# Non-Invasive Analyses of Altered Schaedler Flora in C57Bl/6J and Balb/c Mice to Monitor Hygiene Status of a Housing Facility

## TL;DR

This study shows that analyzing the Altered Schaedler Flora (ASF) in mice can help detect infections and monitor hygiene in animal facilities.

## Contribution

The study introduces ASF analysis as a practical tool for detecting unwanted infections in mice based on gut microbiome changes.

## Key findings

- ASF bacterial groups show significant quantity changes in infected versus non-infected mice across different housing areas.
- Strain-specific differences in ASF composition were observed between C57Bl/6J and Balb/c mice.
- ASF analysis using qPCR kits provides rapid and accurate microbiome profiling for health monitoring.

## Abstract

Transgenic animal models are crucial for precise genetic research. The gut microbiota plays a vital role, affecting digestion, metabolism, immune development, and pathogen exclusion. The microbiome’s composition varies with environmental factors and can significantly impact research outcomes, necessitating standardization for further microbiome research. The ‘Altered Schaedler flora’ (ASF), consisting of eight bacterial groups, was defined after analyzing the whole gut microbiome of laboratory mice. These ASF models, showing stability across generations, are used to establish baseline microbiome conditions to simplify comparability, as only a relatively small data set is available (many groups of bacteria tend to constantly change in composition and occurrence). Our data show a significant difference in the quantity of ASF groups when comparing laboratory mice held in specific pathogen-free housing conditions to mice housed in areas with proven pathogen contact. It is also interesting to note that there were strain-specific differences between the two mouse lines tested. In conclusion, it can be said that an in-house ASF analysis is a good tool for detecting an unwanted infection. However, a baseline must first be defined for the respective animal strain and husbandry area.

The composition of the gut microbiome, defined by environmental factors, significantly affects research outcomes, with variations observed across animal facilities. Efforts to standardize led to the definition of the ‘Altered Schaedler flora’ (ASF), comprising eight bacterial groups. Our data highlights the variability of ASF under pathogen contact. Feces from two wild-type strains (C57Bl/6J and Balb/c mice) with and without proven infection was collected in two different animal facilities and analyzed. The data show a significant difference in the quantity (either reduction or increase) of the eight ASF bacterial groups when comparing infected and non-infected mice across different housing areas (SPF-specific pathogen-free, quarantine, and conventional-experimental areas) within a facility, as well as in comparison to another facility. Furthermore, strain-specific differences are also evident, with certain ASF groups showing a reduction in quantity at one facility but an increase at the other, comparing the same housing area. Comparative studies across facilities confirmed the necessity of baseline determination for accurate ASF analysis. Performing ASF analysis, facilitated by in-house qPCR (quantitative polymerase chain reaction) kits, offers prompt and precise microbiome profiling, enhancing experimental accuracy and health monitoring in animal research settings.