Identification of a bacteria - How to determine wich bacteria you are working with (Mar/29/2009 )
Hallo all,
due to a recent topic here I was wondering how you would indentify what bacteria you are working with.
How would you start the proces ?
What tests would you do first?
What flowcharts would you use to determine wich bacteria it is?
(We all know that you can simply send a sample to some accredited lab where they can do a dna test or something to determine what it is, but not all of us can do this)
I have always had the luck to know what bacteria I was working with (havent worked with bacteria a lot though) but what if you havent got this luck.
We all know about Bergey's, but do we all know how to use this book? For someone who has never used it, it might seem difficult or even impossible to use it.
To be honest, I havent used it that many times and most of the times I know where to look because I allready had some help or info on the bacteria.
I once asked a teachter, who also worked in a microbiologylab how to really use the book and he couldnt give me a direct or easy answer 
I have always simply used the following flowcharts: flowcharts but havent really needed to determine something unknown and then looked it up at Bergey's.
pito on Mar 29 2009, 01:10 PM said:
due to a recent topic here I was wondering how you would indentify what bacteria you are working with.
How would you start the proces ?
What tests would you do first?
What flowcharts would you use to determine wich bacteria it is?
(We all know that you can simply send a sample to some accredited lab where they can do a dna test or something to determine what it is, but not all of us can do this)
I have always had the luck to know what bacteria I was working with (havent worked with bacteria a lot though) but what if you havent got this luck.
We all know about Bergey's, but do we all know how to use this book? For someone who has never used it, it might seem difficult or even impossible to use it.
To be honest, I havent used it that many times and most of the times I know where to look because I allready had some help or info on the bacteria.
I once asked a teachter, who also worked in a microbiologylab how to really use the book and he couldnt give me a direct or easy answer
I have always simply used the following flowcharts: flowcharts but havent really needed to determine something unknown and then looked it up at Bergey's.
I'm not a microbiologist but isn't it a bit outdated? I used this "Analytical Profile Index", a standardized, miniaturized version of all the enzymatic tests long time ago...easy but quite rough. Anyway today I'd look for a characteristic/unique DNA sequence for the bacteria and try to amplify it with a PCR.
hobglobin on Mar 29 2009, 01:23 PM said:
pito on Mar 29 2009, 01:10 PM said:
due to a recent topic here I was wondering how you would indentify what bacteria you are working with.
How would you start the proces ?
What tests would you do first?
What flowcharts would you use to determine wich bacteria it is?
(We all know that you can simply send a sample to some accredited lab where they can do a dna test or something to determine what it is, but not all of us can do this)
I have always had the luck to know what bacteria I was working with (havent worked with bacteria a lot though) but what if you havent got this luck.
We all know about Bergey's, but do we all know how to use this book? For someone who has never used it, it might seem difficult or even impossible to use it.
To be honest, I havent used it that many times and most of the times I know where to look because I allready had some help or info on the bacteria.
I once asked a teachter, who also worked in a microbiologylab how to really use the book and he couldnt give me a direct or easy answer
I have always simply used the following flowcharts: flowcharts but havent really needed to determine something unknown and then looked it up at Bergey's.
I'm not a microbiologist but isn't it a bit outdated? I used this "Analytical Profile Index", a standardized, miniaturized version of all the enzymatic tests long time ago...easy but quite rough. Anyway today I'd look for a characteristic/unique DNA sequence for the bacteria and try to amplify it with a PCR.
In general, I have to agree with you, but still: pcr isnt always possible in some labs (sounds strange I know, but still or they dont know how to work with the dna, pcr in general, dont have enough info on it or experience on using the dna profile).
The test (alanytic profile index) you speak of is also good, but sometimes just not good enough or not there to be used.
I know you are right , but still: sometimes its just not possible to use pcr, dna sequencing or the test.
(there are a lot of smaller labs that are still working with simple equipment and small funds)
I speak out of experience really. I was lucky to work with a fungus when I did my thesis and I knew with what I was working, but some other students did not have this luck and they had to find out what bacteria it was and they had no pcr to use (nor the info on it in general) and they did not have an test kit. They had to do some basic tests to look what it might be (gram staining, shape and some basic fermentation tests) and that was it.
You can always start by seeding on MacConkey agar plates and you'll know if its Gram-negative and if it can do lactose fermentation.
But if you've got the budget for it, use API or better yet, CHROMagar plates. They are amazing!!!!
Here are 3 examples for CHROMagar plates I found in google
