Amateur Soap Microbiology and my new Friend

I thought soap was supposed to be *clean*!

lumpy yellow microbial colonies growing on the soap inside of a hand-soap dispenser
People usually assume soap gets rid of funky microbes that might grow on things, so I was very amused several months ago when I spotted something growing on top of the soap in one of the household hand-soap dispensers. As of today, it looks as pictured at left. That lumpy yellow and brown mass atop the the soap looked to me like some sort of soap-sodden mold, and have been saving the dispenser specifically in the hopes that someday I’d have a microscope and could take a look at it. Meanwhile, the mass spread, and slowly started releasing some kind of yellow pigment into the soap.

Incidentally, I kind of doubt this indicates some sort of failure on the part of the manufacturer of the soap. I don’t recall for certain, but I think I may have opened the dispenser at one point to transfer some of the soap to another nearly-empty dispenser. When the mass started growing originally, it was a single spot, which suggests a single spore or speck of dust floating in and landing on the surface. Hey, it happens. Anyway, I’ve therefore blanked out the name of the manufacturer since I don’t think they really have anything to do with this.

VWR VistaVision Microscope
This mysterious growth upon my soap remained mysterious until today. Thanks to the Minister of Domestic Affairs and VWR (who managed to find me a really good deal), I finally got to actually get a close look at that lumpy mass. Meet my new friend Minnie (pictured at right). I could gaze into those eyes for hours. I couldn’t afford a darkfield condenser, and I sure as heck couldn’t afford to upgrade to phase-contrast gear, but I can add either one later if the opportunity presents itself. I also can’t afford the overpriced proprietary digital camera attachments either, though working around that is a whole other project. Until I identify an affordable model that plays well with Linux or work out how to modify a webcam into an ocular attachment,
I’ll have to settle for a trick…

It turns out if you take a digital camera and set it for close-up photos, you can actually stick the camera lens right up to the eyepiece and often get a serviceable picture.. Now, I had to subject the pictures I got today to moderately heavy processing to bring out the detail a bit better, but at least part of that is just me working on learning how to optimize the camera settings for this kind of use.

Equipped with some surplus slides and cover-slips donated by a kind professor who had some extra packages, I opened up the soap container and smeared a little of the yellow crud on a couple of them. One I just slapped a coverslip on for direct observation – the other I smeared over a slide and let dry with the intention of staining using the tiny, previously-unused vial of methylene blue left over from a very old plastic toy microscope. While the latter dried, I took a look at the wet mount hoping to finally see the mold mycelia that I had been expecting…

There wasn’t enough contrast to bother trying to get a photo, but it was obvious at 400x that what I was looking at was bacteria, not mold. Nerdly joy at learning something by looking in the microscope that I wouldn’t have otherwise known ensued, along with happiness as I realized this meant I had a perfect excuse to dig out my recent shipment from the Maker Shed – materials for doing a “Gram Stain”. Incidentally, the “Maker Shed” had the supplies on the way to me within hours of my ordering it, and they have lots and lots of cool stuff. I highly recommend it. Anyway, I got to do a “Gram Stain” for the first time in a couple of years (and the first time ever outside of a school lab). Want to see?

Mystery Microbe, I see you!

Gram-stained bacteria
Here it is – the nasty yellow goo that infected my bottle of hand-soap. My staining technique was a little off since I’m out of practice – the way I interpret the results is that what I’ve got here is neither a member of the Firmicutes (i.e. “Gram positive”) nor – probably – Actinobacteria. I really can’t guess at more than that, though. I think the few “Gram-positive”-looking cells there are artifacts of insufficient decolorization. I know I still had a surplus of the purple “Crystal Violet” stain still on the slide at the end. (How did I know? I’ll show you at the end…). The irregular bluish bits towards the bottom are, I believe, just bits of stuff from the soap itself.

Meanwhile, this pretty much satisfies my curiousity about the Mystery Soap-Infecting Microbe. There’s certainly a lot more I could investigate, but my developing Hillbilly Biotech lab is really intended to support my interest in intentional food microbiology and perhaps evenutally some small-scale non-food industrial microbiology. I have some remaining curiousity about the yellow pigment and whether or not it might be useful for something, but I’m doubting there is any food or beverage I might want to grow this stuff in and therefore don’t have much use for it. Still, I’ll keep the bottle around for a while before I throw it out in case I think of something fun to do with it. If I end up being really interested in the identity of the bug growing on it, I should be able to find a liquid that I can grow a big mess of it in, then run it through a simple DNA extraction process. Then all I need to do is find someone who can supply PCR primers, a thermocycler, and sequencing services cheap. It might sound like I’m being facetious, but I wouldn’t be surprised these days if I manage to find somewhere that’d do it for $20/sample or less. I may eventually do this will the Mystery Soap Bug anyway, since I hope to be running through this process with cultures of sourdough, yogurt, cheese, vinegar, and brewing microbes that I develop myself. For now, though, it’s just nice to be playing with microbiology equipment again. And now fully independently! Wheeeeeeee!!!!!!

