How scientists decipher COVID-19 — Part 1: Brief Overview
Introduction
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.
Context
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
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?
- Medical
Disease research in relation to microorganism, disease treatment, disease diagnosis, drug development etc. - Animal
Animal development, animal food effective ratio, disease prevention etc. - Agriculture
biogeochemical cycles, crop growing management, crop diseases prevention and treatment, soil etc. - Environment
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
Research History
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
Method Overview
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).
Applications
- Analyze community genetic diversity and abundance.
- Understand molecular structural and functional diversity.
- Explore the relationship between microbes and the environment/host.
- Explore novel genes.
Sequencing process
- Sampling.
- DNA extraction.
- Connect to sequencing adapters.
- Sequencing.
Terminology
Genome（基因组）
The complete set of genes in a cell or living thing.
Microbes （微小生物）
The microorganisms of a particular site, habitat, or geological period.
Community structure （群落结构）
The composition of each microbes and its relationship.
References
Metagenomic Research Overview (Chinese)
Continue Reading
How scientists decipher COVID-19 — Part 2: Sanger and Next Generation Sequencing
How scientists decipher COVID-19 — Part 3: IDseq
Special thanks to Phoenix Yin (Microbiology@UBC | Pre-med student) for answering all my questions and proofreading this article.
