Microbial Population Biology

Open access blog network focused on the population biology of bacteria and viruses

April 17, 2014
by Vaughn
1 Comment

Last weeks of class

Dear all,

Please note the comments on the last assignment in which some of you provided links to interesting material related to the host microbiome project.

As a reminder, Exam 2 is on Tuesday 4/22, same format as last time, emphasizing material from the 2nd half of the class. Any questions, please comment here.

The lectures are updated for your review and help with the open-notes format.

We have the option of talking about environmental metagenomics or more host microbiome work on Thursday 4/24. The following week, each research group will present their proposed study in 5 minutes, with time for 2 minutes for questions/feedback. We’ll organize these details on Thursday 4/24, but realize there’s a benefit from going on Tuesday 4/29 in that you’ll have more time to update your draft.



April 9, 2014
by Vaughn

Bonjour, microbiome fans

Dear all,

In my absence I certainly don’t want to deprive you of learning about the amazing ongoing research focused on the microbiomes of humans and other species.

Here are the links to your available media.

1) Science Friday podcast with Curtis Huttenhower, “Mapping the Microbial Make-Up of Healthy Humans.”

2) Science Friday podcast with David Relman, “A Community of Thousands — In Your Gut

3) TEDMED talk by Jonathan Eisen, “Who are ‘Me, Myself, and Us?‘” Also here.

4) TED talk by Paul Ewald (my old advisor): “Can we domesticate germs?

5) NPR video: “Exploring the Invisible Universe that Lives on us and in us” (not loading right now)

6) Harvard outreach video, Peter Turnbaugh; “Dining with Trillions of Microbial Friends.”

Or, anything else you can find. Please pick at least THREE (3). Most are pretty short and all are very entertaining.

For next week, bring notes from what you learned to class.

A reminder, lab reports are due this week, as is your 1/2 page outline of your grant proposal.

Here are a few pictures having arrived here in Nimes, Fr, of ruins from the 1st century BC to the 1st century AD.

coliseum tower

March 31, 2014
by Vaughn
1 Comment

April 1 class (no fooling)

Hi folks,

Please be sure to comment on your partner’s blog on recombination by tomorrow, and maybe some other student blogs as well! There’s some great analysis to share.

Tomorrow we’ll talk about bacterial sociality and coordination, and begin our focus on the Myxococcus xanthus system. Please read this paper (assigned last Thursday) for tomorrow. On Thursday, you’ll pick one of the follow-up papers linked to the syllabus to analyze.


March 20, 2014
by Vaughn

Recombination, small and large: why sex?

Dear all,

For next week, first, please re-read the article assigned for last week carefully. You did a nice job highlighting the key findings but you all need to put the pieces together for yourself. In addition, focus on the Fisher-Muller hypothesis for the evolution of sex. Under what conditions would speeding up the assembly of new mutations (“in with the good”) be advantageous?

Now, thinking about when “in with the good” and “out with the bad” might be most useful, please find a different scientific article (if you haven’t already), link directly to it, and summarize its key findings on your blog. Explicitly state what hypothesis related to the evolution of sex or altered recombination rates the paper examines. Try to draw connections between these articles, or if this is impossible, link your new article to some other scientific knowledge. We’ll discuss what you learned in class next week.


March 18, 2014
by Vaughn
1 Comment

Back from break schedule

Hi gang,

A reminder: we won’t meet during lecture on Thursday 11:10-12:30; instead, we’ll do a mix of classroom and lab exercises from 2-4 in our normal lab room.

Please come prepared by reading the assigned paper by Tim Cooper, and in anticipation of this weekend’s blog on “Why Sex?” please search for an example in biology (not necessarily microbiology) in which rates of recombination vary, and be prepared to discuss it. Use a variety of search schemes, beginning with PubMed.

See you Thurs.


PS: Check out this abstract, which is highly relevant to the first half of the class. Bummer that our library doesn’t subscribe to new issues. #openaccess

March 2, 2014
by Vaughn

Exam 1 2014

Dear all,

I’m looking forward to seeing you Tuesday for the review in preparation of Thursday’s exam (worth 15%). Please come prepared with questions other than “will this be on the test,” because it’s open-blog, paper, notes, etc, so it’s all fair game. I’ll be posting slides from last week asap.

Regarding exam structure, you can expect about 15 questions, most multi-part or requiring a few sentences or a figure.  See the exam page for a bit more info, which I’ve updated with some useful review questions.

Please prepare by reviewing the central concepts and points from each lecture and from each assigned reading.  Since it is open-book the exam will require application and synthesis and not just regurgitation of facts.  I encourage you to spend some time with the materials so that you will be efficient with them during the exam.

You will need to review and interpret some of the literature that I reviewed in class, ie the papers that I reviewed in lecture but that we did not discuss in recitation. You will also have to draw figures that illustrate concepts or findings, since a picture is worth 1,000 words.


February 20, 2014
by Vaughn

Chance, history, and adaptation

Dear all, very nice job dissecting the Travisano et al “Chance, History, and Adaptation” paper today. For this week’s blog, please write on:

1. Do you believe that microevolutionary models, such as the one described in this paper, can shed light on macro-scale processes? Why/why not?

2. What other (macro)evolutionary phenomenon would you like to test with microbes? For example, how would you modify the design of this experiment, and why?

In addition, if you are interested please find my recent Primer on specialization in the Lenski long-term evolution experiment, published this week in PLoS Biology. This is not required.

February 17, 2014
by Vaughn

Snow shuffle

Hi gang,

Our schedule has been made even more complex with the last cancellation, and I expect that many of you are wondering what you’re supposed to be doing. So here’s a review and update:

1) Please comment on a classmate’s blog (or more than one) this week, if you haven’t already. Comments should continue the conversation and thought process.

2) Visit the updated schedule at the Syllabus. This week, we will be covering what we’ve learned from a few major experiments using experimental evolution and how it applies to our understanding of evolution, in general. Your readings include 1) a review of the Lenski long-term experimental evolution project from Lenski himself, via his blog and 2) the Travisano et al study of chance and history in adaptation. We will dissect the latter reading in detail in lab.

3) Next week, I’ll be in Europe so my two PhD students will give lectures on evolution of the mutation rate (which pertains to all organisms) and evolution in biofilms. Relevant readings are posted. While I’m abroad I will post some self-assessment questions for you to begin reviewing for the exam the following week. On Tuesday 3/4, I’ll give a review of the first 1/2.

Questions? Comment here, email, or ask in class! See you tomorrow.

February 5, 2014
by Vaughn

MLST: practical application of the species question

Dear class,

Tomorrow (thursday) in Lab we’ll be working on a computer laboratory that tackles “the species question” head-on.  The lab is MLST-lab-2014.  I’ll bring paper copies, but feel free to download and complete on your computer.

In lecture, we’ll talk about HGT, recombination, and the problem of homology.  And for this weekend, I ask that you consider:

Where do bacterial species come from?  And more to the point, how did your favorite bacterial species (or set of species) come to be?  Please venture out into the primary scientific literature and provide a working link to the paper.

Thus far, you have done a terrific job on your blogs and I’m just now catching up. Keep it up!


February 4, 2014
by Vaughn

Lectures updated

Hi all, I’ve posted the updated lectures along with snapshots of the whiteboards in class. I hope these are helpful to pair with your notes. I’ll work to post slides in a more timely fashion, ahead of time if possible. Have a great snow day.