EMERGING ISSUES IN MICROBIAL DIVERSITY
WE TEACH
MICROBIOLOGY
BUT WE LEARN
FROM MICROBES
SALT LAKE CITY, MAY 2002
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
FACTORIES
FOOD AND FUEL
DISEASE
MICROBES
ENZYMES,
VECTORS,
PROCESSES (PCR)
BIOTERRORISM
DRUGS
EVOLUTION
BIOREMEDIATION
WHY STUDY?
The Limits of Life
Diversity
Cellular Interactions and Communities
Evolution
Disease
Microbial Physiology
Biotechnology and Bioterrorism
LIMITS OF LIFE
Temperature: 4-130?
pH: 1-10?
Genetic: 20-78% G+C
Pressure
Chemical and physical stress
An example of microbes growing under stress:
lichens in an extreme environment.
Notre Dame, Paris.
DIVERSITY
Microbial ecology of biological niches
Metagenomes
Unidentified microbial divisions
Small eukaryotes
Unrealised potential
DIRT TO PAYDIRT
IDENTIFICATION
MICROBES
APPLICATIONS
(MICROBIAL
(BIOCATALYSIS,
BIOTRANSFORMATION)
CATALOGUE)
DIRT
METAGENOME
DNA
rDNA SEQUENCE
CATALOGUE
GENES & PATHWAYS
INTERACTIONS
Symbiosis
Antagonism
Commensalism
Do all of these responses happen
in microbial communities?
THE ROLES OF MICROBES IN
THE EVOLUTION OF HIGHER LIFE FORMS
AND THE CONSTANT EVOLUTION OF MICROBES:
Morphogenesis
Developmental programmes
Regulatory networks
Pathogenesis
“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 TRANSFER
HOW CAN IT BE ESTABLISHED?
1.
2.
3.
4.
5.
6.
7.
Demonstration in the laboratory or the environment
Sequence or motif similarity (DNA or protein)
Islands of distinct base composition
Nucleic acid hybridisation
Association with movable elements
Extrachromosomal association
Phenotypic and behavioral similarities
Disease
Pathogenesis
Prevention
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 repair
Target 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
INCREASING SELECTION, STRESS, HYPERMUTATION
SENSITIVE
M (?)
RESISTANCE (low)
M
A
(compensation)
RESISTANCE (medium)
(compensation)
RESISTANCE (high)
(compensation)
MULTIDRUG
RESISTANCE
(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, BUT
SMALL IS BEAUTIFUL, TOO!
Tantalus Range, B.C.
Genomes, GCs and Small Molecules
75
Streptomycetes
67
Pseudomonas
50
Escherichia
66
GENERALISTS
Mycobacteria
37
SPECIALISTS
Staphylococcus
52
Neisseria
42
Chlamydia
40
Mycoplasma
2
4
Genome Size (Mb)
6
(%G+C)
8
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)
OH
O
H
O
N
OH
H
O
O
OCH3
V. harveyi N-(b-hydroxy-butyryl)L-homoserine lactone
3-hydroxypalmitic acid ester
from Ralstonia solanacearum
Br
Br
Inhibitory furanone
from marine algae
Delisea pulchra
Br
O
O
HO
C
O
H2C
H2C
HN
NH2
C
CH
H2C
C
O
O
O
H2C
HN
NH
O
CH2
CH
O
HN
C
HN
HN
C
O
C
O
NH2
CH
O
H2C
OH
CH
CH3
CH
O
CH
C
HO
CH2
S
H
Bacillus subtilis CSF (ERGMT)
CH3
AgrD1 thiolactone signaling peptide
from Staphylococcus aureus
Signaling molecule diversity (II)
from Pseudomonas aeruginosa:
O
H
O
N
O
O
H
H
O
N
H
O
N-butyryl homoserine
lactone (PAI-2)
O
N-(3-oxo-dodecanoyl)-Lhomoserine lactone (PAI-1)
H
H
H
O
O
N
O
NH
HO
NH
N
O
H
NH
O
H
OH
H
2-hydroxy-3 heptyl-4-quinolone
(PQS)
cyclo (D Ala-L-Val)
cyclo (L-Pro-L-Tyr)
Cyclic dipeptides
Role of antibiotics in the development of resistance
Selection
Phage
induction
Induced
mutagenesis
Virulence
ANTIBIOTICS
Gene transfer
Gene delivery
Mutagenicity
Transposition
Biofilms
Biology is much more than
DNA, RNA,
proteins and membranes!
Perlman's rules (1980)
The microorganism is
always right
your friend
a sensitive partner
There are NO stupid microorganisms.
can
Microorganisms
do anything.
will
Microorganisms are
smarter than
wiser than
more energetic than
chemists,
engineers,
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
ENTEROMICS
METAGENOMICS
BIOGEOMICS
VIROMICS
ARCHEOMICS
GNOMICS
FUNCTIONAL
GENOMICS
METABOLOMICS
PHYSIOMICS
PROTEOMICS
SYSTOMICS
TRANSPOSOMICS
GLYCOMICS
ARRAYOMICS
(TRANSCRIPTOMICS)
RNOMICS