Stephen writes:

The formula for conversion of OD to E. coli cells per ml is essentially correct but based on incorrect assumptions.

“This calculator uses the extinction coefficients for E.coli and Yeast cultures to calculate the cell concentrations from the Optical Density (OD600) reading taken with a spectrophototometer”.

The majority of light generated by the spectrophotometer is not being absorbed by the yeast or bacteria BUT being scattered! It is incorrect to state that live or dead cells have an extinction coefficient when they are in the path of light with a wavelength of 600 nm.   Extinction coefficients are generated as the result of light absorption according to Beer’s law:” Beer’s Law states that molar absorptivity is constant (and the absorbance is proportional to concentration) for a given substance dissolved in a given solute and measured at a given wavelength.”

The other assumption that the calculator uses incorrectly is that the size of the cells is not accounted for….if E. coli is grown in an enriched culture medium e.g. Trypticase soy broth versus a minimal medium e.g. MOPS, the sizes of the cell are very different. Those cells grown in enriched medium are much bigger than those in minimal medium.  Thus there are distinct differences in the amount of light scattered I.e. depending on number and size of the cells.  In addition the amount of light scattered does not distinguish between intact live cells vs intact dead cells.

The more accurate way to use the calculator is to be sure to teach that the data generated should be made for each type of cell under specific growth conditions including the type of culture medium.  Moreover, the calculator is based on light scattering NOT extinction coefficients.


Stephen M Boyle

Emeritus Professor, Microbiology

Virginia Tech

Anthony writes:

Late last night in that little interval between exhaustion and sleep after showering, I take a cat for a little walk in the hallway,  I then sit on the steps with her for a few minutes.  My thoughts strayed to Chimpanzees, wondering how they bear a tropical climate without bathing.  Might there be something in their skin microbiome that naturally cleansed?  Might here be the means to wage war against MRSA, analogous to the Merck’s goldmine found just under the green of a Japanese golf course?

I’d forgotten my conversation with myself until you mentioned in TWiM 168 about the dairy farmers showering less a day.  Might the richness of their superficial flora extend past the nose?  Might that make less frequent bathing possible?


Answer… “Only in the last hundred years have we made bathing a daily practice. Are we overdoing it? According to Dr. Richard Gallo, chief of the dermatology division at the University of California, San Diego,“Good bacteria are educating your own skin cells to make your own antibiotics. . . and they produce their own antibiotics that kills off bad bacteria.” (NY Times “The Great Unwashed“)  Gallo believes showering not only removes lipids and oils that keep your skin from drying out, showering also removes some of the good bacteria.  Commensal skin bacteria as the probiotic of the cutaneous immune response, Expert Review of Dermatology, 5:3, 251-253, DOI: 10.1586/ edm.10.24

Anthony writes:

E. coli deaths from romaine contamination

Would rinsing help?

Shinichiro Enomoto writes:

Thank you for discussing our paper. I used to listen to TWIV and TWIM regularly when I had a long commute. I would have loved to hear Elio’s thoughts on our work. I am his fan and do not mean any disrespect towards Dickson. As per Dickson, we would love to know where Sodalis praecaptivus lives after injection.  

However, injection into the thoracic cavity is artificial and we don’t know the true lifestyle of the S. praecaptivus. With these caveats, I imagine that the bacteria live throughout the hemolymph, as I have recovered colonies from an amputated leg. We don’t know if they are intracellular, though we have preliminary data that suggests that the bacteria can survive for few days in mouse lymphocytes.

We regard the S. praecaptivus as a “protosymbiont” and consider it  ancestral to many of the insect symbionts.   The two relatively “young”  symbionts, S. glossinidius
(of tsetse fly) and Candidatus Sodalis peirantonious (of rice weevil) have different homes and lifestyles.  Ca S. pierantonius lives in bacteriomes, near the gut and near the ovaries, it is suspected that the one near the ovaries gets transmitted and one near the gut provides amino acids (

In contrast S. gossinidius, lives in the hemolymph and bacteriomes have not been detected. And this bacterium is facultative and has been cultured without the host.  Moreover it was recently shown that even paternal transmission can occur ( Given enough time, S. praecaptivus
appears capable of evolving into different lifestyles. But it is also possible that there are many protosymbionts that are already specialized towards different insect hosts.

Shin Enomoto