Triskelion #2

This is the second post in a series called Triskelion. The triskelion is an ancient symbol consisting of a triple spiral (or legs) exhibiting rotational symmetry. The triskelion has different meanings across cultures, but all meanings revolve around a rule of 3’s. In this series, I’ll share three things — a paper, a quote, and a thought. I'll post these whenever I can fill up the three branches of the triskelion. I hope you enjoy.

1.    A Paper

von Schwartzenberg, R.J., Bisanz, J.E., Lyalina, S. et al. Caloric restriction disrupts the microbiota and colonization resistance. Nature 595, 272–277 (2021). https://doi.org/10.1038/s41586-021-03663-4

As an intermittent faster myself, I find myself thinking a lot about the links between fasting and my own microbiome because there are some pretty perceptible (ahem) effects. Thus, I was super excited to read this recent work out of Peter Turnbaugh’s lab that explains the connections between caloric restriction and the gut microbiome. There’s something for everyone in this paper—too much to go over here.

A few things I found interesting:

  1. Caloric restriction led to increased microbial richness (Fig. 1c) and an enrichment of transport functions (Fig. 1d). Natural low-nutrient environments are dominated by transport functions, so it’s interesting to see that as calories are restricted, a similar enrichment of transport functions is observed. It would be interesting to investigate how stable and resilient these changes are over time.

  2. Caloric restriction led to an enrichment of short-chain fatty acid production (SCFA) genes, but an overall decrease in SCFA concentrations. Another reminder that differential abundances in genes (or transcripts, for that matter) do not always relate to what the microbes are doing.

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2.    A Quote

The perspective below can be applied not only to software, but to research more broadly. This is why we’ll always post preprints of our work ahead of publication. “Good enough” trumps “perfection” in most cases.

From David Heinemeier Hansson

“After two decades of open source participation, I’ve found it easier to cultivate community collaboration around software that’s obviously a little broken. Waiting until the project is pristine before sharing it with the world creates an aura of perfection that intimidates and alienates. So releasing before every bug has been squashed, every feature filled in, every facet documented meticulously improves the odds that it’ll attract the interest of others to help make all that happen.

That’s not a license to release a busted mess, don’t get me wrong. But it is an invitation to consider exactly how long to wait before you share with the world. And your own bar for the quality of the contributions, especially in the early days. Where getting more that’s mostly right rather than less that’s entirely so helps create momentum.”

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3.    A Thought

Is a dormant organism really “dormant” if it never resumes growth? What regulates whether it can exit dormancy? Is it possible to distinguish which cells have the capacity to exit dormancy vs those that cannot from molecular data?

I’m sure I’m not the first person to ruminate on this chicken-egg conundrum. But I’ve been thinking a lot about it recently—especially as it pertains to non-spore forming microbes. What do you think? Share it below!

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