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. 2024 Aug 14;32(8):1444–1454.e6. doi: 10.1016/j.chom.2024.07.010
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological Samples
Infant and maternal fecal samples This study N/A
Cord blood samples This study N/A
Critical Commercial Assays
QIAamp Fast DNA Stool Mini kit QIAGEN Cat#51604
NEBNext® Ultra™ II DNA Library Prep Kit New England Biolabs Cat # E7370L
Deposited Data
Metagenomic sequencing data of CS Baby Biome This study European Genomics-Phenome Archive:EGAC00001003433
Original code for microbiome, SCFA and BA analysis This study https://zenodo.org/records/11537223https://github.com/GRONINGEN-MICROBIOME-CENTRE/CS_BABY_BIOME
Original code for microbiome profiling Gascesa et al.20 https://github.com/GRONINGEN-MICROBIOME-CENTRE/DMP/tree/main/microbiome_profiling
Software and Algorithms
REDCap Harris et al.21 http://www.sciencedirect.com/science/article/pii/S1532046408001226
blockrand Snow22 https://CRAN.R-project.org/package=blockrand t
KneadData Huttenhower Lab https://github.com/biobakery/kneaddata
Bowtie2 (version 2.4.2) Langmead and Salzberg et al.23 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
FastQC toolkit (version 0.11.9) Babraham Bioinformatics https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
MetaPhlAn4 Blanco-Míguez et al.24 https://github.com/biobakery/MetaPhlAn/tree/8338b344239a296e6654f8770d012e250106ab70
StrainPhlAn4 Truong et al.25 https://github.com/biobakery/MetaPhlAn/wiki/StrainPhlAn-4
HUMAnN (version 3.6) Beghini et al.26 https://github.com/biobakery/humann
ShortBRED Kaminski et al.27 https://github.com/biobakery/shortbred
metaWRAP (version 1.3.2) Uritskiy et al.28 https://github.com/bxlab/metaWRAP
dRep (version 3.4.2) Olm et al.29 https://github.com/MrOlm/drep
CoverM (version 0.6.1) Woodcroft, B30 https://github.com/wwood/CoverM
RGI (version 6.0.3) Alcock et al.31 https://github.com/arpcard/rgi
lmerTest (version 3.1-3) Kuznetsova et al.32 https://CRAN.R-project.org/package=lmerTest
vegan (version 2.6-2) Oksanen et al.33 https://github.com/vegandevs/vegan/
TCAM Mor et al.14 https://github.com/UriaMorP/tcam_analysis_notebooks
MCMCglmm (version 2.34) Hadfield34 https://github.com/jarrodhadfield/MCMCglmm
Phangorn (version 2.11.1) Schliep35 https://CRAN.R-project.org/package=phangorn
pwrss (version 0.3.1) Bulus, M36 https://CRAN.R-project.org/package=pwrss
R (version 4.3.1) R Core Team37 https://www.r-project.org/
Other
Clincial Trial Registration https://clinicaltrials.gov/study/NCT06030713?cond=NCT06030713&rank=1 NCT06030713