Carbon nanomaterials (CNMs) can positively regulate seed germination and enhance plant growth. However, clarification of the impact of plant organs containing absorbed CNMs on animal and human health is a critical step of risk assessment for new nano?agro-technology. In this study, we have taken a comprehensive approach to studying the effect tomato fruits derived from plants exposed to multi-walled carbon nanotubes (CNTs) have on gastrointestinal epithelial barrier integrity and their impact on the human commensal intestinal microbiota using an <
em>
in vitro<
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cell culture and batch human fecal suspension models. The effects of CNTs on selected pure cultures of <
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Salmonella enterica<
/em>
Typhimurium and <
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Lactobacillus acidophilus<
/em>
were also evaluated. This study demonstrated that CNT-containing fruits or the corresponding residual level of pure CNTs (0.001 ?g ml<
sup>
?1<
/sup>
) was not sufficient to initiate a significant change in transepithelial resistance and on gene expression of the model T-84 human intestinal epithelial cells. However, at 10 ?g ml<
sup>
?1<
/sup>
concentration CNTs were able to penetrate the cell membrane and change the gene expression profile of exposed cells. Furthermore, extracts from CNT-containing fruits had minimal to no effect on human intestinal microbiota as revealed by culture-based analysis and 16S rRNA sequencing.