The tremendous importance of microbiota in microbial homoeostasis, alterations in metabolism and both innate and adaptive immune systems has been well established. A growing body of evidence support that dysbiosis or compositional changes in gut microbiota is linked to the ageing of stem cells in terms of dysregulations of metabolism, aberrant activation of the immune system as well as promoting epigenetic instability of stem cell. In this concise review, we elucidate recent emerging topics on microbiotic alterations and underlying mechanisms in stem cell ageing.