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 06

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

The evolution of evolutionary thought Jan 08
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

Discussion session : Context & Historical Baggage Jan 10

Phylogenetic analysis How to do a phylogenetic analysis Step 1: Deciding on sequences for analysis Jan 13
Step 2 : Obtaining the sequence data
Step 3 : Identifying homologous residues
Alignment problem set

Step 4 : Tree-construction
Tree construction problem set
Jan 15
Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set
Example analysis : ES-2

Discussion session : Phylogenetic Analysis problems sets Jan 17

MLK Day - No class Jan 20

Complications Alternative substitution models Jan 22
Alternative treeing algorithms

Discussion session : Tasmanian Devil Disease and Stickers Tumor Jan 24

Alternatives to ssu-rRNA Jan 27
Other methods for identification

What does this all mean? A review of "The Big Tree" Jan 29
Rooting the Universal Tree
The caveat - horizontal transfer

Discussion session : Arsenate-based Bacteria? Jan 31

Midterm Exam #1 Feb 03

The Bacteria Primitive Thermophilic Bacteria Phylum Aquificae (Aquifex and relatives) Feb 05
Phylum Thermotogae (Thermotoga and relatives)
Other primitive thermophiles
Thermophilic ancestry of Bacteria
Life at high temperatures

Discussion session : The Hot Spring of Yellowstone
The Hot Springs of Yellowstone slideshow
Feb 07

Green Phototrophic Bacteria Phylum Chloroflexi (Green non-sulfur Bacteria) Feb 10
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation

Proteobacteria Class α-proteobacteria Feb 12
Class β-proteobacteria
Class γ-proteobacteria
Class δ-proteobacteria
Class ε-proteobacteria
The concept of Proteobacteria

Discussion session : The Black Death Feb 14

Gram-positive Bacteria Phylum Firmicutes (Low G+C Gram-positive Bacteria) Feb 17
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Spirochaetes & Bacteroids Phylum Spirochaetes Feb 19
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Discussion session : Nanobacteria, Fact or Fiction? Feb 21

Deincocci, Chlamydia & Planctomycetes Phylum Deinococci (Deinococcus/Thermus) Feb 21
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 Feb 26
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 : The Prion Theory - ONLINE ONLY, NO CLASS TIME Feb 28

Eukaryotes Unikonts Mar 03

Viruses & Prions The origin of viruses Mar 05

Discussion Session canceled - No class Mar 07

Spring Break - No class Mar 10
Mar 12
Mar 14

Archaea Phylum Euryarchaea Mar 17
Phylum Nanoarchaeum

Phylum Crenarchaea Mar 19
Phylum Korarchaea
Archaea as...

Discussion session : Pelagibacter ubique : SAR11 Mar 21

Midterm Exam #2 Mar 24

Microbial Populations The identifications of uncultivable organisms Determining the phylotype of the Octopus Spring pink filaments organism Mar 26
Cultivation and isolation of the pink filaments organism, Thermocrinus ruber

Discussion session : The Great Tree of Life Mar 28

Sequence-based microbial surveys

(454 sequencing)
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Mar 31

The Human Microbiome Apr 02

Discussion session : The human microbial hand-ome Apr 04

Flourescent in situ hybridization surveys A phylogenetic FISH survey of Chloroflexi in wastewater sludge Apr 07

Molecular fingerprinting of microbial populations Denaturing Gradient Gel Electrophoresis

Different bacteria in different temperature zones of a Tibetan hot spring. Apr 09
Terminal Restriction Fragment Length Polymorphism
Realtime PCR
Changes in oral microflora after treatment for peridontal disease

Discussion session : Class microbiome project Apr 11

Linking phylotype and phenotype Stable Isotope Probing Apr 14
Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

Metagenomics Apr 16
Evidence for a new type of phototrophy in the sea

Spring Holiday - No class Apr 18

Genomics How to sequence a genome Thermotoga maritima and evidence for lateral gene transfer Apr 21

Metagenomics The metagenome of the Sargasso Sea

Origins The time scale A 3.2 billion year old fossilized ecoystem Apr 23
The Last Common Ancestor
The RNA World
The emergence of Life

Final Exam at 8:00AM! Apr 28