Mark had some great questions about the motivation of the experiment, the day-to-day routine of keeping it going, and interesting things we have observed during its history. It was incredible fun.

I encourage you to check out other episodes of Matters Microbial here:

• https://www.microbe.tv/mm/

Mark has had conversations with many interesting guests over the years, and he also has a collection of stickers, art, and pins that is second to none in promoting “microbial centrism for micronauts”.

Apply HERE at careers.msu.edu

Act now, this opportunity only comes around once every 10,000-60,000 (E. coli) generations!

‘Evolution under a microscope’ going strong at MSU by Bethany Mauger

P.S. The sign is viewed backwards in the photo, it is 82,007 from the other side!

Time flies, and Devin Lake just froze down the 82,500-generation samples last week.

Evolve, E. coli, evolve!

Episode: 12 Tiny Worlds

To recognize everyone’s efforts, we’ve created the LTEE Leaderboard! (Follow the link for the interactive version.)

If we zoom out, the most overwhelming signal is that Lenski lab manager Neerja Hajela is the all-time LTEE champion with 4349 transfers. That’s more than 1/3 of all LTEE transfers to date, a feat than is unlikely to ever be equaled! As we can see from the plot over time, Neerja did the transfers on most weekdays from 1996 to 2018.

There were other historical epochs marked by other Lenski lab managers: Lynette Ekunwe (1427 transfers), Sue Simpson (950 transfers), and Devin Lake (838 transfers). So far, only one member of the Barrick lab, Jack Dwenger (407 transfers), cracks the top ten at 7th. The plot also shows some gaps (when the experiment was paused for a move or pandemic) and a plateau (when we allowed populations that were behind to catch up).

We can also use the LTEE Leaderboard to slice and dice the data. For example, what does the leaderboard look like when we restrict it to transfers that were done on the weekend (Saturday or Sunday)?

Longtime LTEE researcher Zack Blount wins this category and we see some new graduate students and postdocs appear in this top 10 list.

You can even use the LTEE Leaderboard to figure out who did a transfer on a specific day in history. Darwin Day (February 12th) in 1993? Ryszard Korona.The Ides of March (March 15th) in 2009? Zack Blount.

Our plan is to continue to periodically update the LTEE Leaderboard, at least once a year when it is time to determine bragging rights for our annual Barrick lab Year in Review group meeting.

P.S. Your humbled-by-his-small-contribution author only clocks in at 26th on the all-time list with 78 transfers.

Data Acknowledgements and Availability

Thanks especially to Zack Blount and Devin Lake for digging through many years of LTEE notebooks and compiling the spreadsheet that made creating the LTEE Leaderboard possible. Code for the LTEE Shiny app and a CSV file of the underlying data are available on GitHub (https://github.com/barricklab/LTEE-leaderboard).

It’s been a great team effort keeping the experiment running smoothly. There have been no significant interruptions in the daily transfers or suspected contamination events for over a year now!

Jack Dwenger who “coached” the LTEE from November 2022 to July 2024 has taken a position at Penn State to pursue his interests in chemical ecology. Before Jack left, he trained Alexa Morton so she could step in as their new coach without missing a beat. The LTEE is in good hands. Alexa is a veteran of the 2023 UT Austin iGEM team and a recent Dean’s Honored Graduate.

The Olympics theme has had everyone debating how the 12 different populations of the LTEE would fare against one another in different events. Some are easy to judge: Ara–3 wins the only medal in citrate utilization, and it’s DNF (did not finish) for the other 11 populations. Some events will only be decided after more research: Which population has accumulated the most mutations? Which population has the highest fitness when competing for glucose? Which population has the most complex ecology? Which population has the largest cells?

The 80,000-generation populations are waiting in the freezer to be revived for future experiments that will answer these questions.

*One of the twelve populations (Ara–3) is 2,500 generations behind and another (Ara+6) is 500 generations behind due to past contamination incidents like the one discussed here. The last time we had to roll back any of the populations was October 2023.

Of course, the LTEE E. coli were going about their normal business and replicating during the event, a few hours after their daily transfer. We noted the eclipse in the lab notebook, but just to note the passing of time on human and astronomical scales rather than because it would affect their evolution.

The next total solar eclipse over Austin won’t be for hundreds of years… which is hundreds of thousands of E. coli generations, and also many human ones.

