Could you change the title of the article? It's not the title of the paper, and isn't really the most significant finding. The paper itself is a wonderful initial survey of bacterial diversity which is much more important than the trivial observation that we can't identify all the organisms (although I believe that observation should be followed up with more intensive analysis).
The current headline is vastly more entertaining -- and it attracts a lot of non-life-sciences readers (like me) who are willing to linger and learn a bit about bacterial diversity.
Write a narrow headline, get a narrow audience.
In this case, I'll defend the current headline as "virtuous click-bait." That's a rarity, but nice when it happens.
We changed the title to a phrase from the first sentence of the abstract, which seems more accessible than the paper title. We often treat the opening sentence of an article as a kind of subtitle for HN purposes.
I wouldn't call wallflower's title ("Half the DNA on the NYC Subway Matches No Known Organism") egregiously editorialized, though, since that finding was the one the article itself highlighted.
This is the difference between product and marketing. Marketing is taking a product and figuring out how to position to the right audience. If that means highlighting a single feature and letting users/readers discovery the breadth, that's an acceptable tradeoff if it gets the job done.