EMERGING ISSUES IN MICROBIAL DIVERSITY

SALT LAKE CITY, MAY 2002

WE TEACHMICROBIOLOGY

BUT WE LEARNFROM MICROBES

SOME PERTINENT COMMENTS

"the microbe always has the last word""all life in the biosphere depends on microbes"

"all microbiology is environmental microbiology"

THE HIDDEN WORLDS OF MICROBIOLOGY• The number of prokaryote cells in the biosphere (but not the universe?) is

estimated to be 6,000,000,000,000,000,000,000,000,000,000 (6 x 1030).• These contain 50% of the earth's carbon, 90% of nitrogen and phosphorus, and

more than 108 species.• In our colons, there are about 1012 bacteria, not all of which have been

identified.• To date, only 1,500 microbes are known to cause disease in humans or animals.

• There are <109 bacteria in 1 gram of soil.

• A gram of soil contains 1,000-5,000 different species of bacteria.

But what of the eukaryotic microbes?Recent studies show a vast hidden diversity of fungi and protists in the biosphere.

SOME APPLICATIONS

FACTORIESFOOD AND FUEL

DISEASE

BIOREMEDIATION

ENZYMES, VECTORS,

PROCESSES (PCR)MICROBES

BIOTERRORISMDRUGS

EVOLUTION

WHY STUDY?

The Limits of LifeDiversity

Cellular Interactions and CommunitiesEvolutionDisease

Microbial PhysiologyBiotechnology and Bioterrorism

LIMITS OF LIFE

Temperature: 4-130?pH: 1-10?

Genetic: 20-78% G+CPressure

Chemical and physical stress

An example of microbes growing under stress:lichens in an extreme environment.Notre Dame, Paris.

DIVERSITY

Microbial ecology of biological nichesMetagenomesUnidentified microbial divisionsSmall eukaryotesUnrealised potential

DIRT TO PAYDIRT

IDENTIFICATION MICROBES APPLICATIONS

(MICROBIAL

CATALOGUE)

(BIOCATALYSIS,BIOTRANSFORMATION)

DIRT

rDNA SEQUENCECATALOGUEMETAGENOME DNA

GENES & PATHWAYS

INTERACTIONSSymbiosis

AntagonismCommensalism

Do all of these responses happen in microbial communities?

THE ROLES OF MICROBES INTHE EVOLUTION OF HIGHER LIFE FORMS

AND THE CONSTANT EVOLUTION OF MICROBES:

MorphogenesisDevelopmental programmes

Regulatory networksPathogenesis

“Why worry about life in space (astrobiology, etc.) when terrestrial microbes can provide clues as to the origins and evolution of eukaryotic differentiation?”

A bacterial mouth!!?(Momma et al. J. Bact. 2000)

HORIZONTAL (LATERAL) GENE TRANSFERHOW CAN IT BE ESTABLISHED?

1. Demonstration in the laboratory or the environment2. Sequence or motif similarity (DNA or protein)3. Islands of distinct base composition4. Nucleic acid hybridisation5. Association with movable elements6. Extrachromosomal association 7. Phenotypic and behavioral similarities

Disease

PathogenesisPrevention

Treatment and Resistance

Know the enemy• Life cycle and ecology of infectious microbes• Evolutionary lineage• Environmental changes associated with infection• Host-range variation• Diagnosis• Mechanisms of host/pathogen interaction• Mechanisms of resistance• Host susceptibility determinants• CELLULAR MICROBIOLOGY!

Cellular microbiology: the interaction of prokaryotes and eukaryotes

ANTIBIOTIC RESISTANCE MECHANISMS 2001

Decreased influx*Increased efflux*

Enzymatic inactivation*Sequestration*

Target modification*Target by-pass*

Target repairTarget amplification

Biofilm formation? Intracellular localisation

*can be acquired by horizontal gene transfer

From where?THAT IS THE QUESTION!

Aspects of Antibiotic Resistance

The clinical problem (Medicine)Why it happened (Human nature)

How it happened (Genetics)Mechanisms (Biochemistry)

Origins (Speculation)Solutions (Politics)

HOW BUGS BECOME ANTIBIOTIC RESISTANT:THE PATHWAY TO BECOMING UNTREATABLE

SENSITIVE INC

REA

SING

SELECTIO

N, STR

ESS, HYPER

MU

TATIO

N

RESISTANCE (low)

M (?)

