Microbial Genomics Microbial Genomics Michael J. Stanhope, Michael - - PowerPoint PPT Presentation

Microbial Genomics Microbial Genomics

Michael J. Stanhope, Michael J. Stanhope,

• Pop. Med. Diagnostic
• Pop. Med. Diagnostic Sci

Sci. .

Fleischmann et al. 1995. Science 269: 496

Outline Outline

• Introduction

Introduction

• Microbial diversity

Microbial diversity

• Universal Tree of Life

Universal Tree of Life

• Bacterial genome size

Bacterial genome size

• Core and pan genomes

Core and pan genomes

• Horizontal Gene Transfer (HGT)

Horizontal Gene Transfer (HGT)

• Mechanisms of HGT

Mechanisms of HGT

• Detecting HGT

Detecting HGT

• Comparative genomics of

Comparative genomics of Streptococcus Streptococcus

• Comment on genome sequencing technology

Comment on genome sequencing technology

• E.g. of 454 bacterial genome sequence

E.g. of 454 bacterial genome sequence

• Applications of microbial genomics

Applications of microbial genomics

Introduction Introduction

• Microbial diversity

Microbial diversity

Microbial diversity Microbial diversity

• Superficial inspection, bacteria and

Superficial inspection, bacteria and archaea archaea hardly seem diverse hardly seem diverse

http://www.ucmp.berkeley.edu/archaea/archaeamm.html

Microbial diversity Microbial diversity

• But metabolic diversity great, particularly

But metabolic diversity great, particularly energy generating energy generating

• Even within a species; e.g.

Even within a species; e.g. E E. . coli coli: :

• Fermentation or respiration; respire aerobically or

Fermentation or respiration; respire aerobically or anaerobically anaerobically; glucose or lactose as sole carbon source ; glucose or lactose as sole carbon source – – transforming sugar into amino acids, vitamins, transforming sugar into amino acids, vitamins, nucleotides nucleotides

Microbial diversity Microbial diversity

• Energy generating metabolism in bacteria:

Energy generating metabolism in bacteria:

• Alcohol fermentation

Alcohol fermentation

• Lactic acid fermentation

Lactic acid fermentation present in eukaryotes

present in eukaryotes & prokaryotes & prokaryotes

• Aerobic respiration

Aerobic respiration

• Oxygenic photosynthesis

Oxygenic photosynthesis

• Anaerobic degradation of carbohydrates through the

Anaerobic degradation of carbohydrates through the Embden Embden-

• Meyerhof pathway.

Meyerhof pathway.

• Other fermentation pathways e.g.

Other fermentation pathways e.g. phosphoketolase phosphoketolase pathway pathway

• Anaerobic respiration

Anaerobic respiration

• Lithotrophy

Lithotrophy ( (inorganics inorganics as source of energy) as source of energy)

• Anoxygenic

Anoxygenic photosynthesis photosynthesis

• Methanogenesis

Methanogenesis (H (H2

2 as energy source and produces methane)

as energy source and produces methane)

• Light driven

Light driven nonphotosynthetic nonphotosynthetic photophosphorylation photophosphorylation

Microbial diversity Microbial diversity

• prokaryotic cells on Earth = 6 X 10

prokaryotic cells on Earth = 6 X 1030

30

• Prokaryotic cellular carbon = 60

Prokaryotic cellular carbon = 60-

• 100% of estimated

100% of estimated carbon in terrestrial and marine plants. carbon in terrestrial and marine plants.

• Abundant in environments where eukaryotes are rare

Abundant in environments where eukaryotes are rare

• How many species?

How many species?

• Definition of species?

Definition of species?

