How scientists decipher COVID-19 — Part 1: Brief Overview

Illustration from depositphotos

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:

  1. Maintaining the balance of ecological equilibrium and biodiversity.
  2. 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:

  1. DNA content aspect (Metagenomics)
  2. RNA expression aspect (Metatranscriptomics)
  3. Protein expression aspect (Metaprotemics)
  4. 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?

  1. Studying the difference of microbial community structures and compositions.
  2. Obtaining and analyzing the difference among environmental and host samples.
  3. Studying the difference among species/genus.
  4. Studying the functions of microbial community structure.

What areas can metagenomic research be applied to?

  1. Medical
    Disease research in relation to microorganism, disease treatment, disease diagnosis, drug development etc.
  2. Animal
    Animal development, animal food effective ratio, disease prevention etc.
  3. Agriculture
    biogeochemical cycles, crop growing management, crop diseases prevention and treatment, soil etc.
  4. Environment
    Smog, water pollution, gas pollution decomposition, prevention and control of desertification.
  5. Biological energy source
    Natural antibiotic selection, Gene mining.
  6. Extreme environment
    Glaciers, frozen soil, hydrothermal vent.

What are the current research trends?

  1. Application expansion
    Human disease, biological energy source, environment restoration, biotech, agriculture, animal nutrition, biological defense, extreme environment, and ethics
  2. In depth functional analysis
  3. Discovery of new genes
    Antibiotics, enzyme, new drug
  4. Multi-omics research

Research History

The following is a brief timeline of metagenomics research history:

  1. 1998: The idea of Metagenomics is proposed
  2. 2007: Launched Human Microbiome Project
  3. 2008: Launched MetaHIT Project
  4. 2010: Launched Earth Microbiome Project
  5. 2013: Launched iHMP
  6. 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

  1. Analyze community genetic diversity and abundance.
  2. Understand molecular structural and functional diversity.
  3. Explore the relationship between microbes and the environment/host.
  4. Explore novel genes.

Sequencing process

  1. Sampling.
  2. DNA extraction.
  3. Connect to sequencing adapters.
  4. 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.

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Product Designer | Content Creator | Currently seeking my unfair advantage | This is my sanctuary to let my thoughts flow

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Zunshi Wang

Zunshi Wang

Product Designer | Content Creator | Currently seeking my unfair advantage | This is my sanctuary to let my thoughts flow

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