Yes, I’m a nerd. And proud of it!

What’s next?

Now that I finally have a microscope, I no longer have any excuse for not getting to work on the rest of my Hillbilly Biotech lab. Just this weekend I was pricing out Hillbilly Autoclaves. I picked up a cheap air pump and air stone
for potentially building an aerobic bubble-column fermenter (for quick growth of yeast starters or a working model of a “Fring’s Acetator®”-style vinegar generator. I still want to build an ozone generator for sanitization and to get a pH meter. I’d like to also get my hands on some wheat, barley, and rye seeds to sanitize, sprout, and grow here as the first stage of developing a truly local sourdough culture, plus arrange to have several pounds of plain flour irradiated to sterilize it.

I’m also like summer to be over. Yes, I’m writing this in Winter, but it’s not until later in the summer to autumn that locally-grown fruits will start becoming available, and locally grown fruits ought to be an ideal source of local brewing and baking yeasts and bacteria. Finally, I’d like to find a wealthy patron (or matron, I’m no sexist…) who would sponsor me so I could just pursue food-microbe bioprospecting and research full-time…

Oh, yes, and I need to get around to finishing Episode 4 of my little podcast project, especially since episode 4’s topic is a fundamental microbiology technique.

Comments welcome below – thanks for reading!

Oh, and as a reward for getting all the way to the end, here’s a picture that I thought was pretty – crystals of “Crystal Violet” and iodine. I told you I had too much left on the slide…
Crystallized dye left on the slide

Nerd Reading Spasm!

Did I mention the place I work has some amazingly spiffy perks for a nerd like me?

Last night, I was poking around pubmed looking for references to yeast and erythritol (namely, do yeast interact with it, and will they metabolize it?) I found precisely one relevant reference. From 1975. In a Czechoslavokian microbiology journal. A no-longer-existent Czechoslovakian microbiology journal. Even though it was a journal published in English, I didn’t figure I’d be able to find the article I was looking for. It did turn out that the greedy (insert long string of profanity here) anti-open-access “SpringerLink®” Netherlands organization has an electronic copy of the article…which I can get limited access to for a short time for a mere $34.00. Not going to happen, obviously.

Just in case the college had a subscription that would let me get to the article at no extra cost, I checked. No such luck. But…

…The campus medical science library just two buildings over from where I work has dead-tree editions of essentially the entire journal! Im name des Nudelmonster! Instead of paying $34.00, I got a photocopy of the article for about $0.50. Bonus: As I had hoped, the article[1] reports that erythritol is not metabolized by yeasts, although it is taken up to a small extent. That means I can add erythritol (or xylitol or sorbitol or whatever) to must or wort, and it’ll still be there when the yeast finish, leaving the resulting beverage still sweet. Hooray!

Plus, I was also able to get access to an electronic copy of a review of the uses of poly-?-glutamate[2], which I was bemoaning not having access to over on an interesting Small Things Considered post recently.

Speaking of reading, one thing I really could use are any worthwhile books on the general subject of applied/industrial microbiology, bioprocess engineering, fermentation, and so on. “Worthwhile” here means practical texts that are A)primarily about microbiological processes (as opposed to, say, bioengineering of plants) B)Reasonably technical, and C)Either “not very old” or “very old indeed” (I collect old science books).

I’m not a fan of’s abuses of the patent system, but I’m in a hurry since it’s past my bedtime already. Therefore, purely as a sampling of the kinds of books that sounded interesting to me, here is a selection in more or less random order of books that came up in a quick search on Anybody out there have any other suggestions?

Continue reading Nerd Reading Spasm!

I Hate You, Carl Zimmer!

Carl Zimmer wrote a book. Of course, that’s no reason to hate him, and I don’t hate him for that.

His book is all about Escherichia coli (“E.coli”). The friggin’ “Microsoft” of the biotech world. Accursed E. coli, hogging up all the print space and protocol development and sucking up electricity for -80°F freezers. I mean, come on people! You could be doing transformation of B. subtilis and related organisms instead, which form nice, sturdy endospores which you can dry out and keep in an any cool, dry place, no -80°F freezer needed! Or you could use something like Agrobacterium tumefaciens, and as a bonus be able to then transfer your nice transformed genes into plants, too! But NOOOOOooo….it’s always “E.coli, E.coli, E.coli.” DAMN YOU, E.COLI!

