Abstract
Germ-free rodents colonized with microbiotas of interest are used for host-microbiota investigations and for testing microbiota-targeted therapeutic candidates. Traditionally, isolators are used for housing such gnotobiotic rodents due to optimal protection from the environment, but research groups focused on the microbiome are increasingly combining or substituting isolator housing with individually ventilated cage (IVC) systems. We compared the effect of housing systems on the gut microbiota composition of germ-free mice colonized with a complex microbiota and housed in either multiple IVC cages in an IVC facility or in multiple open-top cages in an isolator during three generations and five months. No increase in bacterial diversity as assessed by 16S rRNA gene sequencing was observed in the IVC cages, despite not applying completely aseptic cage changes. The donor bacterial community was equally represented in both housing systems. Time-dependent clustering between generations was observed in both systems, but was strongest in the IVC cages. Different relative abundance of a Rikenellaceae genus contributed to separate clustering of the isolator and IVC communities. Our data suggest that complex microbiotas are protected in IVC systems, but challenges related to temporal dynamics should be addressed.
Highlights
Day 168 End of study as wells as for experimental facilities, aiming for maintaining mouse cohorts with a stable complex microbiota over time
Colonization was efficient in isolators and individually ventilated cage (IVC), but unique taxa were detected in both systems compared to the inoculum
Additional 50 sparsely dispersed and very low abundance taxa were found in the isolator and IVCs, which were not detected in the inoculum (Fig. 2b)
Summary
Day 168 End of study as wells as for experimental facilities, aiming for maintaining mouse cohorts with a stable complex microbiota over time. We colonized GF parent mice with a complex specific pathogen free (SPF) microbiota, housed them in IVCs or in an isolator, and bred them to pass the microbiota on to the offspring. That the IVCs could be protected from environmental contamination to an extent where this would not cause major compositional shifts in the gut microbiota compared to the gnotobiotic isolator over a period of five months. We based this hypothesis on the assumption that a complex microbiota, once stabilized in the mice, would be relatively resistant to compositional changes caused by the potential introduction of low abundance contaminating bacteria happening during husbandry procedures, such as cage changes
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