E. coli in the Long View

E. coli has been with us for untold generations — more of theirs than ours, to be sure — and we have evolved together in both commensal and adversarial ways.

E. coli lives in the short now. Like many of its bacterial peers, Escherichia coli can take as little as twenty minutes to reproduce in ideal laboratory conditions. Despite these brief individual lives, E. coli, an impressively diverse bacterial species that includes both harmless and rather harmful strains, has a long history that intertwines deeply with humans and our guts. Two recent scientific studies —  one reaching centuries back and another observing thousands of generations’ worth of evolution in the now — provide important insight into the past, present, and future of our sometimes contentious relationship with E. coli.

The first study, published this month in Communications Biology, uses an unlikely source to uncover the oldest genome of E. coli as of yet found. The study, which comes from a team of international scientists, drew its sample of E. coli from a gallstone found in the mummy of Giovanni d’Avalos, a middle-aged Neapolitan nobleman who died in 01586. d’Avalos lived an unremarkable life: unlike his father Alfonso, who served ably under Spanish King and Holy Roman Emperor Charles V in the Italian wars, d’Avalos received no great distinction in his forty-eight years of life in and around Naples and the Southern Mediterranean. Instead, history and biology remember him for the swath of health conditions he acquired in his last decade of life, including most notably an acute case of cholecystitis, the inflammation of the gallbladder.  

Gallstones have many possible causes, but E. coli is among the most prominent.  And in the long-buried gallstones of Giovanni d’Avalos, the researchers found exactly that. After extracting genetic material from the still-preserved, dark brown gallstones and filtering out human DNA, the researchers found that the most common bacterial species present in the DNA samples was E. coli.

From there, the study explores how these sixteenth century microbes differ from their modern relatives. How have the untold hundreds of thousands or millions of generations reshaped the E. coli genome? The researchers found that the gallstone E. coli sample had DNA that fit best in the species’ Phylogroup A, a clade within the species associated with other historical strains, strains found in less industrialized communities, and gout-causing strains.

Yet the d’Avalos sample differed in significant ways from A-group E. coli of more recent vintage. For one, they lacked the array of antimicrobial resistance genes that contemporary strains usually carry. The people of early modern Italy did not have easy access to effective antibiotics, which were only invented in the 01930s —  . The particular variety that found its way into d’Avalos’ gallbladder also lacked many of the virulence factors associated with common harmful strains like Shiga toxin-producing E. coli, indicating it was instead a commensal strain — typically benign in human bodies — that made an opportunistic leap into gallstone infection in a time of bodily stress. Most studies that have explored ancient DNA have focused on more obvious pathogens like Yersinia pestis, the bacteria that caused the Black Plague and many subsequent epidemics. By analyzing a more benign set of pathogens, the study opens up the door to a deeper understanding of how our microbial passengers have evolved with us.

The other recent E. coli study is less ancient in its provenance, but no less an example of long-term thinking in our understanding of our microbial counterparts. It draws on one of the most significant long-form experiments in biological history: the E. coli long-term evolution experiment (LTEE), which has been running for nearly 35 years since its 01988 inception at Richard Lenski’s laboratory at the University of California, Irvine. Since then, the experiment has moved with Lenski to Michigan State University, where the strains of bacteria involved in the experiment lived for more than three decades. As of June 02022, the experiment has withstood yet another move to Jeffrey Barrick’s lab at the University of Texas at Austin.

The twelve lineages of Lenski's Long-term Evolution Experiment in 02006. Courtesy of Brian Baer and Neerja Hajela, Creative Commons Attribution-Share Alike 1.0 Generic

The LTEE’s set-up is potent in its simplicity. In 01988, Lenski set up 12 populations of (non-pathogenic) E. coli,  beginning from a single haploid cell each, in 12 identical glucose solutions —  enough nutrients for the bacterial populations to grow 100-fold in a few hours. Every day since, lab members have transplanted 1% of the prior day’s population to a new set of media, allowing the cycle to continue anew. To keep a record of the experiment’s evolutionary development, each population is frozen every 500 generations (approximately every 75 days) using a cryoprotectant for protection and stored at -80° F, a fossil record of samples that can be reawakened for further study, in a process that the lab considers a sort of “time travel.”

A timeline of the LTEE with generation times for comparison

The experiment, originally intended to track evolution for 2,000 generations, has now been running for more that 75,000 generations. To put this in more familiar terms, that’s the generational distance between modern-day humans and Homo erectus. It hasn’t been a constant run over the course of its three-plus decades; the beginning of the Coronavirus Pandemic in 02020 and, less catastrophically, the move from Irvine to Lansing, Michigan in 01992 caused interruptions of six months each.

Despite these short breaks, the experiment’s extreme longevity has allowed for a wealth of scientific discovery in the form of more than 150 scientific publications from 01991 until this year.  In a recent interview, Lenski noted that the experiment has shown both evolution’s reproducibility and the “striking divergences” it can produce. While the 12 lines have shown similar overall increases in fitness relative to the baseline ancestor, they have not all followed the same path, with one out of twelve having evolved the surprising ability to consume citrate in addition to glucose around generation 31,500.

The most recent paper out of the LTEE, by post-doc Minako Izutsu and Lenski, tests one of the foundational questions of evolution: the comparative roles of initial genetic diversity and future mutations in determining fitness. Variation within a population is a necessary fuel for natural selection — without it, there’s nothing to select for — but that variation can come from two sources in a controlled experimental environment. Variation can be baked into a study due to the initial mix of individuals in an experimental population, or can arise through mutation as it progresses. Izutsu and Lenski’s study explores whether initially non-diverse populations can “catch up” to their more diverse counterparts in terms of fitness. It compares 4 different treatments of bacteria: cloned samples with no initial diversity, lines from 50,000 generations into the LTEE, and mixed versions of both the clones and the lines.

Over the course of the 2,000 generations of the experiment, the 72 lines in the new experiment all gained similar amounts of relative fitness. During the first 100 generations, the more diverse, mixed lineages adapted to new conditions much more quickly, but by the 500th generation this initial advantage wore away as mutations occurring during the experiment proved to have a more long-lasting effect.

The experiment’s results, and perhaps the grander enterprise of the LTEE itself, speak to the power of evolutionary time to break through what may seem like immutable starting characteristics. E. coli has been with us for untold generations —  more of theirs than ours, to be sure — and we have evolved together in both commensal and adversarial ways. Whether in noble gallstones or controlled lab conditions,  E. coli will continue to evolve with us.

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The Long Now Foundation is a nonprofit established in 01996 to foster long-term thinking. Our work encourages imagination at the timescale of civilization — the next and last 10,000 years — a timespan we call the long now.

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