Microbiota composition of simultaneously colonized mice housed under either a gnotobiotic isolator or individually ventilated cage regime.
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.
Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.|Internal Research and Development, Taconic Biosciences, 4623 Lille Skensved, Denmark.
Randi
R
Lundberg
National Food Institute, Technical University of Denmark, 2860 Søborg, Denmark.
Martin I
MI
Bahl
National Food Institute, Technical University of Denmark, 2860 Søborg, Denmark.
Tine R
TR
Licht
Internal Research and Development, Taconic Biosciences, 4623 Lille Skensved, Denmark.
Martin F
MF
Toft
Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark.
Axel K
AK
Hansen
D000375:Aging / Q000502:physiology; D000818:Animals; D044822:Biodiversity; D016000:Cluster Analysis; D015169:Colony Count, Microbial; D005243:Feces / Q000382:microbiology; D005260:Female; D000069196:Gastrointestinal Microbiome; D005856:Germ-Free Life; D006799:Housing, Animal; D008297:Male; D008810:Mice, Inbred C57BL; D010802:Phylogeny; D013997:Time Factors; D014691:Ventilation