Microbial Identification software: SUMMARY

vernon VERNON at micro.uct.ac.za
Thu Feb 17 05:11:34 EST 1994


Dear Netters,

A couple of weeks ago I posted the following request:

> I was wondering whether any of you out there know of software (pc)
> which allows one to identify bacteria based on their physical and
> biochemical characteristics.  In other words, the software functions
> as a taxonomic key. I am interested in both commercial and shareware
> programs.  Any assistance in this regard will be much appreciated.

I was asked by a number of people to send them a summary of the
responses I received.  I have done so below.

However, to sum up what I have found, the program
MICRID and MICRIDX developed by Scott Kellogg has proved to be the
BEST microbial identification (free) software available.  The program
allows for the identification of over 1000 bacterial species, and
best of all, allows one to add their own custom made matrices
(derived from those in Bergey's Manual) which include the types of
bacteria you would be expecting to find in a given sample; ie. sea
water samples will include Aeromonads, Vibrio's, Pseudomonads, etc.
I have tested this program and have found it to be easy to use,
accurate, and extremely flexible.  I have the author's permission
to distribute the software if requested.  Thus, if you would like to try
MICRID then please send me an e-mail message and I will forward a zipped
copy to you.

The other program that I have tested is the CDC program called BACTID.  This
is easy to use, etc.  The only limitation is that it only identifies
clinicallly important Enterobacteria, and therefore, is not of use
to those of you who are wanting to identify environmental isolates.

-----------------------------------------------------------------------------
SUMMARY:
--------

Do you know the PC program developed at the CDC in Atlanta a couple
of years ago for the typification of Enterobacteria ?  It takes into
consideration the biochemical reactions and calculates the probability for
the isolate to meet the characteristics of the Enterobacteriacea on the
database.

If you need it, I possibly could zip, uuencode and send it by E-Mail.

Sincerely,

                        Claudio.


--------------------------------------------------------------
Dr. Claudio L. Stiebel (DVM)   | Departamento de Zoonosis
                               | Municipalidad de San Martin
HOME: +54 1 752-6647           | (133) Almeyra, N* 2399
WORK: +54 1 750-0202           | 1650 San Martin
E-MAIL: cls at mgsmdz.sld.ar      | ARGENTINA
--------------------------------------------------------------

----------------------------------------------------------------------

We described a program in Letters in Applied Microbiology 10:259
1990 to identify Lactic Acid Bacteria based on comparison of observed
characters with a data matrix. This could be modified to use any other
data matrix, if this is available - this in my experience is the
limiting factor is the use of computers in identification rather than
the program. Our program is available free on receipt of a floppy
disk, or could probably be sent by email.
Hope this is some use.

Best wishes
Raymond Cox
Biochemistry/Odense University/Denmark
fot at dou.dk<

----------------------------------------------------------------------


I have a bacteria/yeast computer identification system I wrote
several years ago (1434 species).  If you are interested email me and
I'll send you a zipped copy.


=========================================
Scott T. Kellogg, Dept. of Microbiol., Mol. Biol. & Biochem.
Univ. of Idaho, Moscow, ID 83843
Internet: kellogg at crow.csrv.uidaho.edu
Phone: 208-885K-6966      Fax: 208-885-6518

----------------------------------------------------------------------


Hi,

I just caught your note in bionet regarding software
for bacterial classification.

Dr. Dennis Lye of the Department of biology, Northern Kentucky
University, Highland Heights, KY  41099 USA has a user friendly
program that is used in undergraduate (biology majors and nursing
majors) microbiology classes.

It uses the application Hypercard, and is specifically for
MacIntosh computers. I think he is distributing it as freeware.
I've used it before, and it does a good job of getting
students to genus, - some to species. It is based on physical and
chemical characteristics typically performed in intro labs.

He is on sabbatical this year, but is on campus frequently.

The department phone number is
606-572-5110.

Good luck - hope this helps.

Melane Riedinger
Department of Biology
Northeastern Illinois University





More information about the Bio-soft mailing list