I am trying to calculate the growth rate of F. succinogenes from OD measures: can anyone tell me how to proceed: I tried to use GrowthRate software of Bellingham research institute but I had a problem with OD limit (1 is the limit). Is there any other software? If not what equation can I use to proceed?
Ines - see the attached file for an example of this I wrote down a while back...
Perhaps a more helpful/automatic file is attached here as well...
You can change any value in red font to achieve your desired situation.
There is a reason why an OD of 1 is the limit: for most cultures of bacteria the number of cells isn't proportional to the OD at this point. Depending on the species, the proportional relationship may not even hold beyond an OG of 0.4 or 0.5. I don't know if that's the case for your species.
I did find a paper which suggests that F. succinogenes hits late-log growth around an OD(645 nm) of 0.3 to 0.4. It's linked below.
http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2009.01565.x/full
Hello Ines,
From a theoretical point of view i recommend you to read the book "Brock: biology of microorganisms" is one of my favorites and I think all these concepts (growth rate, generation time, etc.), are well explained and you can find there the equations which are very easy to understand.
Then, I agree with Harry, depending on the species you can find some differences when you try to calculate all these parameters. It also depends on the culture conditions you are using. So, the best tips I can think about are:
1) use plate counting (and direct microscope counting if you have a Neubauer chamber), together with OD measurement to construct a valid growth curve. Make sure these results are reproducible.
2) if you change the experimental conditions I recommend you to get a new growth curve each time (I used several culture media during research and the growth rate was changed in almost any case).
3) when you take two points from your growth curve to calculate the growth rate make sure you are taking these point from the exponential phase.
I hope you find this helpful. Good luck!
Thank you guys i really find all your comments very useful.
Concerning the GrowthRate software of Bellingham research institute, i made two mistakes so i guess that why i had 1 as OD limit (i think it was an error message).
Actually, i had to replace , by . in my txt file for the program to read it
and second mistake, i should of eliminate all the 0 values and keep only the first one at T0. for exemple :
original corrected
Time OD Time OD
0 0,00 0 0,00
0,5 0,00 4,5 0,01
1,5 0,00 5,5 0,01
2,5 0,00 6,5 0,02
3,5 0,00 7,5 0,03
4,5 0,01
5,5 0,01
6,5 0,02
7,5 0,03
We've used GATHODE to analyse groth of K.pneumoniae in 96-well format (386-wells also possible). This python based software (free) was created for yeast's Growth Phenotyping Assay but working pretty well for other suspension cultures.
The non-linear relations of cell concentration and OD>0.4 could be corrected.
The raw OD600 data were obtained with TECAN plate reader and exported as tables in ASCII format. Analysis allow us to fit exp function and calculate doubling time, growth rate and lag time.
If you still interesting in this type of software please see attached article for details.
Article Protocols and Programs for High-Throughput Growth and Aging ...
by the way, same results could be obtained via transformation raw OD data in Magellan software from TECAN. First transform OD dynamics to LN(OD). Calculate maximum linear slope and time of this. The time of reaching 5-10 % LN(OD) give us same to lag time data.
We've tested this approach on couple computers, but Magellan software calculate transformation very slow.
I enthousistically recommend the GROWTHRATES software.
The publication
doi:10.1093/molbev/mst187.
growth rates made easy
Hall BG
The software
https://sourceforge.net/projects/growthrates/files/
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