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
Chapter 1 of the textbook
Course Overview Jan 07

Context & Historical Baggage

Chapter 2 of the textbook
What is Microbial Diversity?
The fundamental similarity of all living things

The evolution of evolutionary thought Jan 09
Taxonomy and phylogeny
The false eukaryote/prokaryote dichotomy

Phylogenetic analysis How to do a phylogenetic analysis

Chapters 3 and 4 of the textbook
Step 1: Deciding on sequences for analysis Jan 12
Step 2 : Obtaining the sequence data
Step 3 : Identifying homologous residues
Alignment problem set

Step 4 : Tree-construction
Tree construction problem set
Jan 14
Step 5 : Interpreting the phylogenetic tree
Tree interpretation problem set
Example analysis : ES-2

Discussion session : New antibiotic discovery Jan 16

MLK Day - No class Jan 19


Chapters 5 and 6 of the textbook
Alternative substitution models Jan 21
Alternative treeing algorithms

Discussion session : Phylogenetic Analysis problems sets Jan 23

Alternatives to ssu-rRNA Jan 26
Other methods for identification

What does this all mean?

Chapter 7 of the textbook
A review of "The Big Tree" Jan 28
Rooting the Universal Tree
The caveat - horizontal transfer

Discussion session : The Hot Spring of Yellowstone
The Hot Springs of Yellowstone slideshow
Jan 30

Midterm Exam #1 Feb 2

The Bacteria Primitive Thermophilic Bacteria

Chapter 8 of the textbook
Phylum Aquificae (Aquifex and relatives) Feb 04
Phylum Thermotogae (Thermotoga and relatives)
Other primitive thermophiles
Thermophilic ancestry of Bacteria
Life at high temperatures

Discussion session : Arsenate-based Bacteria? Feb 06

Green Phototrophic Bacteria

Chapter 9 of the textbook
Phylum Chloroflexi (Green non-sulfur Bacteria) Feb 09
Phylum Chlorobi (Green sulfur Bacteria)
Phylum Cyanobacteria (Blue-green algae)
Other Green phototrophs
Bacterial photosynthesis
Carbon fixation


Chapter 10 of the textbook
Class α-proteobacteria Feb 11
Class β-proteobacteria
Class γ-proteobacteria
Class δ-proteobacteria
Class ε-proteobacteria
The concept of Proteobacteria

Discussion session : The Justinian Plague Feb 13

Gram-positive Bacteria

Chapter 11 of the textbook
Phylum Firmicutes (Low G+C Gram-positive Bacteria) Feb 16
Phylum Actinobacteria (high G+C Gram-positive Bacteria)
Bacterial Development
Bacterial Multicellularity

Spirochaetes & Bacteroids

Chapter 12 of the textbook
Phylum Spirochaetes Feb 18
Phylum Bacteroids (Sphingobacteria, or Bacteroides/Flavobacterium/Cytophaga)
Bacterial Motility

Discussion session : The Prion Theory Feb 20

Deincocci, Chlamydia & Planctomycetes

Chapter 13 of the textbook
Phylum Deinococci (Deinococcus/Thermus) Feb 23
Phylum Chlamydiae (Chlamydia and relatives)
Phylum Planctomycetes (Planctomyces & relatives)
Reductive evolution in parasites

Bacterial phyla with few or no cultivated species

Chapter 14 of the textbook
Phyla with few cultivated species Feb 25
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? Feb 27


Chapter 16 of the textbook
Unikonts Mar 02

Viruses & Prions

Chapter 17 of the textbook
The origin of viruses Mar 04

Discussion Session canceled - No class Mar 06

Spring Break - No class Mar 09
Mar 11
Mar 13


Chapter 15 of the textbook
Phylum Euryarchaea Mar 16
Phylum Nanoarchaeum

Phylum Crenarchaea Mar 18
Phylum Korarchaea
Archaea as...

Discussion session : Pelagibacter ubique : SAR11 Mar 20

Midterm Exam #2 Mar 23

Microbial Populations The identifications of uncultivable organisms

Chapter 18 of the textbook
Determining the phylotype of the Octopus Spring pink filaments organism Mar 25
Cultivation and isolation of the pink filaments organism, Thermocrinus ruber

Discussion session : The Great Tree of Life Mar 27

Sequence-based microbial surveys
(including 454 sequencing)

Chapter 19 of the textbook
Molecular phylogenetic analysis of bacterial symbionts of the deep-sea hydrothermal vent scaly snail Mar 30

The Human Microbiome Apr 01

Spring Holiday - No class Apr 03

Flourescent in situ hybridization surveys
Chapter 20 of the textbook
A phylogenetic FISH survey of Chloroflexi in wastewater sludge Apr 08

Molecular fingerprinting of microbial populations

Chapter 21 of the textbook
Denaturing Gradient Gel Electrophoresis

Different bacteria in different temperature zones of a Tibetan hot spring. Apr 08
Terminal Restriction Fragment Length Polymorphism
Realtime PCR
Changes in oral microflora after treatment for peridontal disease

Discussion session : The human microbial hand-ome Apr 10

Linking phylotype and phenotype

Chapter 22 of the textbook
Stable Isotope Probing Apr 13
Identification of ciliate grazers of autotrophic Bacteria in ammonia-oxidizing activated sludge by RNA stable isotope probing

Metagenomics Apr 15
Evidence for a new type of phototrophy in the sea

Discussion session : Class microbiome project Apr 17


Chapter 23 of the textbook
How to sequence a genome Thermotoga maritima and evidence for lateral gene transfer Apr 20

Metagenomics The metagenome of the Sargasso Sea


Chapter 24 of the textbook
The time scale A 3.2 billion year old fossilized ecoystem Apr 22
The Last Common Ancestor
The RNA World
The emergence of Life

Discussion session : Tasmanian Devil Disease and Stickers Tumor Apr 24

Final Exam at 9:00AM! May 01