• Lack diagnostic morphological characteristics

Lack diagnostic morphological characteristics

• Exchange genetic material in unique and unusual ways

Exchange genetic material in unique and unusual ways

• Same species = 70% DNA

Same species = 70% DNA-

• DNA hybridization

DNA hybridization

• Underestimating prokaryotic diversity

Underestimating prokaryotic diversity

• Practical limitations in counting

Practical limitations in counting

• 1% cultivable

1% cultivable

Introduction Introduction

• Universal Tree

Universal Tree

Universal Tree of Life Universal Tree of Life

• 1980

1980’ ’s Carl s Carl Woese Woese, , phylogenetic phylogenetic analysis of all analysis of all forms of cellular life; forms of cellular life; ssrRNA ssrRNA

• Found in all cells

Found in all cells

• Present in thousands of copies and easy to isolate

Present in thousands of copies and easy to isolate

• Complementary to sequence of gene

Complementary to sequence of gene

• Sequence can be compared to reveal similarity and

Sequence can be compared to reveal similarity and differences differences

• Defined three cellular domains of life:

Defined three cellular domains of life:

• Eukaryotes

Eukaryotes

• Eubacteria

Eubacteria (Bacteria) (Bacteria)

• Archaeabacteria

Archaeabacteria ( (Archaea Archaea) )

Pace, NR. 1997. Science 276:734

http://whyfiles.org/022critters/archaea.html

Genome Size Genome Size

Genome size Genome size

• 405 complete bacterial genomes on NCBI

405 complete bacterial genomes on NCBI

• Carsonella

Carsonella ruddii ruddii (159,662) (159,662) – – Burkholderia Burkholderia xenovorans xenovorans (9.73 Mb) (9.73 Mb)

• Genome size / ecological niche

Genome size / ecological niche

• Smaller genomes,

Smaller genomes, endocellular endocellular parasites or parasites or symbionts symbionts

Genome size Genome size

• Mutually obligate

Mutually obligate endosymbiotic endosymbiotic associations with associations with animal hosts animal hosts

• bacteriocytes

bacteriocytes

Distel and Cavanaugh. 1994. J. Bact. 4:1932.

Genome size Genome size

Nakabachi et al. 2006. Science 314:267

Genome size Genome size

• Free living bacteria, genome size correlates with

Free living bacteria, genome size correlates with species metabolism & width of ecological niche species metabolism & width of ecological niche

• Pathogenic species, narrow range of hosts, small

Pathogenic species, narrow range of hosts, small genomes; e.g. genomes; e.g. Helicobacter, Helicobacter, Streptococcus Streptococcus

• Anaerobic bacteria, restricted metabolism, e.g.

Anaerobic bacteria, restricted metabolism, e.g. methanogens methanogens, small genomes. , small genomes.

• Aerobic organisms, and opportunistic pathogens,

Aerobic organisms, and opportunistic pathogens, higher diversity of genome size; e.g. higher diversity of genome size; e.g. Pseudomonas Pseudomonas (6 (6 Mb) Mb)

pan and core genomes pan and core genomes

• Core

Core

• Genes present in all strains

Genes present in all strains

• Pan (from Greek meaning whole)

Pan (from Greek meaning whole)

• Dispensable genome composed of genes

Dispensable genome composed of genes absent from one or more strains and genes absent from one or more strains and genes unique to particular strains unique to particular strains

Bacteria chromosomes Bacteria chromosomes

• Most, single circular chromosome, but

Most, single circular chromosome, but exceptions: exceptions:

• E.g.

E.g. Streptomyces Streptomyces, , Borrelia Borrelia, , Agrobacterium Agrobacterium, , linear chromosomes linear chromosomes

• Linear plasmids

Linear plasmids – – e.g. e.g. Klebsiella Klebsiella, , Escherichia Escherichia, , Thiobacillus Thiobacillus

• Linearity: enhances genomic plasticity?

Linearity: enhances genomic plasticity?

