2. Outline
• How has genomics improved the power of
Microbiology to understand microbes?
• What new concepts and paradigms have been
advanced?
• Future challenges
3. Outline
• How has genomics improved the power of
Microbiology to understand microbes?
• What new concepts and paradigms have been
advanced?
• Future challenges
4.
5. r-strategists
• Fast growers
• Easy to retrieve in pure culture
• Not very abundant in the environment
• Sporadic blooms
• E.g. Roseobacter, Alteromonas
K-strategists
• slow growers
• Dificult to retrieve in pure culture
• Very abundant in the environment
• Steady numbers
• E.g. Pelagibacter, Prochlorococcus
18. Some Alteromonas genomes
Flagella glycosylation
O-chain
O-chain related
Alteromonas australica
98,6%
Alt170
ANI
75,0%
A. macleodii
80,7%
AltATCC
82,6%
Alt199
1.0 Mbp
2.0 Mbp
3.0 Mbp
4.0 Mbp
19. What do you learn from the genome
• General features (Size, GC content, tetranucleotide frequencies, coding density, etc)
• Precise phylogenetic/taxonomic placement
22. What do you learn from the genome
• General features (Size, GC content, tetranucleotide frequencies, coding density, etc)
• Precise phylogenetic/taxonomic placement
• Predictions for metabolism (e.g transporters)
• Prediction for ecology (survival
strategies, environmental
parameters, motility)
25. • Na+ driven respiratory chain or transport
unusual in freshwater or soils
• Rhodopsins or photolyases
• Transporters
• Motility
• Low pI halophiles
26. What do you learn from the genome
• General features (Size, GC content, tetranucleotide frequencies, coding density, etc)
• Precise phylogenetic/taxonomic placement
• Predictions for metabolism (e.g transporters)
• Prediction for ecology (survival
strategies, environmental
parameters, motility)
29. What do you learn from the genome
• General features (Size, GC content, tetranucleotide frequencies, coding density, etc)
• Precise phylogenetic/taxonomic placement
• Predictions for metabolism (e.g transporters)
• Prediction for ecology (survival
strategies, environmental
parameters, motility)
• Biotechnological potential
33. Outline
• How has genomics improved the power of
Microbiology to understand microbes?
• What new concepts and paradigms have been
advanced?
• Future challenges
34. THE BACTERIAL PAN-GENOME: a new paradigm in Microbiology
Welch et al, 2002
Pan-genome
Core
genome
Flexible
genome
44. Outline
• How has genomics improved the power of
Microbiology to understand microbes?
• What new concepts and paradigms have been
advanced?
• Future challenges
45. Third generation*
Microbiology
• Know
(rather than the
meager 0.1%)
• Know their
(rather
than a single strain)
• Understand their
in nature (rather
than in the lab)
• Understand their contribution to the
*
First generationPhysiology 1865-1952
Second generation Molecular Biology 1952-1995
Third generationGenomics and Metagenomics 1995-