Introduction Microbial digestion is of key importance for ruminants, and disturbances can affect efficiency and quality of products for human consumers. Ruminal biohydrogenation of dietary unsaturated fatty acids leads to a wide variety of specific fatty acids. Some dietary conditions can affect the pathways of this transformation, leading to trans -10 fatty acids rather than the more usual trans -11 fatty acids, this change resulting in milk fat depression in dairy cows. Materials and methods We combined data from an induced and spontaneous trans -10 shift of ruminal biohydrogenation, providing new insight on bacterial changes at different taxonomic levels. A trans -10 shift was induced using dietary addition of concentrate and/or unsaturated fat, and the spontaneous milk fat depression was observed in a commercial dairy herd. Results and discussion Most changes of microbial community related to bacteria that are not known to be involved in the biohydrogenation process, suggesting that the trans -10 shift may represent the biochemical marker of a wide change of bacterial community. At OTU level, sparse discriminant analysis revealed strong associations between this change of biohydrogenation pathway and some taxa, especially three taxa belonging to [Eubacterium] coprostanoligenes group , Muribaculaceae and Lachnospiraceae NK3A20 group , that could both be microbial markers of this disturbance and candidates for studies relative to their ability to produce trans -10 fatty acids.