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Inside the Laboratory for Extraordinary Microbes

๐ŸŒˆ Abstract

The article discusses the history and significance of the bacterium Escherichia coli (E. coli), which has become the most widely used microbe in molecular biology research. It also highlights the work of Cultivarium, a non-profit organization that aims to make "extraordinary" microbes, beyond just E. coli, more accessible to scientists.

๐Ÿ™‹ Q&A

[01] E. coli's Discovery and Rise in Molecular Biology

1. What was the original discovery of E. coli, and how did it become the most widely used microbe in molecular biology?

  • E. coli was first discovered in baby poop by German pediatrician Theodor Escherich in 1885, who originally called it "bacterium coli commune" before it was renamed Escherichia coli in his honor.
  • Before World War II, few scientists used E. coli in their experiments, but in the 1950s, at the dawn of molecular biology, scientists gained a new appreciation for it as an organism that was easy to work with and quick to grow.
  • After the Hershey-Chase experiment in 1952 indicated that DNA was the source of genetic material, the use of E. coli in research swelled, and it became the de facto microbe for molecular biology.

2. Why does the article suggest that E. coli may not be the best organism for advancing scientific progress?

  • The article notes that humanity has only discovered an estimated 0.001% of all microbes, and many of biology's most useful tools have come from "weird" or "non-model" microbes, not just E. coli.
  • The article suggests that a myopic focus on E. coli has trapped molecular biologists in a ditch, as they tend to work with organisms that are easier to handle rather than exploring the potential of more unusual microbes.

[02] Cultivarium's Efforts to Democratize Access to Extraordinary Microbes

1. What are the key steps Cultivarium takes to make "extraordinary" microbes accessible to scientists?

  • Cultivarium orders microbes from the ATCC (American Type Culture Collection) catalog, sequences their genomes, and then works to grow and transform them using robots and custom-built machines.
  • The team spends a significant amount of time (around 90%) trying to understand the optimal growth conditions and genetic engineering techniques for each microbe, as the requirements can be highly specific and difficult to predict.
  • Cultivarium's goal is to make their findings and data on these microbes freely available to the scientific community, in the hope that it will lead to new discoveries and breakthroughs.

2. How does Cultivarium's work with computational models help advance their mission?

  • Cultivarium has trained a computational model that can predict the optimal growth conditions for microbes, even when only a small portion of their genome is known.
  • This model was able to make accurate predictions about factors like oxygen tolerance and optimal temperature for microbes that were not included in the original training dataset, demonstrating the potential to make reasonable assumptions about the growth requirements of entirely new taxonomic groups of microbes.
  • Cultivarium hopes that by democratizing access to a broader range of microbes and the data to work with them, other researchers will be able to discover useful tools and drive scientific progress.
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