5. Microbes are small
Size
* They are small, by definition
* Were not really known until
microscope invention
6. But there are LOTS of them
Numbers
* 100 million in gram of soil
* More cells on Earth than stars
in universe
* More biomass than plants,
animals
* 10x cells on humans than
human cells
* 50x10^6 viruses/ml sea water
16. Sequencing and Microbes
• Sequencing is useful as a tool in studies
of microbial diversity for many reasons
• It is complimentary to other means of
study
• Four major “ERAs” in use of
sequencing for microbial diversity
studies
18. Era I: rRNA Tree of Life
Bacteria
• Appearance of
microbes not
informative (enough)
• rRNA Tree of Life
Archaea identified two major
groups of organisms
w/o nuclei
• rRNA powerful for
many reasons, though
not perfect
Eukaryotes
Barton, Eisen et al. “Evolution”, CSHL Press. 2007.
Based on tree from Pace 1997 Science 276:734-740
19. Diversity III: Phylogenetic
• Three main kinds of organisms
• Bacteria
• Archaea
• Eukaryotes
• Viruses not alive, but some call them
microbes
• Many misclassifications occurred
before the use of molecular methods
20. The Tree of Life
2006
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
21. The Tree of Life
2006
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
46. rRNA PCR
DNA
extraction PCR
Makes lots Sequence
PCR of copies of rRNA genes
the rRNA
genes in
sample
rRNA1
5’...ACACACATAGGTGGAGC
TAGCGATCGATCGA... 3’
Phylogenetic tree Sequence alignment = Data matrix
rRNA2
rRNA1 rRNA2
rRNA1 A C A C A C 5’..TACAGTATAGGTGGAGCT
rRNA4 AGCGACGATCGA... 3’
rRNA3 rRNA2 T A C A G T
rRNA3
rRNA3 C A C T G T 5’...ACGGCAAAATAGGTGGA
E. coli Humans rRNA4 C A C A G T TTCTAGCGATATAGA... 3’
Yeast E. coli A G A C A G rRNA4
5’...ACGGCCCGATAGGTGG
Humans T A T A G T
ATTCTAGCGCCATAGA... 3’
Yeast T A C A G T
54. Genomes Revolutionized Microbiology
• Predictions of metabolic processes
• Better vaccine and drug design
• New insights into mechanisms of
evolution
• Genomes serve as template for
functional studies
• New enzymes and materials for
engineering and synthetic biology
67. Weighted % of Clones
0
0.1250
0.2500
0.3750
0.5000
Al
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np eob ria
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ot ac
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RecA
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Fi act ria
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Major Phylogenetic Group
Sp rof
Sargasso Phylotypes
iro lex
i
Fu cha
D
304: 66. 2004
Metagenomic Phylotyping
ei so et
no ba es
co ct
cc er
Euus ia
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a h
Venter et al., Science
C rcherm
re
na aeous
rc t
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75. Acknowledgements
• $$$
• DOE
• NSF
• GBMF
• Sloan
• DARPA
• People, places
• DOE JGI: Eddy Rubin, Phil Hugenholtz et al.
• UC Davis: Aaron Darling, Dongying Wu
• Other: Jessica Green, Katie Pollard, Martin
Wu, Tom Slezak, Jack Gilbert
Notas do Editor
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Small organisms - too small to see without help\n giant microbes\n \n Mostly live as single cells\n \n Many different kinds (more on this in a bit)\n \n VIruses not included by some, but I think they count\n \n (Show flu bug slide)\n \n
Small organisms - too small to see without help\n giant microbes\n \n Mostly live as single cells\n \n Many different kinds (more on this in a bit)\n \n VIruses not included by some, but I think they count\n \n (Show flu bug slide)\n \n
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Do lots of nasty things\n Get all the good names by the way b/c mostly known through their diseses\n Yersinia pestis\n Vibrio cholerae\n Bacillus anthracis\n Smallpox - ok not all\n Mycobacterium tuberculosis\n Mycobacterium leprae\n Clostridium tetanus\n Clostridium botulinum\n
Mutualists (though names not so good)\n N2 fixation\n C fixation - Chloroplasts inside plants are actually symbiotic bacteria\n Digestion - ruminants and all cellulose\n\n
Cloud of microbes living in / on organisms\n More microbial cells than human\n
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Microbes run the planet\n All photosynthesis\n Number of microbial cells\n
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Composite tree of life based on diverse data\nmain point - euks monophyletic\n\nSignif LGT in euks, but mostly bacterial genes\nso bulk of euk genome is vertically transmitted\nand we can use these gene to reconstruct their history\n
Composite tree of life based on diverse data\nmain point - euks monophyletic\n\nSignif LGT in euks, but mostly bacterial genes\nso bulk of euk genome is vertically transmitted\nand we can use these gene to reconstruct their history\n
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Many prokaryotes cannot be grown and cannot get them from harsh envts, or replicate the envt (i.e volcanic)\nHow do we approach this problem?\n\nResearcher go to various areas to collect samples from envt\n\nGet samples, put into tube\n
Send it out for sequencing, do an alignment with your gene and blast it (search for other organisms) with a similar sequence\n
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Functional prediction using a gene tree is just like predicting the biology of a species using a species tree\n
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This is a tree of a rRNA gene that was found on a large DNA fragment isolated from the Monterey Bay. This rRNA gene groups in a tree with genes from members of the gamma Proteobacteria a group that includes E. coli as well as many environmental bacteria. This rRNA phylotype has been found to be a dominant species in many ocean ecosystems.\n