• Multichromosome

Multichromosome spp spp.; e.g. some .; e.g. some proteobacteria proteobacteria with free living, opportunistic with free living, opportunistic lifestyle lifestyle

Horizontal Gene Transfer Horizontal Gene Transfer

Horizontal Gene Transfer Horizontal Gene Transfer

• Genetic exchanges between different evolutionary

Genetic exchanges between different evolutionary lineages lineages

• 1944 Avery et al., DNA can be absorbed by

1944 Avery et al., DNA can be absorbed by microorganisms microorganisms (Studies on the chemical nature of the substance inducing

(Studies on the chemical nature of the substance inducing transformations of transformations of pneumococcal pneumococcal types. J. Exp. Med.79:137)

• types. J. Exp. Med.79:137)
• Extent or degree is much debated

Extent or degree is much debated

Mechanisms of HGT Mechanisms of HGT

http://fig.cox.miami.edu/Faculty/Dana/bacfun.jpg

Detecting HGT Detecting HGT

• Phylogenetics

Phylogenetics

• Gene tree that differs significantly from

Gene tree that differs significantly from species tree species tree

• Compare all gene trees; gene trees that are

Compare all gene trees; gene trees that are significantly different from majority are significantly different from majority are putative LGT putative LGT

Detecting HGT Detecting HGT

Detecting HGT Detecting HGT

• Best sequence match detection (BLAST)

Best sequence match detection (BLAST)

• Rapid, but of limited use, since sequence

Rapid, but of limited use, since sequence similarity not necessarily correlated with similarity not necessarily correlated with evolutionary history. evolutionary history.

Bacteria to Vertebrate Horizontal Gene Transfer??

“Hundreds of human genes appear likely to have resulted from horizontal transfer from bacteria at some point in the vertebrate lineage.” International Human Genome Sequencing Consortium. Initial Sequencing and Analysis of the Human Genome. Nature 409, 860 (2001).

Bacteria to Vertebrate HGT Bacteria to Vertebrate HGT --

• Implications (

Implications (If True If True) )

• HGT bacterial genes became fixed in

HGT bacterial genes became fixed in vertebrates through insertion into germ cells vertebrates through insertion into germ cells (because somatic cell HGT genes would be lost (because somatic cell HGT genes would be lost within a generation). within a generation).

• Foreign bacterial genes can co

Foreign bacterial genes can co-

• opt vertebrate
• pt vertebrate

regulatory regions and transcription factors. regulatory regions and transcription factors.

• Humans could accumulate foreign, perhaps

Humans could accumulate foreign, perhaps deleterious, genes from bacterial infections deleterious, genes from bacterial infections and/or GM foods and/or GM foods. .

Nature Human Genome Issue Nature Human Genome Issue

• International Human Genome Sequencing

International Human Genome Sequencing Consortium (IHGSC) Consortium (IHGSC)

• 113 genes that are likely examples of bacteria

113 genes that are likely examples of bacteria to vertebrate HGT (horizontal gene transfer). to vertebrate HGT (horizontal gene transfer).

• Conclusion based on BLASTP alignment scores.

Conclusion based on BLASTP alignment scores. Best sequence match detection (BLAST) Best sequence match detection (BLAST)

Phylogenetic evidence in support

• f bacteria - vertebrate HGT

Human Vertebrate Bacteria1 Bacteria2 Bacteria3 Bacteria4 Bacteria5 Bacteria6 Non-vert Eukaryote Non-vert Eukaryote Paralog

Phylogenetic evidence rejecting bacteria - vertebrate HGT

Bacteria1 Bacteria2 Bacteria3 Bacteria4 Bacteria5 Bacteria6 Human Vertebrate Non-vert Eukaryote Non-vert Eukaryote Paralog

Why did the IHGSC conclude Why did the IHGSC conclude bacteria to vertebrate HGT? bacteria to vertebrate HGT?

• Equated BLAST ranking with evolutionary

Equated BLAST ranking with evolutionary relatedness. relatedness.

Detecting HGT Detecting HGT

• Nucleotide compositional analysis

Nucleotide compositional analysis

• Based on premise that DNA fragments

Based on premise that DNA fragments

• btained through HGT retain sequence
• btained through HGT retain sequence

characteristics of donor genome characteristics of donor genome

• Advantage is it only requires genome

Advantage is it only requires genome sequence from 1 sequence from 1 spp spp. .

