Quiz Review

What are the two main types of high-throughput sequencing approaches used to analyze microbial populations?

• Amplicon sequencing and shotgun metagenomics

• Metagenomics and transcriptomics

• Sanger sequencing and flow cytometry

• 16S rRNA profiling and PCR cloning

Why is it challenging to determine the taxonomy of fungi and archaea in metagenomic analyses?

• They lack any genetic material suitable for sequencing

• Their genomes are too small to be detected in environmental samples

• They are underrepresented in reference genome databases
  
  

• They cannot be separated from bacterial sequences by current sequencing technologies

What gene is most commonly used in amplicon sequencing for microbial communities?

• ITS2
  
  

• rbcL

• 16S rRNA
  
  

• COI
  
  

What is one limitation of 16S rRNA sequencing?

• It can't sequence DNA
  
  

• High cost
  
  

• Limited taxonomic resolution

• Requires culturing
  
  

What is one of the main advantages of metagenomic shotgun sequencing?

• Faster PCR cycles
  
  

• Functional profiling of microbial communities

• Better microscope images

• More accurate culturing methods
  
  

What is a major challenge of functional annotation in metagenomics?

• Too much host DNA

• Lack of known gene functions

• Poor DNA extraction methods
  
  

• No available databases
  
  

What is a MAG in metagenomic analysis?

• A manually curated genome from cultured microorganisms

• A reference genome used for taxonomic classification
  
  

• A genome reconstructed from metagenomic data through assembly and binning

• A genetic marker used to identify antimicrobial resistance

What does the assembly quality metric N50 represent?

• The average length of all contigs in the genome assembly
  
  

• The length of the shortest contig in the assembly
  
  

• The length of the contig such that 50% of the total genome length is contained in contigs of that length or longer
  
  

• The total number of contigs in the assembly

How can bacterial replication rate be inferred?

• RNA expression
  
  

• DNA methylation
  
  

• Number of ribosomes
  
  

• Read coverage near the origin of replication

What technique helps distinguish live from dead cells?

• PCR

• PMA treatment
  
  

• RNA-Seq
  
  

• CRISPR-Cas