| Summary: | Industrially originated trans-fatty acids (I-<i>t</i>FAs), such as elaidic acid (EA), and ruminant trans-fatty acids (R-<i>t</i>FAs), such as <i>trans</i>-palmitoleic acid (TPA), may have opposite effects on metabolic health. The objective was to compare the effects of consuming 2–3% I-<i>t</i>FA or R-<i>t</i>FA on the gut microbiome and fecal metabolite profile in mice after 7 and 28 days. Forty C57BL/6 mice were assigned to one of the four prepared formulations: lecithin nanovesicles, lecithin nanovesicles with EA or TPA, or water. Fecal samples and animals’ weights were collected on days 0, 7, and 28. Fecal samples were used to determine gut microbiome profiles by 16S rRNA sequencing and metabolite concentrations by GC/MS. At 28 days, TPA intake decreased the abundance of <i>Staphylococcus</i> sp55 but increased <i>Staphylococcus</i> sp119. EA intake also increased the abundance of <i>Staphylococcus</i> sp119 but decreased <i>Ruminococcaceae</i> UCG-014, <i>Lachnospiraceae</i>, and <i>Clostridium sensu stricto</i> 1 at 28 days. Fecal short-chain fatty acids were increased after TPA while decreased after EA after 7 and 28 days. This study shows that TPA and EA modify the abundance of specific microbial taxa and fecal metabolite profiles in distinct ways.
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