Comparative Genomics of Comparative Genomics of Streptococcus Streptococcus

Streptococcus Streptococcus genomes genomes

• 26 genomes (public) from 6

26 genomes (public) from 6 spp spp

• S.
• S. pneumoniae

pneumoniae (2), (2), S.

• S. agalactiae

agalactiae (8), (8), S. S. pyogenes pyogenes (11), (11), S.

• S. thermophilus

thermophilus (3), (3), S.

• S. mutans

mutans (1), (1), S.

• S. suis

suis (1) (1)

Adaptive potential of bacteria Adaptive potential of bacteria

• 1. Darwinian or positive selection, favoring
• 1. Darwinian or positive selection, favoring

the fixation of advantageous mutations the fixation of advantageous mutations

• 2. acquisition of new genetic material by
• 2. acquisition of new genetic material by

lateral DNA exchange lateral DNA exchange

• 3. gene regulation
• 3. gene regulation

Core genome Core genome

• LGT of bacterial genomes, possibly key

LGT of bacterial genomes, possibly key factor in adaptation factor in adaptation

• Nonetheless, core genome, possibly relatively

Nonetheless, core genome, possibly relatively LGT free LGT free

• Focus on adaptation often centered on

Focus on adaptation often centered on species specific loci species specific loci

• Selection pressure on core genome not

Selection pressure on core genome not explored explored

Molecular selection Molecular selection

• Powerful statistical methods for detecting

Powerful statistical methods for detecting adaptive molecular evolution (Yang and Nielsen) adaptive molecular evolution (Yang and Nielsen)

• Nonsynonymous

Nonsynonymous substitution rate elevated above the substitution rate elevated above the synonymous rate as evidence for positive selection synonymous rate as evidence for positive selection

• Fixation of advantageous mutations, driven by NS

Fixation of advantageous mutations, driven by NS =>evolutionary innovations =>evolutionary innovations

• Our goal

Our goal: assess positive selection pressure : assess positive selection pressure across core genome components of across core genome components of Streptococcus Streptococcus, while concomitantly assessing , while concomitantly assessing levels of recombination within core genome levels of recombination within core genome

Pipeline Pipeline (part 1)

(part 1)

Pipeline Pipeline (part 2)

(part 2)

Estimated pan & core genome Estimated pan & core genome sizes sizes

• S. agalactiae
• S. pyogenes

Alignable core genome size for interspecific analysis = 260

Genes under positive selection: Genes under positive selection: between species between species

32.13 32.13 71 71 221 221 (S. (S. pneumoniae pneumoniae, , S.

• S. suis

suis) ) 16.92 16.92 44 44 260 260 S.

• S. pyogenes

pyogenes 10.77 10.77 28 28 260 260 S.

• S. agalactiae

agalactiae 23.46 23.46 61 61 260 260 S.

• S. thermophilus

thermophilus 34.23 34.23 89 89 260 260 S.

• S. suis

suis 28.08 28.08 73 73 260 260 S.

• S. pneumoniae

pneumoniae 12.69 12.69 33 33 260 260 S.

• S. mutans

mutans % under PS % under PS nbr nbr under PS under PS nbr nbr analyzed analyzed Lineage Lineage

Genes under positive selection: Genes under positive selection: S. S. agalactiae agalactiae

% under PS % under PS nbr nbr under PS under PS nbr nbr analyzed analyzed Lineage Lineage 0.00 0.00 1212 1212 515 515 0.08 0.08 1 1 1212 1212 CJB111 CJB111 0.08 0.08 1 1 1212 1212 2603V/R 2603V/R 0.00 0.00 1212 1212 A909 A909 0.08 0.08 1 1 1212 1212 H36B H36B 0.08 0.08 1 1 1212 1212 NEM316 NEM316 0.00 0.00 1212 1212 18RS21 18RS21 0.58 0.58 7 7 1212 1212 COH1 COH1

Genes under positive selection: Genes under positive selection: S.

