Schedule

This schedule is subject to change as the semester progresses; click on the title of any posted Topic or Module to go to that web page.

Section Topics Modules Date

Introduction Course Overview Course Overview Jan 7

Context & Historical Baggage What is Microbial Diversity?

The fundamental similarity of all living things

The evolution of evolutionary thought Jan 9

Taxonomy and phylogeny

The false eukaryote/prokaryote dichotomy

Discussion session : Context & Historical Baggage Jan 11

Dr. Brown is out of town - No class Jan 14

Jan 16

Jan 18

Martin Luther King Day - No class Jan 21

Phylogenetic analysis How to do a phylogenetic analysis Step 1: Deciding on sequences for analysis Jan 23

Step 2 : Obtaining the sequence data

Step 3 : Identifying homologous residues
Alignment problem set

Discussion session : Devil's Disease & Sticker's tumor Jan 25

Step 4 : Tree-construction
Tree construction problem set Jan 28

Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set

Example analysis : ES-2

Complications Alternative substitution models Jan 30

Alternative treeing algorithms

Bootstrapping

Discussion session : Phylogenetic Analysis problems sets Feb 1

Alternatives to ssu-rRNA Feb 4

Other methods for identification

What does this all mean? A review of "The Big Tree" Feb 6

Rooting the Universal Tree

The caveat - horizontal transfer

Discussion session : The Hot Spring of Yellowstone
The Hot Springs of Yellowstone slideshow Feb 8

Midterm Exam #1 Feb 11

The Bacteria Primitive Thermophilic Bacteria Phylum Aquificae (Aquifex and relatives) Feb 13

Phylum Thermotogae (Thermotoga and relatives)

Other primitive thermophiles

Thermophilic ancestry of Bacteria

Life at high temperatures

Discussion session : Arsenate Bacteria? Feb 15

Green Phototrophic Bacteria Phylum Chloroflexi (Green non-sulfur Bacteria) Feb 18

Phylum Chlorobi (Green sulfur Bacteria)

Phylum Cyanobacteria (Blue-green algae)

Other Green phototrophs

Bacterial photosynthesis

Carbon fixation

Proteobacteria Class α-proteobacteria Feb 20

Class β-proteobacteria

Class γ-proteobacteria

Class δ-proteobacteria

Class ε-proteobacteria

The concept of Proteobacteria

Discussion session : The Black Death Feb 22

Gram-positive Bacteria Phylum Firmicutes (Low G+C Gram-positive Bacteria) Feb 25

Phylum Actinobacteria (high G+C Gram-positive Bacteria)

Bacterial Development

Bacterial Multicellularity

Spirochaetes & Bacteroids Phylum Spirochaetes Feb 27

Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)

Bacterial Motility

Discussion session canceled - No class Mar 1

Spring Break - No class Mar 4

Mar 6

Mar 8

Deincocci, Chlamydia & Planctomycetes Phylum Deinococci (Deinococcus/Thermus) Mar 11

Phylum Chlamydiae (Chlamydia and relatives)

Phylum Planctomycetes (Planctomyces & relatives)

Reductive evolution in parasites

Bacterial phyla with few or no cultivated species Phyla with few cultivated species Mar 13

Phyla with no cultivated species

Phylogenetic groups at all levels are dominated by uncultivated sequences

How much of the microbial world do we know about?

Discussion session : Nanobacteria: Fact or Fiction? Mar 15

Eukaryotes Unikonts Mar 18

Plantae

Chromalveolates

Rhizaria

Excavates

Viruses & Prions The origin of viruses Mar 20

Discussion session : The Prion theory - End of the controversy? Mar 22

Archaea Phylum Euryarchaea Mar 25

Phylum Nanoarchaeum

Phylum Crenarchaea Mar 27

Phylum Korarchaea

Archaea as...

Spring Holiday - No class Mar 29

Midterm Exam #2 Apr 1

Microbial Populations The identifications of uncultivable organisms Determining the phylotype of the Octopus Spring pink filaments organism Apr 3

Cultivation and isolation of the pink filaments organism, Thermocrinus ruber

Discussion session : Pelagibacter ubique : SAR11 Apr 5

Sequence-based microbial surveys

(454 sequencing) Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Apr 8

The Human Microbiome Apr 10

Discussion session : The human microbial hand-ome Apr 12

Flourescent in situ hybridization surveys A phylogenetic FISH survey of Chloroflexi in wastewater sludge Apr 15

Molecular fingerprinting of microbial populations Denaturing Gradient Gel Electrophoresis

Different bacteria in different temperature zones of a Tibetan hot spring. Apr 17

Terminal Restriction Fragment Length Polymorphism

Realtime PCR

Changes in oral microflora after treatment for peridontal disease

Discussion session : Class microbiome project Apr 19

Linking phylotype and phenotype Stable Isotope Probing Apr 22

Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

Metagenomics Apr 24

Evidence for a new type of phototrophy in the sea

Discussion session : Final exam review session Apr 26

Final Exam at 8:00AM! May 8

Section	Topics	Modules	Date


Introduction	Course Overview	Course Overview	Jan 7

	Context & Historical Baggage	What is Microbial Diversity?
		The fundamental similarity of all living things

