KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Bacterial and virus strains
Staphylococcus epidermidis from infant stool	This paper	N/A
Clostridioides difficile from infant stool	This paper	N/A
Biological samples
Fecal samples from preterm infants	This paper, Warner et al.34, La Rosa et al.40	Neonatal Microbiome and Necrotizing Enterocolitis cohort
Chemicals, peptides, and recombinant proteins
Critical commercial assays
DNeasy PowerSoil Pro Kit	Qiagen	Cat #47014
Nextera XT kit	Illumina	Cat #20034197
NucliSENS easyMAG system	bioMerieux	Cat #89130–520
Turbo DNase	Thermo Fisher	Cat #AM2238
QIAseq FastSelect – 5S/16S/23S kit	Qiagen	Cat #335925
NEBNext Ultra II Directional RNA Library Prep kit for Illumina	NEB	Cat #E7760
Deposited data
metagenomes, metatranscriptomes, and metagenomic-assembled genomes	This paper	BioProject PRJNA799247
Fecal metagenomic DNA	Gibson et al.11	BioProject PRJNA301903
Fecal metagenomic DNA	Gasparrini et al.12	BioProject PRJNA489090
Experimental models: Cell lines
Experimental models: Organisms/strains
Oligonucleotides
Recombinant DNA
Software and algorithms
Trimmomatic v0.366	Bolger et al.74	https://github.com/timflutre/trimmomatic
Deconseq v4.37	Schmieder et al.75	https://deconseq.sourceforge.net/
MetaPhlAn3 v3.0	Beghini et al.76	https://github.com/biobakery/MetaPhlAn/tree/3.1.0
HUMAnN3 v3.0	Beghini et al.76	https://github.com/biobakery/humann
ShortBRED	Kaminski et al.77	https://github.com/biobakery/shortbred
MetaSPAdes	Nurk et al.80	https://github.com/ablab/spades
Bowtie2	Langmead et al.81	https://github.com/BenLangmead/bowtie2
samtools	Li et al.82	https://www.htslib.org/
MetaBat2	Kang et al.83	https://bitbucket.org/berkeleylab/metabat/src/master/
checkM	Parks et al.84	https://ecogenomics.github.io/CheckM/
Quast	Gurevich et al.85	https://github.com/ablab/quast
dRep	Olm et al.87	https://github.com/MrOlm/drep
mash	Ondov et al.88	https://github.com/marbl/Mash
R statistical software v4.0.4 - v4.4.0	R core team	https://www.r-project.org
Rstudio	Rstudio	Posit.co
MaAslin2	Mallick et al.51	https://github.com/biobakery/Maaslin2
DirichletMultinomial	Holmes et al.91	https://bioconductor.org/packages/release/bioc/html/DirichletMultinomial.html
inStrain	Olm et al.42	https://github.com/MrOlm/inStrain
pyani	Pritchard et al.89	https://github.com/widdowquinn/pyani
Repeat measures PERMANOVA	Lloyd-Price et al.21	https://bitbucket.org/biobakery/hmp2_analysis/src/master/
Other
Analytic scripts and data	This paper	https://github.com/dantaslab/NICUExposome 10.5281/zenodo.12737979