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Background  The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study its effects on depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated for their characteristics and bacterial microbiome changes.    Results  The 16S ribosomal RNA gene sequencing of fecal microbiota showed that RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure. RbCl significantly enhanced the abundances of  Rikenellaceae ,  Alistipes ,  Clostridium XlVa  and sulfate-reducing bacteria including  Deltaproteobacteria ,  Desulfovibrionales ,  Desulfovibrionaceae  and  Desulfovibrio , but significantly inhibited the abundances of  Tenericutes ,  Mollicutes ,  Anaeroplasmatales ,  Anaeroplasmataceae  and  Anaeroplasma  lineages. With regarding to the archaea, we only observed two less richness archaea  Sulfolobus  and  Acidiplasma  at the genus level.    Conclusions  Changes of fecal microbes may in part contribute to the anticancer or anti-depressant effects of RbCl. These findings further validate that the microbiome could be a target for therapeutic intervention.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02095-4.

Rubidium chloride modulated the fecal microbiota community in mice