Batch cultures of Lactococcus lactis NCDO 2118 and IL 1403 were performed in a Couette bioreactor operated in the modulated wavy vortex flow and the turbulent regimes. This study provides an overall analysis taking into account both mechanical stress and mixing in a Couette bioreactor. A unique phenotypic aspect has been proved to occur only in the modulated wavy vortex flow regime for the two studied strains, namely that the cells become entrapped in a filamentous form. No change in the metabolic behavior of the cells has been observed. The polymeric matrix has been microscopically observed through FISH and fluorescent lectin binding, showing cells entrapped in a glycoconjugate matrix. All hypotheses regarding insufficient mixing as a cause of this phenotype have been discarded, leading to the conclusion that this particular phenotypic feature is essentially due a combined effect of mechanical stress and flow structure. Particle size measurement during the fermentation course indicates that formation of filamentous form results from a continuous aggregation started in the early stages of the cultivation. According to our results a minimum shear is required to induce the ability for cells to aggregate. Then, it appears that both flow structure and mechanical stress (shear) are responsible for the appearance of such a filamentous form. As far as the authors know, this is the first experimental evidence of a bio polymerization induced by the flow structure. Biotechnol. Bioeng. 2011;108: 559-571. (C) 2010 Wiley Periodicals, Inc.