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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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microRNA profilingSmall RNA sequencing

Discovery of infectious and commensal floraMetagenomic sequencing

Discovery of inherited and acquired structural variationPaired end sequencing

Targeted polymorphism and mutation discovery

Targeted genomic resequencing

Large-scale polymorphism discovery

Reduced representation sequencing

Comprehensive polymorphism and mutation discovery in individual human genomes

Complete genome resequencing

Examples of applicationsCategory

Applications of Next Generation Sequencing

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Multiplex sequencing of samples from multipleindividualsMolecular barcoding

Nucleosome positioningNuclease fragmentation and sequencing

Genome-wide mapping of protein-DNA interactions

Chromatin immunoprecipitation–sequencing (ChIP-Seq)

Determining patterns of cytosine methylation in genomic DNA

Sequencing of bisulfite-treated DNA

Quantification of gene expression and alternative splicing; transcript annotation; discovery of transcribed SNPs or somatic mutations

Transcriptomesequencing

Examples of applicationsCategory

Applications of Next Generation Sequencing

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Experimental Approaches in Systems Biology

Proteomics technologies• Mass spectrometry (MS)-based approaches for

identification• Array-based platforms

Metabolomics technologies• Powerful 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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Technical Challenges in Systems Microbiology

Information and data gaps Acquiring information and dataAssuring data qualityMaking systems data applicable and availableA proposal for a systems microbiology database

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Information and Data Gap

Continued genome sequencingData on the functions of the proteins or nucleic acids encoded by these sequencesAccurate gene annotationAccurate quantitative information on a variety of biological parametersData that indicate spatiotemporal relationships between system components

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Information and Data GapData on community architectureData that can reveal design principles and biological networksData that expand the phenotypic characterizations of cells and communitiesData on the natural variability of microbial systemsData on cell cycle or spatial events

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Research in Systems Microbiology

Regulation of biological systemsApplying a systems biology approach to microbial communitiesHypothesis-generating researchMeasuring noise in biological systems

33Convergence of systems and synthetic biology

34Reconstruction, validation and utilization of a metabolic reconstructi

35Phases and data used to generate a metabolic reconstruction

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Procedure to generate a biomass objective function

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Network integration: the interface between different types of reconstruction

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Reconstruction of transcriptional and translational networks

39Timeline of events that resulted in the development of systems biology and synthetic biology

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