Question 1

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

Accepted Answer

It enables the assembly of individual 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 with a species of smaller genome size?

Accepted Answer

Because larger genomes have more unique regions for read mapping.

Question 3

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

Accepted Answer

16S rRNA gene FISH

Question 4

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

Accepted Answer

High strain heterogeneity and repetitive sequences

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 most likely explanation?

Accepted Answer

The bacterium's larger genome size results in more read recruitment.

Question 7

Which imaging technique combines light microscopy and electron microscopy to provide correlative information about microbial cells?

Accepted Answer

CLEM (Correlative Light and Electron Microscopy)

Question 8

What is the main purpose of using virusFISH in environmental microbiology?

Accepted Answer

To link viruses to their specific microbial hosts.

Question 9

Which of the following best describes 'population genomes' in the context of metagenomics?

Accepted Answer

Composite genomes representing a group of closely related organisms from environmental samples.

Question 10

Why is differential coverage across multiple samples useful in metagenomic binning?

Accepted Answer

It helps distinguish between closely related strains based on abundance patterns.

Question 11

Which equation best represents the relationship between the number of sequencing reads ($$R$$), genome size ($$G$$), and abundance ($$A) $$for a given species in a metagenomic sample?

Accepted Answer

$$R = G 	imes A$$

Question 12

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

Accepted Answer

Variable regions

Question 13

What is a major limitation of using 16S rRNA gene FISH for identifying uncultivated microbes?

Accepted Answer

Many regions of the 16S rRNA gene are inaccessible to probes due to complex secondary structure.

Question 14

Which of the following best explains why some ecosystems are too complex for complete genome assembly, even with increased sequencing depth?

Accepted Answer

High diversity and abundance of closely related strains.

Question 15

In a metagenomic study, what is the primary reason for using k-mer analysis?

Accepted Answer

To identify repetitive elements and distinguish between different genomes.

Question 16

Which of the following statements about sequencing in metagenomics is correct?

Accepted Answer

Sequencing is a stochastic process, and species abundance affects read recruitment.

Question 17

A scientist uses correlative electron fluorescence microscopy to study virocells. What is the main benefit of this approach?

Accepted Answer

It allows simultaneous visualization of viral DNA and host cell structure.

Question 18

Which of the following is NOT a determinant of genome assembly success in metagenomics?

Accepted Answer

Protein tertiary structure

Question 19

What is the main reason why mobile genetic elements complicate metagenomic assembly?

Accepted Answer

They increase the number of repetitive sequences.

Question 20

If a metagenomic sample contains 40 Mbps of protist DNA and 1 Mbps of viral DNA, what percentage of sequencing reads would you expect to map to the protist, assuming equal extraction efficiency and random sequencing?

Accepted Answer

$$\frac{40}{41} 	imes 100 \approx 97.6\%$$

Metagenomics: From Composite Genomes to Imaging

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