DVD extras: sponge microbiome

Hey gang, I hope you got the chance to read my first sci-comm piece for Massive Science Consortium. If not, check this link. As we went through the drafts, some sections were trimmed to make the article more focused. I’d like to share with you some of what didn’t make the cut for the published piece.

  1. What the DNA sequence data actually is: First, a bit more detail on sequencing than the article really needed. Pyrosequencing produces a large, complex dataset of genetic code that requires some additional processing. First, highly similar DNA sequences are grouped into operational taxonomic units, or OTUs, that stand in for individual species. Think of OTUs as analogous to identifying a group of cars by their make, model, and year. You have a thorough general idea of the characteristics of the cars without spending the time and effort to find out which have leather seats or backup cameras. For identification, these OTUs are compared to publicly available databases; in this case, the authors used the Ribosomal Database Project. This provided the annotated data from which they compared the amount and diversity of microbes in regularly sanitized sponges versus the others.
  2. Uncritical reporting & misplacing Occam’s razor: A frustrating commonality among the news articles covering the study at the time it was published was the claim that regularly sanitizing the sponges didn’t result in any reduction in bacteria. It’s on the authors as well for misrepresenting that point by stating, “regularly sanitized sponges (as indicated by their users) did not contain less bacteria than uncleaned ones.” One presumes that a regularly sanitized sponge is…well, reused, and therefore reexposed to unsanitary conditions. Nothing in the methods indicates that sponges were sanitized immediately prior to sequencing. Otherwise, it should be obvious that regular cleaning of a sponge won’t render it any less hospitable to microbes in the long term. You don’t take one shower and never get dirty again.
  3. It’s a sample size of 5 ‘regularly sanitized’ vs. 9 ‘unsanitized’ sponges, and You Won’t Believe What Those Terms Actually Mean: In the article I mentioned that the authors compared regular sanitization of sponges with the effect of a course of antibiotics on the gut. I got into why antibiotic resistance and heat/detergent resistance shouldn’t be expected to develop in the same, way, but there’s another argument. If sanitized samples not only showed enrichment of certain OTUs, but also depleted overall diversity, it would be similar to a patient’ after broad-spectrum antibiotic treatment. In the study, regularly sanitized sponges (n=5) averaged less OTUs than unsanitized (n=9), but it is unclear if the difference was significant, and the authors did not discuss this point. In fact, the only way the analogy works is for people or animals chronically on antibiotics, for example due to an immunodeficiency. That analogy doesn’t really extrapolate to most of us and our kitchen sponges. Furthermore, the numbers! This is 14 sponges, from a specific region of Germany, divided again into the two groups ‘regularly sanitized’ and ‘not’. Looking into the methods, the authors noted that ‘regularly sanitized’ was from a questionnaire issued to the sponge donors. ‘Regularly sanitized’ meant checking ‘yes’ on ‘application of special cleaning procedures’, which was further clarified:

“In case of the special cleaning procedures, the users were asked to specify whether they regularly apply special measures to clean their sponge. The procedures mentioned were: heating in a microwave and rinsing with hot, soapy water.”

I was pretty shocked. First off, that means 1, 2, 3, 4, or 5 of the ‘regularly sanitized’ sponges were microwaved –we don’t know!– and we also don’t know if microwaving in particular drives the bacteria difference. I don’t know about y’all, but I exclusively use my sponge with hot, soapy water. What are the ‘unsanitized’ sponge users doing with their sponges, wiping dry? In that case, my sponge is getting sanitized every time I use it, and I hope yours is too.

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So my overall thoughts on the article are that it’s really interesting work and it should be reassuring that there aren’t any actual bacterial baddies lurking in our kitchen sponges. It turns out to be a dynamic microenvironment within the kitchen. I’d like to tsk-tsk the authors for overselling the Chryseobacteria/Moraxella finding in their discussion point; it’s interesting that they overpopulate the ‘regularly sanitized’ cohort, but as discussed here the ‘regularly sanitized’ term doesn’t really mean much and absolutely should have been explained better or gated more stringently.

On a personal level, I really appreciated the opportunity to have my work edited and the personal feedback from the Massive members who edited my work. Looking forward to sharing my next Massive piece, which will definitely be less critical. That’s a hat I’m not that fond of wearing, but I’ll put it on if need be.

PS – I told you my next piece would be about bacteria, but this one was not so related to diet. Mea culpa.

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