Tyler has a long-running Darwin Day event. Many thanks to my hosts, including Brent Bill at UT Tyler and Danielle Pritchard at TJC, and many others who organized events and offered hospitality. I especially enjoyed discussions with students at the TJC STEM Club and hearing about ongoing research projects from students and faculty at UT Tyler. They even have a new faculty member, Wei-Chin Ho, who works on experimental evolution with E. coli!

Lastly, thanks to Tom Hooten for recording and then assembling this video of the lecture. You can check out his channel on YouTube to see videos from other past Darwin Day speakers that they have hosted.

Fortunately, you can also learn about the exciting ongoing MuLTEE (multicellular long-term evolution experiment with “snowflake” yeast) at Georgia Tech from Will Ratcliff in this episode. Here, an only slightly more complex environment (allowing cells to settle) has led to the evolution of nascent multicellular forms with interesting properties. You can also muse about the prospects for life (and multicellular life) in the universe with Joe Graves of North Carolina A&T who has used experimental evolution to examine bacterial resistance to metal nanoparticles.

Episode link: https://bigpicturescience.org/episodes/going-multicellular

Photo Credit: Frank Fox (www.mikro-foto.de)

Check out the video and the article if you want to learn about the LTEE or if you are considering starting your own microbial evolution experiment. The video is also embedded in this post below.

I’m looking forward to sharing these materials with new researchers joining my group who are learning to help maintain the LTEE or beginning to study it, and also with researchers we send these ever-evolving E. coli.

Some highlights:

• We discuss aspects of the design of the LTEE that make it simple and sustainable.
• We document all kinds of expected results: how the flasks appear after growth and the optical densities the evolved E. coli populations reach in different media; photos of the colonies formed by the evolved LTEE populations on various agar plates; and agar plates showing E. coli that form red and white colonies competing for dominance over several transfers and what the changes mean in terms of relative fitness values.
• We created and an R package called fitnessR (available on GitHub) and an Excel spreadsheet (available as a supplemental file) for calculating relative fitness from co-culture competition experiment results.
• We describe alternative procedures for performing competition assays that can be used when the fitnesses of the two competitors are very similar or very different.
• We discuss some ways that the methods of the LTEE have been and are still being updated as technology has changed, and the potential advantages and disadvantages of other evolution experiment setups.

See also: If you are interested in LTEE methods, check out our protocols.io group which has media recipes and will gradually be populated with additional protocols. Rich also has a recent paper out that discusses the design of the LTEE, both in terms of procedures and as an experiment designed to answer questions about evolution (link).

@article{Barrick2023,

title = {Daily Transfers, Archiving Populations, and Measuring Fitness in the Long-Term Evolution Experiment with Escherichia coli},

author = {Jeffrey E. Barrick and Zachary D. Blount and Devin M. Lake and Jack H. Dwenger and Jesus E. Chavarria-Palma and Minako Izutsu and Michael J. Wiser},

doi = {10.3791/65342},

issn = {1940-087X},

year  = {2023},

date = {2023-08-18},

urldate = {2023-08-18},

journal = {Journal of Visualized Experiments},

volume = {198},

pages = {e65342},

abstract = {The Long-Term Evolution Experiment (LTEE) has followed twelve populations of \textit{Escherichia coli} as they have adapted to a simple laboratory environment for more than 35 years and 77,000 bacterial generations. The setup and procedures used in the LTEE epitomize reliable and reproducible methods for studying microbial evolution. In this protocol, we first describe how the LTEE populations are transferred to fresh medium and cultured each day. Then, we describe how the LTEE populations are regularly checked for possible signs of contamination and archived to provide a permanent frozen "fossil record" for later study. Multiple safeguards included in these procedures are designed to prevent contamination, detect various problems when they occur, and recover from disruptions without appreciably setting back the progress of the experiment. One way that the overall tempo and character of evolutionary changes are monitored in the LTEE is by measuring the competitive fitness of populations and strains from the experiment. We describe how co-culture competition assays are conducted and provide both a spreadsheet and an R package (fitnessR) for calculating relative fitness from the results. Over the course of the LTEE, the behaviors of some populations have changed in interesting ways, and new technologies like whole-genome sequencing have provided additional avenues for investigating how the populations have evolved. We end by discussing how the original LTEE procedures have been updated to accommodate or take advantage of these changes. This protocol will be useful for researchers who use the LTEE as a model system for studying connections between evolution and genetics, molecular biology, systems biology, and ecology. More broadly, the LTEE provides a tried-and-true template for those who are beginning their own evolution experiments with new microbes, environments, and questions. },

keywords = {},

pubstate = {published},

tppubtype = {article}

}