Aims: To apply a denaturing gradient gel electrophoretic (DGGE) method to quantify and profile individual strains during a mixed culture fermentation.

Methods and Results: DNA was extracted during the culture of lactic acid bacteria (LAB) and amplified in a multiple competitive PCR (cPCR) using general primers targeting 16S rDNA and DNA from Streptococcus salivarius as competitive DNA. Subsequently the 200‐kb amplified fragments were separated by DGGE. The method was validated in pure cultures and used to profile a mixture of three LAB grown on glucose, soluble starch and glycogen from mussel processing waste. The inclusion of a starch‐ and glycogen‐degrading strain (Lactobacillus plantarum) and a weakly amylotic nisin‐resistant strain (Lact. paracasei) allowed proliferation of the nisin producing Lactococcus lactis which in itself is unable to grow on complex carbohydrates. cPCR–DGGE permitted the monitoring of a different strain succession on the different carbohydrates, related to amylolytic activity and substrate consumption, acid production and nisin production.

Conclusions: cPCR–DGGE is a useful tool for profiling defined mixed cultures of bacteria and hence allows their interaction to be studied.

Significance and Impact of the Study: Provided validation of the method for each specific case, it may be appropriate to monitor and control the reproducibility of any defined mixed culture of bacteria, with the advantage that an increase in the strain numbers to be monitored does not yield an increase in the labour of the procedure.