Changes in oral microbial ecology of C57Bl6 mice associated with sampling methodology and aging

Mouth is an important niche for bacterial colonization. Previous research used mouth microbiota to predict diseases like colon cancer and inflammatory bowel disease (IBD). It is still unclear how the sampling methodology influences microbial characterization. Our aim was to determine if the sampling methods cotton swab or tissue biopsy and the age influence the oral microbial composition of mice. Microbial DNA was extracted and characterized from mouth swabs and tissue biopsies from 2 and 15 months old C57Bl6 SPF male mice kept in the same facility. Our results show statistical different microbial community of the different ages, type of sampling and the two fixed factors age x type of sample (p-value <0.05). At genus level, we identified shifts in the abundance of Actinobacillus, Neisseria, Staphylococcus and Streptococcus and those differences were related to sampling and age. Additionally, the abundance of Streptococcus danieliae, Moraxella osloensis and some unclassified Streptococcus was affected by the sampling method. Although swab and tissue biopsies, identified the common colonizers of oral microbiota, cotton swabbing is a low-cost and practical method, validating the use of the swab as the preferred oral sampling approach.