The epithelia of the intestine perform various functions, playing a crucial role in providing a physical barrier and an innate immune defence against infections. Creating a 3D model of cell co-cultures established with IPEC-J2 cell line and porcine blood monocyte-derived macrophages (MDMs), we are getting closer to mirroring the porcine intestine ex vivo. The effect of Limosilactobacillus reuteri B1/1 and Limosilactobacillus fermentum CCM 7158 on relative gene expression of interleukins (IL-1β, IL-6, IL-8, IL-18 and IL-10), genes encoding receptors for TLR4 and TLR2, tight junction proteins as claudin-1 (CLDN1), occludin (OCLN) and important antimicrobial proteins as lumican (LUM) and olfactomedin-4 (OLMF-4) was monitored in this model. The immunomodulatory potential of newly isolated L. reuteri B1/1 was confirmed as was able to suppress the enhanced pro-inflammatory response to LPS induction in both cell types. L. reuteriB1/1 was even able to up-regulate the mRNA levels of genes encoding antimicrobial proteins LUM and OLFM-4 and to increase TJ-related genes CLDN1 and OCLN, which were significantly down-regulated by LPS-infection in IPEC-J2 cells. Conversely, L. fermentum CCM 7158 which was chosen as an indicator lactic acid bacteria (LAB) strain, increased the mRNA levels of the investigated pro-inflammatory cytokines (IL-18, IL-6, and IL-1β) in MDM, when LPS was simultaneously applied to basally deposited macrophages. Although L. fermentum CCM 7158 induced the production of pro-inflammatory cytokines, synchronous up-regulation of the anti-inflammatory cytokine IL-10 was detected in both lactic acid bacteria LAB strains used in both cell cultures.