Metagenomics

What is the main advantage of culture-dependent methods for studying microorganisms compared to culture-independent methods?

• They can provide pure isolates of microorganisms

• They are more accurate in quantifying the total number of microbes in a sample

• They can detect all microorganisms present in the sample, including uncultivable microorganisms

• They can provide the genetic materials of uncultivable microorganisms

What is the study of a community's entire genetic material directly obtained from an environmental sample?

• Genomics

• Metaproteomic

• Metagenomics

• Metabolomics

Metagenomics is a powerful tool for studying the diversity of microbes in an environment.

Why can't we just culture all microbes to study them?

• Culturing is too expensive

• Not all microbes can be cultured

• The DNA must be sequenced first

• Cultured microbes lose their natural functions

Which of the following is NOT a potential application of metagenomics?

• Identifying new pathogen in disease outbreaks

• Studying the role of microbes in the environment

• Obtaining pure bacterial colony from the environment

• Discovering novel enzymes and bioproducts for industrial processes

Metagenomics is only used for research purposes and has no real-world applications.

• True

• False

The quality and quantity of extracted total DNA are crucial for sequencing and downstream application.

What is the common method for measuring DNA concentration?

• Light microscopy

• Nanodrop spectrophotometer

• Gel electrophoresis

• Polymerase chain reaction

Amplicon sequencing is one of the technique used in metagenomics.

What does it amplify and study?

• The entire genome of all organisms present in the sample

• Only for long DNA fragments

• Specific or conserved regions of the DNA

• Only for short DNA fragments

Shotgun metagenomics refer to:

• Sequencing all DNA fragment present in the total DNA

• Sequencing only the protein-coding regions of genes

• Sequencing only specific region of DNA

• Sequencing only the DNA from a specific organisms of interest

Metagenomic analysis involves the application of different bioinformatics tools.

What does "bioinformatics" refer to?

• The application of computer science to analyze biological data

• The study of living organisms through culturing method

• A type of DNA sequencing machine

• The use of microscope to study bacterial cells

Which of the following bioinformatics tools is typically used for taxonomic profiling of shotgun metagenomic data?

• Trimmomatic

• Kraken2

• MEGAHIT

• metaGeneMark