“Microbiome” is a term used to refer to gut bacteria but also to other inhabitants of the gut, like viruses, fungi, and protozoa. In this article, K. Servick discussed the impact of the microbiome on varying experimental data. The microbes that reside in mice can make it difficult to replicate scientific studies. While mice in the same cage tend to have the same microbes, differences exist between groups, cages, and even individual mice based on a variety of factors (e.g. change in diet, a new stress level, or where and how mice were kept by vendors) that cannot be easily standardized or regulated in an experimental setting.
However, although the microbiome issue can have an effect on inbetween-lab reproducibility, it should not be a problem for evaluating the impact of a treatment for humans. Here, potential drugs and new applications are expected to produce strong and robust effects first in mice and subsequently in humans, that differences like genotypes or microbiological states do not influence the efficacy of a drug. Mice showing those differences due to the microbiome may be used for immunological studies and could help explain some of the differing biological responses to treatment experienced in humans. LINK