REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Newborn fecal samples	Turku University Hospital, Turku, Finland	N/A
Critical commercial assays
PureLink Microbiome DNA Purification Kit	Invitrogen, ThermoFisher Scientific	CAT# A29790
AMPure XP for PCR clean-up (magnetic beads)	Beckman Coulter	CAT# A63882
Quant-iT PicoGreen dsDNA quantitation kit	Invitrogen, ThermoFisher Scientific	CAT# P7589
MO BIO’s PowerSoil DNA Isolation Kit Handbook	QIAGEN	CAT# 12855
5x All-in-One RT MasterMix	abm	CAT# G592
Fast SYBR Green Master mix	Applied Biosystems	CAT# 43-856-12
Total RNA Purification Kit	Norgen Biotek Corp	CAT# 17200
Deposited data
Sequence data	This paper	ENA:PRJEB46240; DDBJ:ERP130461
Experimental models: organisms/strains
Mouse: Swiss Webster	Azrieli Medical Faculty Animal Facility	WT – established colony in the faculty
Software and algorithms
QIIME2	Bolyen et al., 201946	https://qiime2.org/
DADA2	Callahan et al., 201647	https://benjjneb.github.io/dada2/tutorial.html
Other
Mouse Chow: Maintenance Diet	Altromin International	Diet 1324