		The evolution of evolutionary thought	Jan 9
		Taxonomy and phylogeny
		The false eukaryote/prokaryote dichotomy

		Discussion session : Context & Historical Baggage	Jan 11

Dr. Brown is out of town - No class			Jan 14
			Jan 16
			Jan 18

Martin Luther King Day - No class			Jan 21

Phylogenetic analysis	How to do a phylogenetic analysis	Step 1: Deciding on sequences for analysis	Jan 23
		Step 2 : Obtaining the sequence data
		Step 3 : Identifying homologous residues Alignment problem set

		Discussion session : Devil's Disease & Sticker's tumor	Jan 25

		Step 4 : Tree-construction Tree construction problem set	Jan 28
		Step 5 : Interpreting the phylogenetic tree Tree interpretation problem set
		Example analysis : ES-2

	Complications	Alternative substitution models	Jan 30
		Alternative treeing algorithms
		Bootstrapping

		Discussion session : Phylogenetic Analysis problems sets	Feb 1

		Alternatives to ssu-rRNA	Feb 4
		Other methods for identification	Feb 4

	What does this all mean?	A review of "The Big Tree"	Feb 6
		Rooting the Universal Tree
		The caveat - horizontal transfer

		Discussion session : The Hot Spring of Yellowstone The Hot Springs of Yellowstone slideshow	Feb 8

Midterm Exam #1			Feb 11

The Bacteria	Primitive Thermophilic Bacteria	Phylum Aquificae (Aquifex and relatives)	Feb 13
		Phylum Thermotogae (Thermotoga and relatives)
		Other primitive thermophiles
		Thermophilic ancestry of Bacteria
		Life at high temperatures

		Discussion session : Arsenate Bacteria?	Feb 15

	Green Phototrophic Bacteria	Phylum Chloroflexi (Green non-sulfur Bacteria)	Feb 18
		Phylum Chlorobi (Green sulfur Bacteria)
		Phylum Cyanobacteria (Blue-green algae)
		Other Green phototrophs
		Bacterial photosynthesis
		Carbon fixation

	Proteobacteria	Class α-proteobacteria	Feb 20
		Class β-proteobacteria
		Class γ-proteobacteria
		Class δ-proteobacteria
		Class ε-proteobacteria
		The concept of Proteobacteria

		Discussion session : The Black Death	Feb 22

	Gram-positive Bacteria	Phylum Firmicutes (Low G+C Gram-positive Bacteria)	Feb 25
		Phylum Actinobacteria (high G+C Gram-positive Bacteria)
		Bacterial Development
		Bacterial Multicellularity

	Spirochaetes & Bacteroids	Phylum Spirochaetes	Feb 27
		Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
		Bacterial Motility

		Discussion session canceled - No class	Mar 1

	Spring Break - No class		Mar 4
			Mar 6
			Mar 8

	Deincocci, Chlamydia & Planctomycetes	Phylum Deinococci (Deinococcus/Thermus)	Mar 11
		Phylum Chlamydiae (Chlamydia and relatives)
		Phylum Planctomycetes (Planctomyces & relatives)
		Reductive evolution in parasites

	Bacterial phyla with few or no cultivated species	Phyla with few cultivated species	Mar 13
		Phyla with no cultivated species
		Phylogenetic groups at all levels are dominated by uncultivated sequences
		How much of the microbial world do we know about?

		Discussion session : Nanobacteria: Fact or Fiction?	Mar 15

Eukaryotes		Unikonts	Mar 18
		Plantae
		Chromalveolates
		Rhizaria
		Excavates

Viruses & Prions		The origin of viruses	Mar 20

		Discussion session : The Prion theory - End of the controversy?	Mar 22

Archaea		Phylum Euryarchaea	Mar 25
		Phylum Nanoarchaeum	Mar 25

		Phylum Crenarchaea	Mar 27
		Phylum Korarchaea
		Archaea as...

Spring Holiday - No class			Mar 29

Midterm Exam #2			Apr 1

Microbial Populations	The identifications of uncultivable organisms	Determining the phylotype of the Octopus Spring pink filaments organism	Apr 3
		Cultivation and isolation of the pink filaments organism, Thermocrinus ruber	Apr 3

		Discussion session : Pelagibacter ubique : SAR11	Apr 5

	Sequence-based microbial surveys (454 sequencing)	Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail	Apr 8

		The Human Microbiome	Apr 10

		Discussion session : The human microbial hand-ome	Apr 12

	Flourescent in situ hybridization surveys	A phylogenetic FISH survey of Chloroflexi in wastewater sludge	Apr 15

	Molecular fingerprinting of microbial populations	Denaturing Gradient Gel Electrophoresis

		Different bacteria in different temperature zones of a Tibetan hot spring.	Apr 17
		Terminal Restriction Fragment Length Polymorphism
		Realtime PCR
		Changes in oral microflora after treatment for peridontal disease

		Discussion session : Class microbiome project	Apr 19

	Linking phylotype and phenotype	Stable Isotope Probing	Apr 22
		Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing	Apr 22

		Metagenomics	Apr 24
		Evidence for a new type of phototrophy in the sea	Apr 24

		Discussion session : Final exam review session	Apr 26

Final Exam at 8:00AM!			May 8