Of course, none of that is Carl Zimmer’s fault, either, so this is also no reason to hate him.

Now, if his book was lousy, that MIGHT be a reason to hate him, but as far as I can tell there’s no reason to think the book is lousy, so this is no reason to hate him either. In fact, that’s kind of the problem.

No, the reason I Hate Carl Zimmer is that he’s written a book about friggin’, stage-hogging E.coli…and I want it. (Well, a copy of it anyway.) It sounds like a very interesting book. I feel like a Republican who wants a copy of “The Audacity of Hope”. Or a Democrat who wants to plan a vacation to visit the George W. Bush Presidential Library. The cognitive dissonance torments me, and it’s all Carl Zimmer’s fault! CURSE YOU CARL ZIMMER!

Okay, got that out of my system. A review might follow eventually if I manage to get a copy of the book. Meanwhile, for a change of pace, anybody want to hear about my Asterisk setup? Or should I just get back to the fermentation stuff?

P.S. Here’s a bit of trivia for you: “Frig” is apparently an old-English word meaning “to wiggle”…

What really counts as a “microbe”?

Just a brief pre-post before the main one I’ve got brewing now (which will be posted either later today or tomorrow).

A tapeworm: Since when does 30-36 feet long count as 'micro'???Microbiology is the dominating topic of this particular blog, but I don’t think I’ve ever addressed what I consider to really count as “micro”biology. This isn’t necessarily an obvious topic. My old “Microbiology” book from 8 years ago, plus the textbook from last year’s “Pathogenic Microbiology” class both contained large sections discussing organisms that are visible without a microscope. Heck, the “Pathogenic Microbiology” text even had a whole section on spider and insect bites. And, tapeworms? Since when is “over 30 feet long” considered “micro”? As I like to say: It’s time for Microbiology to grow up and move out of Medicine’s basement.

So: Here are the defining features of what I consider to be a “microbe”, at least for purposes of what I tend to discuss here on the blog:

  • Obvious: the organism cannot be effectively examined visually without a microscope and individual organisms can virtually never be observed by the “naked eye”.
  • In nature, a full normal population of a microbe can and will develop from a single live cell, and isolated individual cells are reasonably commonly observed.
  • Microbes do not “eat”.

It’s that last point that prompted me to write this post, mainly because it’s such an important part of why microbes work and how they affect their surroundings, especially when it comes to food microbes. What I mean by “do not eat” is that they are incapable of taking large (microbially speaking) chunks of material into themselves to use. Any cell nutrient for a microbe must be in the form of small molecules, like sugars, small peptides or individual amino acids, and so on that can be easily transported across the cell membranes and through the cell wall where applicable.

The importance of this is that for a microbe to grow on a complicated substance like meat or bread (for example), they have to excrete specialized enzymes that break down the substances out in the environment into simpler components like sugars or small peptides. If a microbe cannot secrete a protein-digesting “protease” enzyme, it can be surrounded by tasty, nutritious proteins and still starve to death. If a microbe can’t secrete an amylase (starch-digesting) enzyme, it doesn’t matter that starch is made of nice yummy glucose molecules because they’re all wadded up into long chains of starch that the microbe can’t get at.

And that, finally, is important because it brings up issues of growing multiple microbes together to accomplish something. Sake, for example, is made by fermenting rice, but rice is made primarily of starch. Saccharomyces yeasts don’t make amylases, so in order to make sake, you also have to add a kind of mold (Aspergillus oryzae, one of the types of white-mold-with-little-black-specks that you may see growing on the bread you’ve left sitting around for too long). A. oryzae is also a microbe and therefore can’t “eat”, but it does produce amylase. Since the amylase is breaking down the starches outside of the cells, this means the released glucose is also available for the yeast to use.

Admittedly, my definition above isn’t perfect. On the one hand, it leaves out protozoa (like amoebae and the well-known Paramecium, both of which actually do take in “chunks” of food, but both of which most people would normally consider to be “microbes”. It also leaves IN things like mushrooms, which are not usually thought of as being “microbes” by people who aren’t microbiologists. And, of course, it leaves me with no excuse not to go and learn something about eukaryotic (“plant”) algae (as opposed to bacteria-algae, a.k.a. cyanobacteria) and diatoms. Suggestions for updating my definition may be left in the comments…

Just something that came up while I was assembling what will be the next post. Stay tuned.