacterial cells are unculturable with current methods.
Are culture-based methods effective for studying the human microbiome? State 3 reasons why or why not.
No, most bacterial cells are unculturable. This is because it is hard to recreate the gut environment, most cells do not like growing in an isolated environment from other microbes, and it is difficult to know the appropriate nutrient requirements.
What are the 4 culture-independent methods used to study the microbiome?
- 16-S rDNA-based sequencing
- Metagenomics
- mRNA sequencing/metatranscriptomics
- Metabolomics
What fundamental question is answered about the microbiome used the 16S rDNA-based sequencing method?
It answers what organisms are in the system, as the 16S gene is held by all bacteria.
What are the two major components of the 16S rDNA gene?
The identical (slow-evolving) region and the variable (fast-evolving) region, which vary between different species.
Describe how 16S rDNA gene anlysis will vary depending on how much precision you want in the results.
If you want results that are more general, say, at the phylum level, not many variable regions are needed. But at the species/strain level, you need many more (likely the whole genome), as they will be near identical.
Explain how 16S DNA gene analysis works.
You amplify the part of the gene you want using PCR then compare the sequence to others from the microbial community or members of its own species from pre-existing databases.
What fundamental question is answered using the metagenomics sequencing method?
What microorganisms are there and what do they have the capacity to do (i.e. which genes are present)
The metagenomic approach is also called the […]
Shotgun approach
How many bacterial phyla are present in the human microbiome?
3-5
What type of graph can be used to depict the type of microbial communities in the microbiome?
A PCOA plot
