The Need to Characterize ‘Near’ Missing Diversity: A Comment on the Subway Microbiome Paper

I’m a few weeks late to the subway microbiome paper which, in internet time is decades, but I’ve noticed two things are missing in the commentary. Before I get to those issues, one of the advantages of being behind the curve is that I can outsource the whole bubonic plague issue to Nick Loman:

However, I think we can fairly confidently conclude that your study provides no compelling evidence of Y. pestis [bubonic plague] being on the subway. The missing part of this discussion is that we already have lots of understanding about the population genomics of Y. pestis and B. anthracis [anthrax] to guide us in interpreting these data. The most important thing to know is that these species are genetically extremely monomorphic, so matches at ~90% nucleotide identity simply cannot be from the same species.

I’ll just add that when I looked at the reads that were supposed to be plague (listed in the post), they looked like ordinary phage proteins and, as Loman notes, weren’t Y. pestis genes. In fact, as Christopher Mason, one of the authors on the paper notes, these sequences are perfectly identical matches to Enterobacter hormaechei, a somewhat distant relative of both the gut commensal, E. coli, and Y. pestis. I find this really interesting, since we don’t know much about E. hormaechei, and what little we do know is based on isolates from sick people, which might not be (probably isn’t) its ‘native habitat’, any more than most E. coli should be thought of as pathogens. So here’s this bacterium, which in the grand scheme of things, is similar to other bacteria we’ve studied, but whose ecology is a complete mystery. It’s great that everyone is focusing on Things We Have Never Seen Before, but there’s still far too much work to be done on things we’ve named, are clinically important, and which we still know very little about.

So that’s the first missing point. Here’s the second:

STAY AWAY FROM 168TH STREET! That no one has mentioned this incredibly important result is clear evidence of a deep, nefarious conspiracy….

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3 Responses to The Need to Characterize ‘Near’ Missing Diversity: A Comment on the Subway Microbiome Paper

  1. Colin says:

    Did they find Platypus sequences or did they use Platypus Conquistador?

  2. Florian says:

    But what about (ninja) turtles?

  3. noddin0ff says:

    Evidence that it was a really, really small alligator…

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