Question 1

Which of the following best describes the main advantage of genome-resolved metagenomics over traditional metagenomics?

Accepted Answer

It enables the assembly of complete genomes from complex environmental samples.

Question 2

In metagenomic sequencing, why does a species with a larger genome size tend to recruit more sequencing reads, assuming equal abundance?

Accepted Answer

Because the probability of a read originating from a species is proportional to its genome size.

Question 3

Which method is most commonly used to identify uncultivated bacteria and archaea in environmental samples?

Accepted Answer

16S rRNA gene sequencing

Question 4

What is the primary challenge in assembling genomes from highly complex metagenomic samples?

Accepted Answer

Insufficient sequencing depth due to high species diversity

Question 5

Which of the following is a key feature of the 16S rRNA gene that makes it useful for microbial phylogeny?

Accepted Answer

It contains both conserved and variable regions.

Question 6

A metagenomic sample contains a bacterium with a 5 Mbps genome and a virus with a 0.05 Mbps genome, both in equal abundance. If 99% of sequencing reads map to the bacterium, what is the ratio of genome sizes?

Accepted Answer

$$\frac{5}{0.05} = 100$$

Question 7

Which of the following best explains why differential coverage is useful in metagenomic binning?

Accepted Answer

It helps distinguish closely related strains by comparing abundance across multiple samples.

Question 8

What is the main purpose of virusFISH in environmental microbiology?

Accepted Answer

To link viruses to their specific microbial hosts using fluorescence in situ hybridization.

Question 9

Which statement about the stochastic nature of sequencing is correct?

Accepted Answer

Species with higher abundance and larger genomes are more likely to be represented in sequencing reads.

Question 10

Why are some regions of the 16S rRNA gene not accessible by probes in FISH experiments?

Accepted Answer

Because the complex secondary structure of the rRNA can block probe binding.

Question 11

Which imaging technique allows for the correlation of light microscopy and electron microscopy data in microbiology?

Accepted Answer

Correlative Light and Electron Microscopy (CLEM)

Question 12

What is a 'population genome' in the context of metagenomics?

Accepted Answer

A genome assembled from sequencing data representing a group of closely related organisms in a sample.

Question 13

Which of the following is NOT a determinant of the ability to assemble genomes from metagenomes?

Accepted Answer

The presence of only eukaryotic organisms

Question 14

A researcher wants to discriminate between different microbial species in a sample. Which region of the 16S rRNA gene should they target?

Accepted Answer

Variable regions

Question 15

Which of the following best describes the process of metagenome-assembled genomes (MAGs)?

Accepted Answer

Genomes reconstructed from metagenomic sequencing data using binning and assembly algorithms.

Question 16

If a metagenomic sample contains 40 Mbps of protist DNA and 1 Mbps of viral DNA, what percentage of total DNA is viral?

Accepted Answer

$$\frac{1}{40+1} 	imes 100 = 2.44\%$$

Question 17

Which of the following is a limitation of using 16S rRNA gene FISH for microbial identification?

Accepted Answer

Some regions of the 16S rRNA gene are inaccessible due to secondary structure.

Question 18

What is the role of k-mer analysis in metagenomic binning?

Accepted Answer

To identify repetitive sequences and assist in grouping similar genomic fragments.

Question 19

Which statement about metagenomic samples is correct?

Accepted Answer

They often contain multiple species with varying genome sizes and abundances.

Question 20

Why is more sequencing required for highly complex ecosystems in metagenomics?

Accepted Answer

To ensure sufficient coverage of all species, especially those with low abundance.

Genome-Resolved Metagenomics and Imaging of Uncultivated Microbes

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