• S. pyogenes

pyogenes

0.92 0.92 9 9 983 983 (SSI (SSI-

• 1, MGAS315)

1, MGAS315) 0.41 0.41 4 4 978 978 (MGAS5005, M1 GAS) (MGAS5005, M1 GAS) 0.22 0.22 2 2 925 925 (MGAS9429, MGAS2096) (MGAS9429, MGAS2096) 0.00 0.00 1297 1297 SSI SSI-

• 1

1 0.00 0.00 1297 1297 M1 GAS M1 GAS 0.15 0.15 2 2 1297 1297 MGAS9429 MGAS9429 0.31 0.31 4 4 1297 1297 MGAS8232 MGAS8232 0.15 0.15 2 2 1297 1297 MGAS6180 MGAS6180 0.08 0.08 1 1 1297 1297 MGAS5005 MGAS5005 0.00 0.00 1297 1297 MGAS315 MGAS315 0.08 0.08 1 1 1297 1297 MGAS2096 MGAS2096 0.08 0.08 1 1 1297 1297 MGAS10750 MGAS10750 0.23 0.23 3 3 1297 1297 MGAS10394 MGAS10394 0.54 0.54 7 7 1297 1297 MGAS10270 MGAS10270 % under PS % under PS nbr nbr under PS under PS nbr nbr analyzed analyzed Lineage Lineage

Recombination Recombination

223 (18%) 223 (18%) 18 18 (1%) (1%) 7 (1%) 7 (1%) 34 (3%) 34 (3%) 222 (18%) 222 (18%)

S.

• S. agalactiae

agalactiae

477 (37%) 477 (37%) 186 186 (14%) (14%) 168 (13%) 168 (13%) 284 284 (22%) (22%) 434 (33%) 434 (33%)

S.

• S. pyogenes

pyogenes

53 (20%) 53 (20%) 11 11 (4%) (4%) 35 (14%) 35 (14%) 54 54 (21%) (21%) 26 (10%) 26 (10%)

interspecific interspecific

SPI U SPI U intragenic intragenic set set SPI SPI ∩ ∩ PHI PHI PHI PHI ∩ ∩ MaxChi MaxChi ∩ ∩ NSS NSS

(set of (set of intragenic intragenic methods) methods)

PHI PHI

( (intragenic intragenic method) method)

SPI SPI (strong

(strong phylogenetic phylogenetic incongruence) incongruence)

Data set Data set

Recombination and positive Recombination and positive selection selection

17 (53%) 17 (53%) 21 (65%) 21 (65%) 25 (78%) 25 (78%) 32 32

S.

• S. pyogenes

pyogenes

4 (40%) 4 (40%) 4 (40%) 4 (40%) 10 10

S.

• S. agalactiae

agalactiae

29 (11%) 29 (11%) 20 (8%) 20 (8%) 43 (25%) 43 (25%) 175 175

interspecific interspecific

PS + PS + intragenic intragenic PS + SPI PS + SPI PS + PS + recombinant recombinant Genes Genes under PS under PS Data set Data set

Pan genome and recombination Pan genome and recombination

• Habitat differences for

Habitat differences for S.

• S. pyogenes

pyogenes and and S. S. agalactiae agalactiae

• Reduced gene pool environment for

Reduced gene pool environment for S. S. pyogenes pyogenes, could result in smaller pan genome , could result in smaller pan genome and potentially more homologous and potentially more homologous recombination recombination

Statistical analysis of PS data Statistical analysis of PS data

• Significant affect of lineage (ANOVA; p<0.0001):

Significant affect of lineage (ANOVA; p<0.0001):

• Majority of

Majority of pairwise pairwise multiple comparisons significantly different multiple comparisons significantly different

