How does one categorize prokaryotes?

If you’re taking or have taken only basic or “medical” microbiology courses, it may seem like bacteria are still classified by ancient 19th-century criteria. Are the bacteria Gram-positive, Gram-negative, Acid-fast? And then, are they round, straight, or bendy? Then, to categorize any further, there’s a bewildering array of culture tests you can go through – some of which seem archaically specific with quaint un-intuitive terminology for the results.

Take “hemolysis“, for example. Considering how wide-ranging the environments are in which different bacteria can live, going through all that effort to see if the bacteria secrete any special substances that have a special effect on sheep red blood cells seems less than helpful. Okay, in fairness, when you’re dealing specifically with disease bacteria with the potential to possibly get into somebody’s bloodstream this test is useful, but in the entire population of all bacteria, this is a ridiculously tiny number of species.
And then there’s the terminology for this one – if the blood cells in the media are popped open but not totally destroyed (the media underneath will be greenish from the iron compounds released from the popped cells) it’s called “?-hemolytic”. If they ARE essentially totally destroyed (the media underneath the bacteria clears completely) it’s “?-hemolytic”. Not bad so far, but what if the bacteria doesn’t visibly destroy the blood cells at all? Why, that’s “?-hemolytic”. No, not “non-hemolytic”, even though that’s what it means. And, no, I have no idea why this is. I’m glad whoever came up with this scheme wasn’t a legislator. Otherwise, people who were accused of being murderers but were proven to be innocent would be declared to have committed “?-homicide”…

Using these kinds of phenotypic tests does have some advantages – most of them have been around so long that they’ve been thoroughly tested, they’re usually pretty easy to do, and if you’re hiring people to do bacterial classification grunt-work, finding people who can handle “mix this stuff together and see if it gets clumpy” is easier and cheaper than finding people to do more complex molecular work. On the other hand, there are some major disadvantages.

Firstly, there doesn’t seem to be any publically-accessible data repository with useful information of this kind that I’ve been able to find, unlike, say, the genetic data readily accessible at Genbank or the RDP-II. Sure, you can sometimes find some of this kind of data in papers describing specific species or strains, but to use this kind of information you have to already have a good idea of what your microbe might be – you can’t just plug “it ‘ferments’ lactose, sucrose, and xylitol, but not sorbitol or fructose, it’s catalase-negative, liquifies gelatin, and grows happily even when there’s tetracycline in it’s culture media” into a decent online database anywhere that I’ve been able to find and get a listing of known possibilities.

The other problem is that a lot of these kinds of traits aren’t necessarily part of the bacterium’s own genome. Bacteria often inherit certain traits from “bonus” DNA that they can pick up from other bacteria (“plasmids”) or from a viral infection. Yes, bacteria can be infected by viruses. Resistance to antibiotics is commonly spread by plasmids (though not always – I seem to recall that Klebsiella pneumoniae, for example, has a penicillin-resistance ability that actually is part of its core genome.) A number of diseases are actually caused by bacteria getting infected with viruses. Maybe your case of Necrotizing Fasciitis isn’t because your Streptococcus pyogenes on your skin, but because your Strep. pyogenes is rabid

The most reliable way available to work out who a microbe is involves comparing versions of a gene that essentially is never moved around between different microbes, but all microbes have. For prokaryotes, the gene in question is the “16s small subunit ribosomal RNA” gene sequence – or just called “16s“. This is what the taxonomy you can find at NCBI for bacteria and archaea is based on.

You know, when I started this post, I was just going to say that I wanted to get a more intuitive understanding of prokaryotic taxonomic groups and to that end was going to put together some posts on particular types of bacteria and archaea. I hope all the “bonus” background that seems to have come pouring forth from my overheated mind is useful.

Anyway, stay tuned this weekend for a post on firmicutes at some point.

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The Author is (currently) an autodidactic student of Industrial and Environmental microbiology, who is sick of people assuming all microbiology should be medical in nature, and who would really like to be allowed to go to graduate school one of these days now that he's finished his BS in Microbiology (with a bonus AS in Chemistry). He also enjoys exploring the Big Room (the one with the really high blue ceiling and big light that tracks from one side to the other every day) and looking at its contents from unusual mental angles.

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