“Top Ten Favorite Microbes” proto-meme…

Dr. Joseph over on the “(It’s a…) Micro World (…after all)” blog posted a list of his ten favorite microbes. After showing up in the comments of his post and being a wiseass about E.coli and Gram staining, the least I can do is participate here. Besides, it’s a great idea. Therefore here are ten of my current favorite microbes:

  • Clostridium acetobutylicum, which is a (perhaps even “the”) classical Industrial Microbiology bacterium, used to produce butanol and acetone. After years of getting forced out by processes for making butanol from oil instead, this critter is starting to get some renewed attention, since butanol can be used for automotive fuels directly in place of or mixed with normal gasoline, unlike ethanol which needs special handling and engine modifications if you want to use more than about 10% of it in your gasoline.
  • Rhodopirellula baltica, because the Planctomycetes are nifty and wierd. They almost have organelles – their genetic material is wrapped in a membrane sort of like a eukaryotic nucleus. Some of them even have another separate membrane-enclosed part where funky things are done with nitrogen. Plus, they confirmed for me that I actually learned something in Microbial Genetics class when I read that R. baltica had 51 different ?-factors encoded in their genome and I understood what that meant…
  • Bacillus subtilis (“natto”) It forms endospores which can remain viable for a long time without any special storage requirements, can generate masses of useful snot made of glutamic acid chemically strung together (poly-?-glutamate), gets used for certain food fermentations, and possesses natural competence (the ability to take up and transform themselves with DNA from the outside world). What’s not to like?
  • Pseudomonas fluorescens because I’ve never entirely lost my childlike fascination with things that glow. Like the name implies, this bug (like other Pseudomonads) secretes an iron-gathering molecule that happens to be fluorescent. Of course, why settle for mere fluoresence when you can have:
  • Vibrio fischeri, which glows in the dark outright. The very first act of genetic engineering I ever did was in a biotech class, where we used bioluminescence genes from this organism to transform boring old E.coli into something that glows in the dark.
  • Saccharomyces cerevisiae, because brewing is probably the oldest industrial/intentional-food-microbiology organism by far. Between bread and beer, this yeast is arguably one of the keys to civilization…
  • Zygosaccharomyces bailii just because I’ve been wondering about the preservative action of benzoic acid and similar food additives, and Z.bailii is not only resistant to benzoic acid, but it appears that it may be able to eat benzoate outright[1]. And that’s just kind of nifty to me.
  • Trichosporonoides megachiliensis, the mold that seems to be at the center of production of my newest food-ingredient toy, Erythritol[3].
  • Aspergillus oryzae, a famous mold used for several food-related fermentations[2] (including the production of various types of jiu – the class of “alcoholic rice-based beverages” to which sake belongs) and the production of a number of useful enzymes.
  • Gluconobacter oxydans, for the production of vinegar as well as gluconic acid, the latter of which I’d like to try making myself someday for my own food or beverage purposes.


In case anyone objects to the inclusion of two molds as “microbes”, here are a couple of honest-to-Woese prokaryotes you can put in their place:

  • Lactobacillus delbrueckii, a classic lactic-acid producing “yogurt” bacterium
  • Pediococcus damnosus, another lactic acid bacterium, responsible for undesirable “ropiness” of wine (wine snot) but on the other hand for desirable flavor and “mouth-feel” characteristics of wild-fermented Belgian lambic ales (and, I seem to recall, aspects of the flavors of some cheeses).

And if anyone objects to having freakish eukaryotes in this list at all, let me know and I’m sure I can easily come up with two more normal organisms (i.e. prokaryotes) to replace the two yeasts, too. I haven’t even touched the Archaea in this list yet, nor the electricity-breathing Geobacter or Geothrix, or….well, lots of others, really.

Oh, and Happy Thanksgiving, y’all.

[1] Mollapour M, Piper PW:”The ZbYME2 gene from the food spoilage yeast Zygosaccharomyces bailii confers not only YME2 functions in Saccharomyces cerevisiae, but also the capacity for
catabolism of sorbate and benzoate, two major weak organic acid preservatives.”; Mol Microbiol. 2001 Nov;42(4):919-30.

[2] US EPA:”Aspergillus oryzae Final Risk Assessment” http://www.epa.gov/biotech_rule/pubs/fra/fra007.htm (last accessed 2008-11-26)

[3] US FDA:”Agency Reponse Letter: GRAS Notice No. GRN 000208″ (accessed 2008-11-26)

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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.

9 thoughts on ““Top Ten Favorite Microbes” proto-meme…”

  1. Nice list! It is amazing — to me at least — how cyclical science can sometimes wind up being (case in point: C. acetobutylicum). The ANAMMOX bacteria (the Planctomycetes you mention) are indeed some nifty organisms, and we do some work with them in the center where I work.

    Your additional organisms made me realize I should have put Oenococcus oeni on my list. O. oeni, whose genome has been sequenced, plays a role in vinification (wine fermentation), used to cut down on acidity. It’s also resistant to high levels of ethanol, and has an interesting mutation system (or lack thereof — mutS and mutL are missing).

    Also, Geobacter rocks as well. I think it’d be cool to eventually power lawn lights in my yard using Geobacter.

  2. ARGH! I forgot all about malo-lactic fermentation (O.oeni among others)! I am filled with shame!

    The fact that microbes are so dang useful is what makes them so interesting to me. One flask full of culture and I am a Supreme Overlord over a population of billions! “Now, my minions! Ethanol! Bring me ethanol! AH, HA HA HA HA HA!”

  3. Here you go Epicanis!!
    [EDIT by Epicanis 20081204T2107-06: inserted an <img src=”http://www.brewerysouvenirs.co.uk/humptydumptybrewery/images/pumpclip%20christmas%20cheer.JPG” /> between the anchor tags so the image would show after all – thanks!]

  4. Thanks for the Christmas Cheer!

    Of course, now I’m all grumpy because wordpress kept mangling my HTML when I tried to insert the image into your comment. (DAMMIT WordPress, if I wanted “&amp;” instead of just “&” I would have typed “&amp;!” to begin with!)

    The Christmas Cheer is still pleasant anyway, though…

  5. Great list!
    Funny you should mention natto. My boss took the lab to a Japanese establishment that served natto so that we could try it. I just couldn’t bring myself to eat it because of the smell, but almost everyone who did eat it was not pleased with the taste or texture. However, one member of our lab loved it and ate almost all of it.

  6. Natto isn’t as bad as it sounds (or looks. or smells…). It’s way better than “rotted soybeans in bacteria-snot sauce” might be expected to. Definitely a rather, uh, “specialized” taste, but it’s worth trying at least once.

    (On a totally unrelated note: looks like a lot of microbiologists besides me avoid Microsoft platforms…)

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