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Help identifying an unknown culture without sequence (student)

isolate unknown microbiology

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#1 mrodom

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Posted 25 November 2013 - 06:17 AM

Hello,

I am hoping some people with more experience than me can point me in the right direction for identifying an isolate. I am a student performing research and have been collecting data on an isolate throughout the quarter, however sequencing was unfortunatly unsuccessful and I do not have time to redo it before the end of the quarter. So, I am hoping that someone can suggest a broad category my isolate may fit into based on the information I have, or perhaps point me to a resource.

Here is the information that I have

Origin: Soil at the edge of a duck pond, located on a horse farm in western Washington state

 

Colonies: Colonies are bright, highlighter pink. Circular with entire margins. Somewhat shiny and slightly translucent. Fairly flat. Fairly consistent size, ~1mm diameter. No distinct scent that I could detect.

 

Cellular morphology: Gram positive cocci. Seem to appear in clumps. There is an interesting "pea pod" structure around some of them where there is a gram-negative staining envelope structure containing 4-6 cells.

 

Aerobic, non-motile. Uses respiration to metabolize sugars. The cells did not grow very well in my metabolism assay, but it appears to be able to metabolize starch, glucose, maltose, sucrose and fructose. And not citrate, lactose, sodium pyruvate or amino acids. It did not show any signs of fermentation of CO2 production.

 

Thank you very much, any suggestions are welcome.



#2 bob1

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Posted 25 November 2013 - 11:59 AM

Capsule stain?

 

If it is highlighter pink - there could be some interesting fluorescent genes in there - potential commercial opportunity.



#3 El Crazy Xabi

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Posted 25 November 2013 - 08:08 PM

Have you performed the classical biochemical tests?

 

If you use the API Biomerieux strips guides you may get a potential ID based on that, though I don't know if you can get them without purchasing the strips.

 

By the way, whenever you describe colonies specify culture conditions and medium. Most bugs change the colony morphology under different conditions, especially in different media



#4 Phil Geis

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Posted 26 November 2013 - 05:39 AM

Rather than shooting in the dark (esp. with API) - suggest you get Bergey's Determinative Manual.  Be a microbiologist.



#5 pito

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Posted 26 November 2013 - 07:29 AM

Check the attachement.

 

I am pretty sure I already posted this here somewhere.

 

Attached Files


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#6 Phil Geis

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Posted 26 November 2013 - 08:35 AM

Thanks Pito - could you post all the groups (esp. > 21)?  As described this isolate may not fall into any of those in the attachment..



#7 pito

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Posted 26 November 2013 - 08:37 AM

Thanks Pito - could you post all the groups (esp. > 21)?  As described this isolate may not fall into any of those in the attachment..

I dont have flow charts for all the groups, just these ones.

Perhaps somewhere, stucked away I have some of the others, but not sure.


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#8 pito

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Posted 26 November 2013 - 08:48 AM

This is also a very usefull book:

Aerobic Bacteriology, and check chapter 3.18

 

also: http://www.med.wayne... Flow Chart.pdf

and: http://www.nebraskam...p/GuideBook.pdf

for some general flowcharts.

Of course, not complete etc but it should do the trick for most students identification problems

 

 

Attached Files


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#9 Phil Geis

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Posted 26 November 2013 - 11:46 AM

Pito - these are probably not useful.  This is not a clinical isolate and by source and morphology is very unlikely to be identified as one. 

 

 

mrodom - suggest you look at the full manual identified by Pito - esp. Groups 21-35.

http://www.barnesand...holt/1100538624



#10 pito

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Posted 26 November 2013 - 11:52 AM

Pito - these are probably not useful.  This is not a clinical isolate and by source and morphology is very unlikely to be identified as one. 

 

 

mrodom - suggest you look at the full manual identified by Pito - esp. Groups 21-35.

http://www.barnesand...holt/1100538624

I know, but I doubt he has access to the full book.

 

And since he is a student, I would find it weird that its not a standard one....

But I have not checked his post in detail anyway so my posts might indeed not be very helpfull, but you never know.


If you don't know it, then ask it! Better to ask and look foolish to some than not ask and stay stupid.


#11 Phil Geis

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Posted 26 November 2013 - 12:29 PM

Isolate appears to be environmental rather than clinical -  reportedly from a pond,  colonies "bright, highlighter pink" and cells apparently sheathed.







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