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. 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.
- Aspergillus oryzae, a famous mold used for several food-related fermentations (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.
 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.
 US EPA:”Aspergillus oryzae Final Risk Assessment” http://www.epa.gov/biotech_rule/pubs/fra/fra007.htm (last accessed 2008-11-26)
 US FDA:”Agency Reponse Letter: GRAS Notice No. GRN 000208″ (accessed 2008-11-26)