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Scott Kelley

I wonder: Do the culture-based studies point out their limitations? If you can grow it, it is necessarily important? If you can't grow it (don't know the growth conditions or it died in transit) is it necessarily unimportant?

If the molecular folks still have to point out limitations with every study they publish, even though these are well known by now, I think the culture-based studies should do the same. For instance, they have been culturing Pasteurella out of sheep's noses for decades and still can't decide whether they kill bighorn sheep. Meanwhile, molecular evidence has surfaced that suggests many other microbes are involved. Completely ignored of course.

And in the indoors, should we just stop studying it because some people get freaked out? Is that the fault of the scientists? Should me not learn what is there, what has been there outside of what we can grow? Can we not be interested in how things move around indoors where we spend 90% of our time?

The real nonsense of this blog is the statement that we should ONLY care when an outbreak of something we understand happens (e.g. Clostridium). Well what about the 100,000 deaths per year due to infections acquired in hospital? These are mostly opportunistic. Where did they come from? How can we stop them? Are surfaces involved? Do the bugs come on clothes from the restroom? Do we know this already? Most of the time, these agents are not identified.

DNA work is a wonderful compliment to what is known already in microbiology. It has expanded our understanding 1000-fold over culture methods in the natural world. It has the potential to do the same in the built environment. Please keep this in mind.

Elio replies:

Let’s first agree about the obvious. When it comes to environmental samples, plate counts only detect the bacteria that can be readily cultivated. This widely recognized and is called the “Great Plate Count Anomaly.” Thus, plate counts severely underestimate the number of species in a sample. Plate counts reveal the presence of only some of the living bacteria in the sample and usually tell of their abundance.

On the other hand, metagenomic analysis of a sample tells us what DNA is present and potentially which genes are in attendance. This is indeed valuable information, as it suggests the biological potential in a sample. It is far more inclusive but, generally speaking, is only suggestive. Unless specialized techniques are used, it does not provide quantitative information, nor does it distinguished between live and dead organisms. Relevant to the paper in question is that many human-associated bacteria die rapidly on drying, although the DNA remains in their carcasses.

It would seem obvious that both approaches should be used in concert, being that they yield different kinds of information. Alas, this is seldom done, as many workers favor one of these approaches over the other. They ought to complement each other. To use an imperfect analogy, think of a large library. A metagenomicist may know the titles of the books, usually with a small amount of information about each, the “cultivator” will have read a few of them.

I suspect that Scott may agree with these general points. He says, with plenty of reason, that everyone should be mindful of the limitations of their studies. It’s true that the plate anomaly is seldom spelled out, but I believe that most people are more aware of the limitations of cultivation techniques than of metagenomics.

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