Tuesday, November 25, 2008

Top Ten Favorite Microbes

In browsing the comment fields of my blog entries, I came across a comment by Rhea, blogger of The Apprenticing Lab Rat that got me thinking.

What are my favorite microbes?

So, I put my thinking cap on, and came up with the following list of my ...

Top Ten Favorite Microbes.

10. Nitrosomonas eutropha - I suppose you could put N. europaea here in this spot as well, they're very closely related. They make up one lineage of the Nitrosomonas genus, which happens to be the lineage you're most likely to find growing in wastewater treatment plants. This genus is also one of two major players (along with Nitrosococcus) in the first phase of ammonia oxidation, which sees the conversion of ammonia to nitrite, a necessary step in the Nitrogen Cycle.

9. Yersinia pestis - Any bug which can pretty much singlehandedly be responsible for what people would forever refer to as the "Black Death" gets my attention and respect.

8. Comamonas badia - Not an organism most people are going to have heard about, though I've blogged about it before. Nothing particularly exciting about this organism other than the fact that it forms flocs. Flocs are useful for wastewater treatment systems as it provides a matrix for organisms to grow on ... call them floating biofilms. If the flocs are of the right composition, they will settle out rapidly, a feature necessary for producing a quality effluent. It's on my list because in some of our genetic characterization studies, we've seen a relative of this organism but have yet to isolate it. I like challenges!

7. Escherichia coli - Come on, Who doesn't like E. coli? Of course, for the purposes of this question, we're excluding those individuals who are currently tied up with a bout of the Aztec two-step. For any gene jockey E. coli is an essential tool for cloning purposes. Heck, I even used E. coli for triparental matings way back when.

6. Legionella - How many organisms do you know that can spread through an air-conditioning system? I know of one in particular, and this one is it.

5. Pseudomonas aeruginosa - As a clinical microbiologist, P. aeruginosa is one of those organisms that is very easy to identify. If it smells like Welch's grape juice, it's P. aeruginosa. That, and it fluoresces. It does have this nasty habit of being very harmful to burn victims though. The damn bug grows just about everywhere, and is a friggin pain in the posterior to eradicate from a system once it takes root.

4. Borrelia burgdorferi - Say that fives times real fast. I've never had Lyme disease, and I never want to either. Spirochetes look cool too.

3. Vibrio cholerae - Two words for you: rice-water stool. Some things/phrases stick with you forever, and those two words are one such phrase I will never forget. I've also always been fascinated with quorum sensing, and this organism along with other Vibrio species, has seen the lion share of such research. V. cholerae was also responsible for helping Robert Koch refine his postulates, as well as bringing about the birth of epidemiology (see John Snow).

2. Neisseria gonorrhoeae - Spent more time working on this organism than any other. It's an exquisite organism, being an obligate human pathogen it has no vector and must rely on one of the few activities that most humans have a proclivity for -- sex -- for transmission. There is a documented case of fomite transmission as well.I crack up everytime I see that. The actual letter ... is a bit disgusting when you read it.

1. Deinococcus radiodurans - The coolest of the cool. Any organism that can take dosages of radiation that would kill a human a couple hundred thousand times over is neat! Not that this organism evolved after Chernobyl. Instead, this "super power" is most likely the result of surviving dessicated environments. That is why this xerophile (arid condition surviving organism) is at the top of my list! All extremophiles rock by the way!

So, what are some of the favorites of everyone else? Hmmm, should I make this a meme?


microbiologist xx said...

Yes! Deinococcus radiodurans IS freaking cool. It would be on my list for sure, along with some spore-formers.

Tom said...

You better put a list together!

Ivan Privaci said...

"Come on, Who doesn't like E. coli?"
ME. I've said it before and I'll say it again - Escherichia coli is The "Microsoft" of the biotech world (and that's not meant to be a compliment, if that's not obvious...) It's only gotten where it is because of the underhanded efforts of γ-proteobacterial supremacists. Bunch of anti-firmicutesites!

Tom said...

Heh. I did notice that I was a bit biased towards Gram negatives in my list (8 out of 10).

Ivan Privaci said...

My next "microbiology microlecture" may have to be on the subject of prokaryotic taxonomy (where I can continue my hobby-crusade against virtually-useless Gram-stain-based taxonomic schemes..."Microbiology needs to grow up and move out of Medicine's basement.")

Speaking of which, your list was also entirely prokaryotes - not that I disapprove of this, being the self-proclaimed Glorious Leader of the Prokaryote Anti-Defamation League.

Still, my own list will have a few of those freakish eukaryotes on it, too. I get away with this by telling myself that a eukaryotic cell is just a well-established prokaryote commune.

Tom said...

