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Microbial MetabolismSystems Microbiology
Ching-Tsan Huang (黃慶璨)Office: Agronomy Hall, Room 111Tel: (02) 33664454E-mail: cthuang@ntu.edu.tw MIT OCW
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Systems Microbiology aims to integrate basic biological information with genomics, transcriptomics, metabolomics, glycomics, proteomics and other data to create an integrated model of how a microbial cell or community functions. (Nature Review Microbiology)Systems Microbiology seeks to identify how microbial functions evolve and how emergent properties in cells and communities arise from seemingly simple, linear genetic sequences.
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Source: U.S. Department of Energy Genome Programs http://genomics.energy.gov.
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Source: U.S. Department of Energy Genome Programs http://genomics.energy.gov.
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Why Systems Microbiology?
Microbial systems are important and ideal models
Microbes offer important lessons about all life forms
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Disciplines Involving Systems MicrobiologyMicrobiologists,Biochemists,Evolutionary biologistsMathematicians,Computer scientists,Physicists,Chemists,Control theorists,Systems engineers,Geochemists,Atmospheric chemists,Chemical and physical oceanographers,Earth scientists, andBiostatisticians.
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Potential Applications of Systems Microbiology
AgriculturesMedicinesNovel energy production systemsMetabolic engineeringBiocontrolPollution and bioremediationBioterrorism and decontaminationMicrobiological detection systemsGlobal monitoring
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Integrated Systems Microbiology
Microbiology
Computer Science
ChemistryEcology
Mathematics
Molecular Evolution
Microbial - Host System
Multi-Disciplinary
Biocontrol/ Bioremediation
Drug Discovery Antibiotic Resistance DiagnosticsVaccines
• Environmental• Industrial Bioreactors
BioenergyBiosensors
Genetics
•Biomedical
10Utilization of Microbial Inoculants to Promote Sustainable Agriculture
Phytostimulation
Production of IAAACC deaminaseIncrease rooting Increase Nitrogen
uptakeReduced fertilizer
usageReduced nitrate
pollution
Biofertilization
Nitrogen fixationPhosphate solubilizationReduced fertilizer usageReduced water pollution
Antimicrobial MetabolitesReduced pathogensReduced diseaseReduced fungicide usage
Biocontrol
Nutrients
SignalsPrimary metabolismSecondary metabolism
Gene expression
Primary metabolism
Secondary metabolism
Microbial Cell Factory
Bioremediation
Clean-up ofcontaminated
soils
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An Integrated Systems Biology Approach to Elucidating the Nature of Molecular Signalling in Microbial-Host Interactions
Environmental signalsMicrobial signalsQuorum sensing
Signalling and regulatory circuits
Eukaryotic Host cells in culture
Pseudomonas aeruginosa
Secondary metabolitesSignal molecules Biofilm formation
Planktonic cells
CytokinesHost signals
Overall Aim:
To establish the importance of microbial and host signalling in determining the outcome of microbial-host interactions.
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From Metagenomes to Ecosystem Functioning
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Strain-resolved proteomics from environmental samples
14From Proteins to Environments
15From Proteins to Environments
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Experimental Approaches in Systems Biology
Sequencing technologiesA capillary-based Sanger method on sequencing platforms.Massively higher throughput, such as 454 pyrosequencing, SOLiD and Solexa
DNA microarrays and high-throughput sequencingSlides containing spatially organized DNA probes with known sequences for the identification and quantification of fluorescently labelled nucleic acids samples.
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Next Generation Sequencing
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Experimental Approaches in Systems Biology
Proteomics technologiesMass spectrometry (MS)-based approaches for identificationArray-based platforms
Metabolomics technologiesPowerful and accurately predictive approaches Bench-scale assays to high-throughput methods
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Evolution of mass spectrometry-based proteomics from microbial isolates to communities
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LC/MS-based Proteomics
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Mass Spectrometry
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Matrix-assisted laser desorption/ionization-based resequencing
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Technical Challenges In Systems Microbiology
Technical bottlenecksSingle cell measurementsIdentifying and accurately measuring metabolitesCultivationData accessibilityComputational limitationsAnnotation and functional characterization of genesProteomicsHigh-throughput technologies
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Tracking and segmenting single cells
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