A well‐balanced gut microbiome is associated with improved health outcomes, but to date, the GM of IUGR piglets have only been sparsely investigated. Here, we investigated GM composition, color of colon content, and blood parameters of 20 IUGR and 20 normal 24‐day‐old piglets. No significant differences were detected in colon microbiota composition between IUGR and the normal piglets with respect to alpha and beta diversity measures. The colon content of these piglets displayed three colors: brown, black, and yellow. Interestingly, the color of the colon content varied with microbial community composition, with significant differences in the relative abundance of taxa belonging to Fusobacteria and Treponema. Fusobacteria were most abundant in yellow fecal samples, with a mean relative abundance around 5.6%, whereas this was 0.51% within brown and 0.02% for the black fecal samples. Fusobacteria positively correlated with total blood protein, albumin, and triglycerides. Contrarily, Treponema was at 0.9% the most abundant in black fecal samples, while present at 0.1% of relative abundance in brown fecal samples and 0.01% in yellow samples, correlating positively with blood iron content. This study indicates that colon/fecal content color can be used as indicator for specific GM and metabolite signatures.