I'm not sure what you mean by Gram-stain-based taxonomic schemes. We're doing some taxonomy on some new strains here in my lab and the "golden standards" for identifying novel species are DNA:DNA hybridization, FAME analysis, and respiratory isoprenoid quinone analysis.

It just so happens that when you do 16S rRNA gene sequencing, Gram negative and Gram positive organisms form these nice monophyletic clades. Well, within their own phyla that is.

Or have I missed something? I am always the last to know ...

Ivan Privaci said...

I'm not sure you can properly use the term "monophyletic" for "Gram Negative". That's "Every phylum Besides the Firmicutes and Actinobacteria", right? (and not even Actinobacteria or the family (order?) of mollicutes in some contexts - most of the time I've run into people using "stain-based" taxonomy, they call the actinobacteria "acid-fast" rather than "High G+C Gram Positive"). I actually tend to think of the Gram Stain as merely a presumptive test for the phylum Firmicutes. All the Gram Stain really tells you is whether your subject organism has a cell wall that is unusually impermeable to your decolorizing solvent or not.

Bear in mind that this really is a "Hobby" crusade of mine and not intended to be taken too seriously.
*(Oh, and I am realizing it may not be obvious that I wasn't suggesting that you needed to be lectured at, either - especially not by the likes of me. I've just been doing some audio recordings for mental exercise recently and I think bacterial taxonomy would be an interesting subject for one...)*

Aside from the amusement I derive from pretending to be horribly offended by the Gram Stain, the only real points behind it are:

#1) "Gram Negative", really, is only slightly more taxonomically useful in my opinion than saying "non-pathogenic" (i.e. they both mean "everything but a small minority of types of bacteria")

#2) I think the importance of "Gram Positivity" (whether that includes "acid-fast" or not) has been grossly inflated by the fact that microbiology even today gets treated too much as a subdiscipline of medicine, where for the most part nearly all of the "relevant" bacteria (the ones that cause diseases in humans and occasionally other food or pet species) really do fit in only three phyla: "Gram Positive" Firmicutes (anthrax, botulism, MRSA...), "Gram Negative" Proteobacteria (E.coli, gonorrhea, salmonella, cholera...), and occasionally the "Gram-biguous" actinobacteria (tuberculosis, "leprosy"...). Syphilis and chlamydia (very small populations within their respective phyla) are exceptions of course. Still, this view makes it easy to forget about all of the OTHER phyla, all of which are also technically "Gram negative".

I suppose it's not going to help my argument, though, when my "10 favorite microbes" list will have 2-4 "Gram Positive" firmicutes and 2 "Gram Negative" γ-proteobacteria disproportionately represented in it.

Tom said...

I couched my comment by saying they form "these" monophyletic clades ... implying multiple. ;)

From a Clinical Microbiology point of view however, this initial test is actually very helpful in a majority of cases. The Gram stain, most often coupled with site of isolation information, sets up your additional tests. Of course, this does merge with your ...

Point #2. I am faced with this issue daily as well. Now, I grew up in a medical microbiology environment, but I now have a much deeper appreciation for applied microbiological organisms and processes. Actually, this is a good idea for another blog post, however since most funding is driven by tax dollars, and people need to be alive to pay taxes ... you can see where the problem arises.

Anonymous said...

From a research PoV it makes sense that you have 8/10 gram (-) sited as rocking bugs...we know waaaay more about them. ( why is that? are gram (+) really that hard to study??)

ALSO...i met Charlie Calisher at the CDC a bit ago...he's been finding himself in VIRUS taxonomy lately. ew. So prop's to you two for being interested in such things...and he might have some interesting things to say about it if you have time to look him up.

I like your list...tho it is missing Listeria monocytogenes and H pylori. :P Good call on P. aeruginosa...fascinating booger with an arsenal of virulence factors. (Besides i'm doing my graduate work on it.)

Hope you are recovering from too much turkey!!

Tom said...

Listeria monocytogenes and H. pylori are both definitely cool bugs. They're probably in my top twenty. I'd also list the bugs my lab is currently in the process of characterizing (and naming) but I'm not sure I want to give up my pseudonymity (if it truly exists) just yet.

Thanksgiving went well. My sister is a great cook (even better than me), and all the wife and I had to do is drive there (I brought Jell-o though!).

BTW: You ARE going to put a list of your Top 10 bugs together, no?

Anonymous said...

This is an awesome meme. My picks

Anonymous said...

Yes. And it's beginning to catch on!! O.o

Tom said...

Nice picks Ed, you too Rhea. Actually, all the picks so far are definitely worthy candidates (can't think there'd actually be any bad candidates).

Unknown said...

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Anonymous said...

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