• Significant affect of biochemical category (p<0.0001)

Significant affect of biochemical category (p<0.0001)

• Amino acid biosynthesis; Biosynthesis of cofactors, prosthetic g

Amino acid biosynthesis; Biosynthesis of cofactors, prosthetic groups, roups, and carriers; Cell envelope; Cellular processes; Central interme and carriers; Cell envelope; Cellular processes; Central intermediary diary metabolism; metabolism; DNA metabolism

DNA metabolism; Energy metabolism; Fatty acid

; Energy metabolism; Fatty acid and and phospholipid phospholipid metabolism; Hypothetical proteins; Protein fate; metabolism; Hypothetical proteins; Protein fate; Protein synthesis; Protein synthesis; Purines Purines, , pyrimidines pyrimidines, nucleosides, and nucleotides; , nucleosides, and nucleotides; Regulatory functions; Signal transduction; Regulatory functions; Signal transduction; Transcription

Transcription;

; Transport and binding proteins; Unknown function Transport and binding proteins; Unknown function

• Significant interaction between lineage and biochemical category

Significant interaction between lineage and biochemical category (p=0.003) (p=0.003)

• (

(S.

• S. pneumoniae

pneumoniae, S. , S. suis suis) DNA metabolism, Transcription, ) DNA metabolism, Transcription, Protein fate Protein fate

Genes selected per lineage Genes selected per lineage

Genes selected on each lineage Genes selected on each lineage

19 unique loci for S. suis; 15 for S. thermophilus; 14 for S. pneumoniae

Lineages with unusual selection Lineages with unusual selection pressure pressure

• S.
• S. suis

suis

• Both gene gain and loss and PS; suggesting

Both gene gain and loss and PS; suggesting evolutionary flexibility evolutionary flexibility – – host jumping? host jumping?

• S.
• S. agalactiae

agalactiae, COH1 , COH1

• Significantly associated with neonatal disease, and of

Significantly associated with neonatal disease, and of recent bovine ancestry recent bovine ancestry

• S.
• S. pyogenes

pyogenes, M3 serotype , M3 serotype

• M3 cause more cases of invasive disease, higher rate

M3 cause more cases of invasive disease, higher rate

• f lethal infections, epidemic tendencies
• f lethal infections, epidemic tendencies
• S.
• S. thermophilus

thermophilus, LMD , LMD-

• 9

9

• ?

?

Streptococcus Streptococcus comparative comparative genomics tentative conclusions genomics tentative conclusions

• Considerable recombination and positive

Considerable recombination and positive selection pressure in selection pressure in Streptococcus Streptococcus core core genome genome

• Several loci identified for

Several loci identified for S.

• S. agalactiae

agalactiae and and S. S. pyogenes pyogenes that could be linked to the specific that could be linked to the specific pathogenic features of these strains pathogenic features of these strains

• Identification and cataloguing of these loci, serve

Identification and cataloguing of these loci, serve as an evolutionary short as an evolutionary short-

• cut for laboratory

cut for laboratory mutation experiments, to assess specific mutation experiments, to assess specific functional significance of these genes. functional significance of these genes.

Sequencing Technology Sequencing Technology

First First “ “shot gun shot gun” ” microbial microbial genome sequence genome sequence

Haemophilus influenzae 1.8 Mb Library of plasmid clones, 1600-2000 bp fragments; sequences of these clones with their many overlaps represent the raw data entered into computer programs (e.g. TIGR assembler) which assemble the genome; remaining gaps closed with other strategies (e.g. long range PCR)

Fleischmann et al. 1995. Science 269: 496

Race for the $1000 genome Race for the $1000 genome

• First to produce $1000 human genome

First to produce $1000 human genome

• J. Craig Venter Science Foundation: $500,000
• J. Craig Venter Science Foundation: $500,000
• X Prize Foundation: $5 million

