Introduction to Microbiome
Transcript of Introduction to Microbiome
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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/
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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.
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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
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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
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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)
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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
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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!
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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)
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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?
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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
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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
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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
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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
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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
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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
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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
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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