I think is very dificult because the porcentage are similar what kind bacteria are) gram positive or Gram negative, of course I belived are bacills Gram positive

Did you grow using the same conditions (media, temperature, incubation time)?

Yes I grew them in the same conditions and they are Gram negative!! does it help?

Although I do not directly work with lipid profiles in bacteria, I have a had considerable interest in it for several years. First, I agree with André above that it is crucial that the bacteria are grown under identical conditions. Lower temperatures often leads to production of more unsaturated fatty acids int eh membrane to keep the fluidity up. Media and growth phase can also make the profiles change. On the other hand, it is not uncommon that he saturation level of the fatty acids are the same (based on similar growth conditions), while the chain length is different (which is more of a strain/species variation resulting from the fatty acid biosynthesis pathways of the bacteria). The latter can be really interesting, suggesting a completely different composition of the fatty acids associated with the membrane and you may well want to expand the studies to look at what head groups they are attached to and what types of lipids are there (cardiolipin, phosphoglycerol, phosphoetnaolamine etc). That could be very informative.

Although they are from the same species and grown under identical conditions, genotypically they are not identical. May be you have to sequence both strains.

Thanks Anders, i'll check again my data but for sure i have around 70% saturated fatty acids and 30% unsaturated fatty acids, and also the growth phase (but i'm pretty sure to have collected the cells at the end of the exponential phase), the temperature is 30 degrees.

Also, how i can figure out what types of lipids are they? it's a bit out off my knowledge.

It is a bitt out of my knowledge too. I know you can look at the different classes of lipids by TLC and you can determine phospholipid content by 32P-labeling of the lipids, but there may well be better ways. One old example of characterization of these lipids can be found in Trombe MC, Laneelle MA, Laneelle G (1979) Lipid composition of aminopterin-resistant and sensitive strains of Streptococcus pneumoniae. Effect of aminopterin inhibition. Biochim Biophys Acta 574: 290-300.

the ratio saturation/unsaturation (S/U) tells you something about the fluidity of the membrane, as both were grown under the same conditions (temp) it indicates that both have the same ratio S/U to keep the membrane in a functional fluid state. The length of the FA species differs apparently which probably reflects differences in the genotype of the two strains. Length of FA is less important for fluidity. A headgroup analysis would also help to see if the strains differ further.

Calculation of saturated and unsaturated fat is based on proportionality between the total area of ​​peaks of fatty acids identified in the chromatogram. Thus the referred situation could occur if an imbalance exist between the amount of fatty acids identified in each sample.

Your question touches on the unresolved issue of what is the boundary of a species (remember there is no general universally agreed definition), so two isolates can be quite different while classified being blonging to the same species, e.g., by 16S rRNA sequence; I have observed with strains having above 99% similar 16S rRNA sequence similarity quite different amount of lipds as well as cell wall) Different strains can have different total amounts of lipids while the ratio is the same. Small differences in the regulation of lipid anabolism/metabolism can change significantly the total amount of lipids. Taking in account the variability of the lipids by growth conditions -- some times minor differences, such as cell size different doubling times so the growth phase is different etc.)

In short: I would not put too much emphasis on your observation, except the lipids play a major role in your research project. In that case: First I would carefully repeat the experiment, i.e., lipid analysis under strictly controlled growth conditions ( e.g., same protein content / cell numbers at harvesting, check microscopically size and morphology while doing a growth curve, etc.)