New Trends in Microbiology

8/8/2019 New Trends in Microbiology

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New Trends in Microbiology

Zhihong Hu

Wuhan Institute of Virology

Chinese Academy of Sciences


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Outline

I. Microbes and Microbiology

II. Environmental Microbiology

III. Microbial Genomics

IV. Emerging Infectious Disease

V. Integrative Microbiology


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I. Microbes and Microbiology


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Microbes are the Basis of Life

Microbes were the first life

form on earth

The root of the tree of life

Microbes have the greatest

genetic and metabolic

diversity

Define the boards of the

biosphere

3.5 billion years old prokaryotic fossil


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0

1000

2000

3000

4000

5000

2000 2005 2010 2015 2020

Total Ethanol

From cellulose

From corn

Bio-Ethanol

Biofuels Will Depend on Microbes


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Microbes are Vital to Human Health

More than 90% of the cells in our bodies are

microorganisms

Necessary for digestion and absorption of nutrients

Critical for the development of vascular and

immune systems

Pathogens of infectious diseases


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Microbiology is Fundamental to Biology

Microbes are ideal model for studying life

science

Microbiology plays important roles in

biochemistry, genetics, evolution, molecular

biology, etc.


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The Tree of Life Before Molecular Microbiology

Five Kingdoms of Life


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II. Environmental Microbiology


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Amann, Ludwig and Schleifer, Microbiol. Rev.59, 1995

~99% of the Microbes on Earth are Uncultured


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Metagenomics:

In situ Microbial Community Analysis

To Understandthe Whole,

One Must Study

the Whole

Newman & Banfield, Science 296, 2002


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Hot Spring in Tengchong,

Yunnan, China (75 oC)Bao et al., Genome Research 12, 2002

Thermoanaerobacter

tengcongensis

Genome ofThermoanaerobacter tengcongensis


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Proteomics ofT. tengcongensis

Wang et al., Proteomics, 2004


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The Significance ofExtremophiles Researches

Origin of life and evolution

Adaptation of life to extreme

environments Life on other planets

Potential applications in

industry, agriculture,

medicine, and environmental

remediation


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Some Ongoing Research Activities

in Environmental Microbiology in China

Metagenomic projects: Continental

subsurface deep drilling, deep sea, hot

springs, human intestinal tract, etc. Genetic bases and survival strategies

of extremophiles


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III. Microbial Genomics


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Can we Define a Minimal set of Genes Essential for Life?

DNA metabolism: 16

RNA metabolism: 106 Protein processing, folding,

secretion: 15

Cellular processing: 5

Energetic and intermediary

metabolism :56

Poorly characterized: 8

Total: 206 genes

Protein-coding genes

in the hypothetical minimal cell:

Gil et al., Microbiol Mol Biol Rev. 68, 2004

Mycoplasma genitalium:

382 protein-coding genes

are essential.

Glass et al., PNAS 103, 2006.


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Transmission and Expansion ofY. pestis in China

Zhou et al., J. Bacteriol 186, 2004

DFR17

G05,06,08

G10

G14

G04

G01,02,03

G08

G07

G09

G09

G09

G10

G11,12

G11,13

G05,11

G14

G?

DFR14,22

DFR

04

DFR03,0

4DFR05

DFR13

DFR06,11,12,13,18,19,20

DFR06,11,12,13,18,19,20

DFR06,07,15,16

DFR10DFR04,21

DF

R

0

2

DFR17

DFR

02

DFR0

9

Antiqua Antiqua

Orientalis

Medievalis


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Cluster I - Synthesis and transportof ribosome proteins

Cluster II - Uptake and utilizationof iron

Cluster III - Sulfur metabolism

Cluster IV - Energy metabolism

Global Gene Transcription Profile ofY. pestis


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Metabolic Pathways

inLeptospira interrogans Lai

Ren et al., Nature 422, 2003


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Deng & Bai, Nat. Prod. Rep., 2006

Metabolic Engineering: Antibiotic Biosynthesis


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IV. Emerging Infectious Diseases


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Mechanisms of Viral Emergence

Transmission tohumans

Inter-human

transmission

and further spread

Virus Intermediate hostAnimal reservoirVector


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The full-length genome sequences

had 99.8% identity to the human SARS-CoV.

Guan et al., Science 302, 2003

Masked Palm Civets Harbouring SARS-CoV

Masked Palm Civets


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He et al., Science 303, 2004

Phylogenetic Analysis Linked Early Cases to Civets


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Song et al., PNAS 102, 2005

Re-emerging of SARS in 2003/2004 were found

Directly Linked to Civets

3 animalsamples

2 humansamples

Very mild symptoms

No human-to-human transmission

Direct/indirect civet contact history


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Qu et al., J Biol Chem, 2005

Viral Adaptation to Human Receptors is

Critical for Human to Human Transmission

Li et al., Science, 2005


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Civets were viral positive in markets but negative in farms

Kan et al., J. Virol., 2005

Civet: Animal Reservoir or Intermediate Host?


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Bats?Bats?

One of the largest and the most diverse groups of

mammals which originated 50 million years ago

More than 80 bat viruses belonging to 10 virus families

were reported

Bats are natural reservoirs of a numbers of viruses such

as Hendra, Nipah, Ebola and rabies


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Li et al., Science 310, 2005


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RBDS1 domainS2 domain

TM Cyto

Bat SARS-like Virus may not Infectious to Human


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Market civet

Human

Bat?Otheranimals

Transmission Chain of SARS-CoV?

Wild civet

Farm civet


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VI. Integrative Microbiology

Microbiology

Bioinformatics

Chemistry

Ecology

Nanotechnology

Geology

Engineering

GeneticsImmunology


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Bioinformatics

GENE EXPRESSION

PROFILES

PROTEIN

INTERACTION DATA

GENE ONTOLOGY

PROTEIN COMPLEX

DATA

PATHWAY DATA


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True-color image of a Trichodesmium bloom (A), the Trichodesmiumderived chlorophyll (B), and modeled N2 fixation (C).

Ecology:Remote Sensing for Tracking Marine Microbial Ecosystem

Capone & Subramaniam, ASM News 71, 2005


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Nanotechnology and Microbiology

Using nanotechnology to study microbiology:

- Imaging single molecules

- Poking and pulling nanoscale objects (laser traps,

optical tweezer)

- Determining spatial organization in living

microbes (AFM, near/far field microscope)

Contribution of microbiology to nanotechnology

Merz et al.,

Nature 407, 2000


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New Trends in Microbiology

Environmental microbiology

Microbial genomics

Emerging infectious disease

Biocomplexity

The origins and history of life

Engineering of microbes to improve the quality of life


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Thank You

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New Trends in Microbiology