X Prize Foundation: $5 million

• 2004; NIH; $70 million grant program

2004; NIH; $70 million grant program

Next generation of sequencers Next generation of sequencers

1000 NA Single-molecule array VisiGen Biotechnologies 500 35 Parallel microchip Solexa 100 30 Map and survey microarray NimbleGen Systems 5 800+ Biochip Network Biosystems 7 850- 1000 Parallel bead array Microchip Biotechnologies 14,000 20,000 Electronic microchip LI-COR Biosciences 3-4 1000 Capillary electrophoresis Applied Biosystems 200 50 Sequencing by ligation Agencourt Bioscience 96 100 Parallel bead array 454 Life Sciences Expected Throughput Mb (million bases)/day Read Length (bases) Format Company Searching for Cheaper Genome Sequencers

from: Service, RF 2006. Science 311:1544

454 sequencing 454 sequencing

from: Margulies et al. 2005 Nature 437:376

• Sequencing by synthesis

(tracks bases as they are added); pyrosequencing

• 300-500 bp pieces, denatured;
• link one strand to plastic bead
• copy using emulsion PCR
• beads are separated on a fibre-
• ptic plate containing approx.

1.6 million wells;

• add sequencing reagents

454 sequencing 454 sequencing

from: Margulies et al. 2005 Nature 437:376

• nucleotides added release

pyrophophate, prompting luciferase & flash of light

• correlating flashes

from each cell with nucleotides presented in flow through, computer tracks sequence growth

Nanopore Nanopore sequencing sequencing

from: Service, RF 2006. Science 311:1544

Example of 454 Bacteria Example of 454 Bacteria Genome Sequence Genome Sequence

Streptococcus Streptococcus canis canis

• Genome sequence data for putative sister

Genome sequence data for putative sister groups to major pathogens often not available groups to major pathogens often not available

• e.g.

e.g. S S. . pyogenes pyogenes; putative sister group ; putative sister group S.

• S. canis

canis

• S.
• S. canis

canis from 454 Life Sciences from 454 Life Sciences

• 103

103 cotigs cotigs, 2,191,310 , 2,191,310 bp bp, 98.5% coverage, 39.6% GC , 98.5% coverage, 39.6% GC

• 100% of the bases with Q40+ rating (99.99%

100% of the bases with Q40+ rating (99.99% accuracy) accuracy)

canis canis / / pyogenes pyogenes genome wide genome wide alignments alignments

canis canis / / pyogenes pyogenes genomic content genomic content comparison comparison

Applications of Microbial Genomics Applications of Microbial Genomics

Comparative genomics and drug Comparative genomics and drug discovery discovery

• Genes need prioritization

Genes need prioritization

• Drug development against a single bacterial species

Drug development against a single bacterial species usually impractical usually impractical

• Gene products, with

Gene products, with orthologs

• rthologs in humans, may lack

in humans, may lack selectivity selectivity

• => compare genomes, find potential drug targets shared by

=> compare genomes, find potential drug targets shared by clinically important range of clinically important range of taxa taxa, & absent or divergent from , & absent or divergent from human host human host

Molecular Epidemiology Molecular Epidemiology

• MLST = multi locus sequence typing; sequence

MLST = multi locus sequence typing; sequence

• f portions of 7 (or more)
• f portions of 7 (or more)

housekeeping genes; housekeeping genes; combination of alleles = combination of alleles = sequence type (ST); sequence type (ST); closely related closely related STs STs (differ by one or two alleles) (differ by one or two alleles) = = clonal clonal complex complex

http://eburst.mlst.net/6.asp

Microarray Microarray gene / presence gene / presence absence absence

• Genome sequence allows gene presence / absence

Genome sequence allows gene presence / absence detection across strains using detection across strains using microarrays microarrays

• E.g.

E.g. Combimatrix Combimatrix 4 X 2K 4 X 2K microarrays microarrays

Gene / presence absence Gene / presence absence hybridization hybridization

Metagenomics Metagenomics

http://chunlab.snu.ac.kr/meta.htm