Offtopic - advice on identifying microorganisms?

[queuetue]

Hi. This isn't beer related, but I thought you might be able to point me in useful directions. When I'm not brewing beer, I'm do hobby experiments in environmental remediation. If this doesn't interest you, please skip the rest of this message, and sorry to take up your time.

Part of what I'd like to be able to do is identify and monitor populations of microorganisms (specific strains of Lactobacilli and Rhodopseudomonas). Unfortunately, I have no lab training at all, and am just looking for good sources to educate myself, determine what equipment I need, and establish controllable protocols.

If anyone has any advice for me, I'd appreciate it - I thought there might be a few amateur (or professional) microbiologists in here.

 

[scinerd3000]

do a google search for open source courses...MIT has some and i also believe harvard and carniage Melon (sp?).Free Online MIT Course Materials | Biology | MIT OpenCourseWare Where are you checking the populations? are you taking about in beer or on the outside or what?

Ive played around in microbiology however i would deffinitly recomend taking a course or two if they have a college in the area with a decent lab....it helps alot! If i remeber correctly, bacillus is gram + and rodshaped. Your probably going to need to make streakplates on agar to seperate colonies and you will need a microscope with a special slide (hemocytometer) to count individual bacterium....Your also going to need a gramstain kit. (4x stains)

 

[ryane]

What type of "home" enviro remediation are you trying to do?

I work in that field, in particular with Chlorinated DNAPLS, but I just cant think of what your trying to do at home

As far as taxonomy, thats tricky, especially at home, we can use clone libraries etc in the lab, youll have to rely on a microscope and that requires a lot of work, and even then you might not get it righ

 

[queuetue]

I'm well outside of the beer universe. Remediation is a bit of misnomer - I'm actually trying to measure the effects of Rhodopseudomonas palustris and various lactobacillii on crop production and gauging their long-term innoculation into the soil. In the short term, I wanted to measure the colony populations of various ferments of indigenous and effective microorganism serums - there's a lot of conflicting information with regard to preparation and I'd like to conduct my own tests.

It's disappointing to hear there isn't any shortcut for an amateur to identify specific strains. I was assuming at worst case, the process was going to involve agar plates and a microscope, but I'm not sure what type of microscope I should start with or which agar media to use for enrichment of specific organisms.

I know this is a long road of education - thanks for your time and whatever direction or resources you can offer.

 

[ryane]

its not that you cannot identify specific strains, its just that its very trick, and some things cannot be seen with a microscope that make a significant difference between strains, now you could probably get in the ballpark fairly easily though

I couldnt tell you which agar/nutrient broth to use, lacto/rhodo should be fairly easy to culture, but others may not culture at all, still its easy/cheap to do a few agars to try things out right? I mean you can even use gelatin/sucrose in a pinch to do this

Seems to be a pretty complex undertaking for home project, mind if I ask what you are trying to accomplish?

 

[menschmaschine]

To see many types of bacteria, you need a microscope that can go to 1000X and do oil immersion. You'll also need a gram stain kit to aid in identification. I've seen lactobacilli at 400X, but they were tiny and difficult to see. If you want to take photos, you need a microscope with micrographing capabilities. Check out Cynmar.com. They should have everything you need.

If you have a science background, then learning lab techniques won't be all that difficult. If not, in addition to microbiology, cell biology might be a good study for you.

 

[BigWhitey_FrostBox]

I recently read a text book called "Brewing Microbioolgy" link which went into some detail about the classification and identification of lactobacillus.

Companies make commercial media for the isolation of these organisms. This selective/ differential media will make it easier to isolate specific colony types. Once you have pure colonies you can use a quick panel of differential media to help you identify the bacteria. In my lab we work with food-borne bacteria and use panels made by Biomerieux (API20E) link. They make a number of panels for the identification of bacteria. As others have mentioned, a microscope and gram stain kit will also come in very handy for the isolation of the bacteria. Good luck, lab supplies and media are expensive

 

[Dr_Deathweed]

It's disappointing to hear there isn't any shortcut for an amateur to identify specific strains. I was assuming at worst case, the process was going to involve agar plates and a microscope, but I'm not sure what type of microscope I should start with or which agar media to use for enrichment of specific organisms.

I know this is a long road of education - thanks for your time and whatever direction or resources you can offer.

This really will not help you unless your garage is a lot cooler than mine, but if you are just looking to identify the presence of certain bacterium, developing a RT-PCR protocol would probably be the easiest, but would not quantify populations in samples. You can always use various media tests to help narrow your populations down, but this is very tedious and involved, and requires culture isolation and purification to be effective.

Microscope and a few staining protocols (grams, acid-fast, etc.) may get you in the ballpark (down to genus), but identifying specific species or serovars requires either PCR or selective culture media. I would HIGHLY recommend getting in contact with a microbiologist if you are interested in this project and are pursuing it on your own. If you are looking at writing it up to be published you will really need their help to develop protocols to make sure that your research is valid.