there are different methods used for extraction, the most prominent one is the use of polymerase chain reaction(PCR),Mass spectroscopy, Gas chromatograpy. sometimes gas chromatograpy with mass spectroscopy may be use for the extraction, this is known as rapid isolation method. this abstract may be useful for you perusal.

Rapid isolation method for lipopolysaccharide and lipid A from gram-negative bacteria.

Abstract

A fast, convenient extraction method for lipopolysaccharide (LPS), using a commercial RNA isolating reagent, allows the isolation of LPS or lipid A from low milligram (dry weight) quantities of bacterial cells. The method avoids the use of specialized equipment and has been used for processing relatively large numbers of samples. The major components of the commercial RNA isolating reagent, Tri-Reagent, are phenol and guanidinium thiocyanate in aqueous solution. The bacterial cell membranes are disrupted with guanidinium thiocyanate, which eliminates the need for mechanical cell disruption (e.g. French press) or heating. LPS and its degradation products, with particular attention paid to its bioactive lipid A portion, were measured and compared with those from the most common conventional extraction method, hot phenol-water. Negative ion quadrupole ion trap and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, fatty acid composition analysis by capillary gas chromatography, total and free phosphate by UV spectrophotometry and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) showed that LPS and lipid A isolated using the Tri-Reagent approach were cleaner and suffered less degradation through loss of phosphate and (or) fatty acyl side chains from lipid A. The Tri-Reagent extraction method generated low free phosphate contamination, 11% of the total phosphate concentration, whereas the hot phenol-water extraction method gave approximately 58% as free, inorganic phosphate. Similar results were observed for the degradation of fatty acyl side chains. The time required by the new method is considerably shorter (two or three days) than that required by conventional hot phenol-water extraction (about two weeks  

Normally one uses either phenol water or phenol chloroform extraction. I used to use phenol water, basically wash the cells with PBS, then resuspend in 55% phenol solution. Incubate at 70C for 15-30min, then centrifuged, and take the aqueous phase. and precipitate with NaAc and ethanol (some uses dialysis to get better purity). Then treat the samples with RNase and DNase, then again with proteinase K. I sometimes repeat the phenol water extraction to get better purity. However, this additional step tends to lose substantial amounts of material. 

Note that you can lose great deal of material if you are working with LPS that produces defective O antigen, they often get drag into the phenol phase due to the increase hydrophobicity. In that case, you will probably need to use a systemic extraction protocol. However, it will require special setup to do so. 

Phenol extraction method will be helpful to get LPS

@Yaoqin Do you have any information about the protein and RNA/DNA content in the extract (if so, how did you measure it? I checked and phenol has absorption peak at ~270nm) Does the remained phenol have any significant effect on the applied enzymes after NaAc precipitation? Thank you in advance!

Hi Yaoqin Hong, Can you share a step-wise protocol of LPS extraction from Gram Negative bacteria. I am planning extraction from Pasteurella multocida.