Key resources table

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Maternal and infant stool samples	Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland	EDIA
Infant serum samples	Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland	EDIA
Breast milk samples	Vincent Obstetrics & Gynecology Department, Massachusetts General Hospital, Boston, MA, USA	OriGiN
Critical commercial assays
PowerSoil DNA Isolation Kit	MoBio Laboratories	Cat#12888-100
Nextera XT DNA Library Preparation kit	Illumina	Cat#FC-131-1096
CalproLab ELISA (ALP)	Calpro AS	Cat#CALP0170
β-Defensin 2 ELISA	Immundiagnostik	Cat#KR6500
MILLIPLEX MAP Human Cytokine/Chemokine Magnetic Bead Panel	Millipore	Cat#HCYTMAG-60K-PX38
Deposited data
Metagenomic sequencing data	This paper	SRA: PRJNA821542
Stool metabolomic profiles	This paper	http://dx.doi.org/10.21228/M8C70Q
Software and algorithms
KneadData v0.7.2	Curtis Huttenhower laboratory	https://huttenhower.sph.harvard.edu/kneaddata/
MetaPhlAn2/StrainPhlAn v2.9.21	Beghini et al. 70	https://huttenhower.sph.harvard.edu/metaphlan/
HUMANn2 v0.11.2	Franzosa et al. 71	https://huttenhower.sph.harvard.edu/humann/
megaHIT v1.1.4-2-gd1998a1	Li et al. 72	https://github.com/voutcn/megahit
Prodigal v2.6.3	Hyatt et al. 73	https://github.com/hyattpd/Prodigal
metaBAT2 v2.15-3-g367a7ef	Kang et al. 74	https://bitbucket.org/berkeleylab/metabat
checkM v1.1.2	Parks et al. 75	https://ecogenomics.github.io/CheckM/
GTDB-Tk v1.0.2	Chaumeil et al. 76	https://github.com/Ecogenomics/GTDBTk
CD-HIT v4.7	Fu et al. 77	http://weizhong-lab.ucsd.edu/cd-hit/
eggNOG-mapper v2.0.1	Huerta-Cepas et al. 78	http://eggnog-mapper.embl.de/
KMA	Clausen et al. 79	https://bitbucket.org/genomicepidemiology/kma