How scientists decipher COVID-19 — Part 1: Brief Overview
If you ever wonder about how scientists decipher the myth behind the novel virus COVID-19, this 3 part series of “How scientists decipher COVID-19” will provide you a brief understanding about:
1. PART 1: The metagenomic field.
2. PART 2: Sanger and Next Generation Sequencing — the methods used to study the virus and its DNA.
3. PART 3: IDseq — an application that aims to empower places that lack economic and technical resources with matchable research capability.
Microbiome refers to the total number of microorganisms in a certain environment. This environment can be soil, atmosphere, water, human, animal or plants.
The microbiome is crucial for us in two aspects:
- Maintaining the balance of ecological equilibrium and biodiversity.
- Closely relevant to the host health of human, animal, plants, and for environmental and food safety.
Areas of Research
There are 4 areas of research within the Microbiome:
- DNA content aspect (Metagenomics)
- RNA expression aspect (Metatranscriptomics)
- Protein expression aspect (Metaprotemics)
- Metabolism, or small molecules aspect (Metabolomics)
Here we will go deeper into understanding the DNA stream — Metagenomics.
Metagenomics is the subject to study the metagenome, or genes found in the environment.
What problems can metagenomic research assist with solving?
- Studying the difference of microbial community structures and compositions.
- Obtaining and analyzing the difference among environmental and host samples.
- Studying the difference among species/genus.
- Studying the functions of microbial community structure.
What areas can metagenomic research be applied to?
Disease research in relation to microorganism, disease treatment, disease diagnosis, drug development etc.
Animal development, animal food effective ratio, disease prevention etc.
biogeochemical cycles, crop growing management, crop diseases prevention and treatment, soil etc.
Smog, water pollution, gas pollution decomposition, prevention and control of desertification.
- Biological energy source
Natural antibiotic selection, Gene mining.
- Extreme environment
Glaciers, frozen soil, hydrothermal vent.
What are the current research trends?
- Application expansion
Human disease, biological energy source, environment restoration, biotech, agriculture, animal nutrition, biological defense, extreme environment, and ethics
- In depth functional analysis
- Discovery of new genes
Antibiotics, enzyme, new drug
- Multi-omics research
The following is a brief timeline of metagenomics research history:
- 1998: The idea of Metagenomics is proposed
- 2007: Launched Human Microbiome Project
- 2008: Launched MetaHIT Project
- 2010: Launched Earth Microbiome Project
- 2013: Launched iHMP
- 2016: Launched the National Microbiome Initiative
Researchers use metagenomic sequencing methods to construct a knowledge base about discovered and undiscovered genes. There are two major ways to sequence DNA: Sanger Sequencing and Next Generation Sequencing (NGS).
- Analyze community genetic diversity and abundance.
- Understand molecular structural and functional diversity.
- Explore the relationship between microbes and the environment/host.
- Explore novel genes.
- DNA extraction.
- Connect to sequencing adapters.
The complete set of genes in a cell or living thing.
The microorganisms of a particular site, habitat, or geological period.
Community structure （群落结构）
The composition of each microbes and its relationship.
Special thanks to Phoenix Yin (Microbiology@UBC | Pre-med student) for answering all my questions and proofreading this article.