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B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y

Introduction to Microbiome

By Jon Jongsik ChunProfessor, Seoul National UniversityCEO, ChunLab, Inc.

Version 2018-01-05

All lectures are available athttps://help.ezbiocloud.net/chun_lecture_kor/

2B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Microbiota

Microbiome

The community of microbial species that live in

a given environment.

All of the genomes inside these microbial cells

are what constitute the microbiota.

3B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Fecal microbiota transplant

Fecal microbiome transplant

Sequencing microbiota

Sequencing microbiome

4B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Microbiota & Microbiome

•Human

•Animal

•Soil

•Water

•Food (e.g. Kimchi)

•Any environment

5B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Holobiont & Holobiome

Assemblages of different species that

form ecological units.

Source: https://blog.thryveinside.com/the-layout-of-the-human-microbiota/

by Lynn Margulis(Endosymbiosis theory)

6B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Great plate anomaly

Sample

Microscopic counting(direct)

Plate counting(by culturing)>>

95 : 5

7B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Unculturable vs. Uncultured

Preferred!

8B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Method for Microbiome Research

• Metagenome (Handelsman et al., 1998)

- The DNA of the total microbiota found in a given

environment/sample

• Metagenomics

- Study of microorganisms by high throughput sequencing without

culturing

- Culture-independent study (no bias by culturing)

9B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

• Most of bacteria are not culturable in routine laboratory conditions.

• In natural environments, even culturable bacteria are not in the

culturable condition (a phenomenon called Viable-But-Non-

Culturable[VBNC])

• No resource for large scale isolation and characterization

Why metagenomics?

10B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

11B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Omics Tools of Microbiome Studies

Microbiome

Direct sampling

Metagenomics

Meta-

transcriptomics

Meta-proteomics

Meta-

metabolomics

CulturingConventional

microbiology

DNA

mRNA

Proteins

Metabolites

Strain/Genome

12B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Goals of Microbiome Studies

Who are they?

What do

they do?

How do

they do?

Taxonomic

Profiling

Functional

Profiling

Mechanism

Study

13B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

New paradigm for human microbiology

Microbiology

Infectious Diseases• Single strain• Culture

Microbiome• Metagenomics (No culturing)• Ecological perspective

14B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

“Microbiome” is booming

Source: Google

0

500

1,000

1,500

2,000

2,500

3,000

3,500

4,000

4,500

5,000

Gut Microbiome Microbiome

Source: PubMed

2000 2014

Public

ations

Microbiome-related publications in PUBMED

“Microbiome” searches by Google

15B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

https://www.nature.com/articles/nrgastro.2017.97

16B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

Microbiome Cookbooks

Source: www.amazon.com

17B I O I N F O R M A T I C S f o r M I C R O B I O L O G Y . C H U N L A B

• Microbiota is a community of microorganisms.

• A microbiome is all DNA of a microbiota.

• Metagenomics is the culture-independent study of a microbiome

through DNA sequencing or other techniques.

• Unlike infectious diseases, microbiome study requires ecological concept

and methodology.

Summary of the Chapter