RESISTANCE (medium)(compensation)

M A

RESISTANCE (high)(compensation)

MULTIDRUGRESISTANCE(compensation) (antagonism)

June 1945:The New York Times

“…..The thoughtlessness of a person playing with penicillin treatment is morally responsible for the death of a man who finally succumbs to infection with the penicillin resistant organism.”

Sir Alexander Fleming

LARGE IS SPECTACULAR, BUTSMALL IS BEAUTIFUL, TOO!

Tantalus Range, B.C.

Genomes, GCs and Small Molecules

Mycoplasma

Chlamydia

Neisseria

Staphylococcus

Mycobacteria

Escherichia

Pseudomonas

Streptomycetes

52

37

66

50

67

75

SPECIALISTSGENERALISTS

Seco

ndar

y M

etab

olite

Pro

duct

ion

42

404 6 82

Genome Size (Mb) (%G+C)

MULTIPLE ACTIVITIES FOR SMALL MOLECULES IN BIOLOGY

Growth inhibitors, allosteric effectors,transcription activators, pheromones,

quorum sensors, insecticides, immunosuppressives, cell-signalling,

hormone analogs, plant growth regulators,surfactants, antivirals, antitumour agents,herbicides, antiparasitics, antihelminthics,antifungals, cholesterol-lowering agents,

and enzyme inhibitors

Signaling molecule diversity (I)

O

O

H

N

H

OO H

OH O

OCH3

O

O

Br

Br

Br

HN

CH

C

H2 C

O

O

CO

HO

HNCHC

CH2

O

O

S

NH

CHC

CH

OOCH3

CH2

H3 C

NH

CH

C

CH2

OH

2CS

CH3

HN

CH

CCH

2O

O

NH

CHC

CH2

O

O

HO

NH

CHC

CH

O

O

HO

CH3

NH2

CH

CH

2 C

O

O

HO

NH2

CH

C

H2C

O

O

H2C

C

HO

O

HN CH

C

H2C

O

O

CH2

H2C NH

C NH2

HN

HN CH

C

H

O

O HN CH

C

H2C

O

O

CH2

S CH3

HN CH

C

CH

OH

O

HO

CH3

AgrD1 thiolactone signaling peptide from Staphylococcus aureus

3-hydroxypalmitic acid ester from Ralstonia solanacearum

V. harveyi N-(β-hydroxy-butyryl)-L-homoserine lactone

Inhibitory furanonefrom marine algae Delisea pulchra

Bacillus subtilis CSF (ERGMT)

Signaling molecule diversity (II)

from Pseudomonas aeruginosa:O

O

H

N

H

O

O

OH

H

N

OO

N-butyryl homoserine lactone (PAI-2)N-(3-oxo-dodecanoyl)-L-

homoserine lactone (PAI-1)

N

NH

O

O

H

H OH

NH

NH

O

O

HH

HN

OOH

H

2-hydroxy-3 heptyl-4-quinolone (PQS) cyclo (L-Pro-L-Tyr)cyclo (∆ Ala-L-Val)

Cyclic dipeptides

Role of antibiotics in the development of resistance

SelectionPhage

inductionInduced mutagenesis

MutagenicityVirulence ANTIBIOTICS

Gene transfer Transposition

Gene delivery Biofilms

Biology is much more thanDNA, RNA,

proteins and membranes!

Perlman's rules (1980)always rightyour frienda sensitive partner

The microorganism is

There are NO stupid microorganisms.

canMicroorganisms do anything.

will

smarter than chemists, Microorganisms are wiser than engineers,

more energetic than etc.

If you take care of your microbial friends, they will take care of your future and you will live happily ever after.

"It is essential that microbiology be perceived and practiced in a way consistent with the natural order of things; microbes are the base for and sustain all other life on this planet. Let us reorganize all of biology around microbiology."

Carl R. Woese 1994

The genealogy of 'omic' sciences(or everyone wants their own "-omic")

GENOMICS

FUNCTIONAL GENOMICS

GNOMICSMETAGENOMICSENTEROMICS VIROMICS

METABOLOMICSPHYSIOMICS

PROTEOMICS

RNOMICS

ARRAYOMICS(TRANSCRIPTOMICS)

ARCHEOMICS

TRANSPOSOMICS

BIOGEOMICS

SYSTOMICSGLYCOMICS