REAGENT or RESOURCE	SOURCE	IDENTIFIER
Critical commercial assays
DNeasy PowerSoil HTP 96 DNA isolation kit	QIAGEN	-
KAPA HyperPlus Kit	Roche	-
Deposited data
Metagenomic sequences of all infant and mother stool samples	This paper	NCBI BioProject: PRJNA698986
Statistical script	This paper	GitHub: https://github.com/clarelou0128/R-statistical-scripts
Software and algorithms
bcl2fastq version 2.20	-	https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html
Sickle version 1.33	-	https://github.com/najoshi/sickle
Bowtie2 version 2.3.5.1	Langmead and Salzberg61	https://github.com/BenLangmead/bowtie2
IDBA-UD version 1.1.3	Peng et al.62	https://github.com/loneknightpy/idba
Prodigal version 2.6.3	Hyatt et al.63	https://github.com/hyattpd/Prodigal
MetaBAT version 2.12.1	Kang et al.64	https://bitbucket.org/berkeleylab/metabat/src/master/
CONCOCT version 1.1.0	Alneberg et al.65	https://github.com/BinPro/CONCOCT
MaxBin version 2.2.7	Wu et al.66	https://sourceforge.net/projects/maxbin/
DasTool version 1.1.1	Sieber et al.67	https://github.com/cmks/DAS_Tool
dRep version 2.6.2	Olm et al.68	https://github.com/MrOlm/drep
tRep version 0.5.3	-	https://github.com/MrOlm/tRep
GTDB-Tk version 1.3.0	Chaumeil et al.69	https://github.com/Ecogenomics/GTDBTk
inStrain version 1.3.4	Olm et al.19	https://github.com/MrOlm/instrain
KofamKOALA	Aramaki et al.70	https://www.genome.jp/tools/kofamkoala/
run_dbcan version 2.0.11	-	https://github.com/linnabrown/run_dbcan
HMMER version 3.3.2	Eddy71	http://hmmer.org/
cath-resolve-hits version 0.16.5	Lewis et al.72	https://github.com/UCLOrengoGroup/cath-tools
BLASTP version 2.10.0	-	https://blast.ncbi.nlm.nih.gov/Blast.cgi
SignalP version 5.0b	Armenteros et al.73	http://www.cbs.dtu.dk/services/SignalP/
TMHMM version 2.0	Krogh et al.74	https://services.healthtech.dtu.dk/service.php?TMHMM-2.0
antiSMASH version 5.1.2	Blin et al.75	https://github.com/antismash/antismash
ABRicate	-	https://github.com/tseemann/abricate
Geneious version 2020.2.4	Kearse et al.76	https://www.geneious.com/
clinker version 0.0.20	Gilchrist and Chooi77	https://github.com/gamcil/clinker
FeGenie	Garber et al.78	https://github.com/Arkadiy-Garber/FeGenie
RStudio	R	https://www.rstudio.com/