Source of human milk (mother or donor) is more important than fortifier type (human or bovine) in shaping the preterm infant microbiome

. 2022 Aug 26;3(9):100712. doi: 10.1016/j.xcrm.2022.100712

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples

Fecal samples	This paper	N/A
Urine samples	This paper	N/A

Chemicals and reagents

ZR BashingBead Lysis Tubes	Zymo Research, USA	Catalog. No. S6003-50
Zymo-Spin IIC Columns	Zymo Research, USA	Catalog. No.C1011-50
BioVendor Extraction buffer	BioVendor, Czech Republic	Catalog No.: C005821

Critical commercial assays

Zymo Quick DNA Fecal Microbe Miniprep kit	Zymo Research, USA	Catalog. No. D6010
ZymoBIOMICS Microbial Community DNA Standard	Zymo Research, USA	Catalog. No. D6305
Genomic DNA from Microbial Mock Community B (Staggered, Low Concentration)	BEI Resources, USA	Catalog. No.: HM-783D
S100A8/A9 (Calprotectin) Human ELISA kit	BioVendor, Czech Republic	Catalog No.: RD191217100R; RRID:AB_10953195; RRID: AB_1227456
F2-Isoprostane ELISA kit	Oxford biomedical research, USA	Catalog No.: EA-85; RRID: AB_10832110
Creatinine microplate assay kit	Oxford biomedical research, USA	Catalog No.: CR-01

Deposited data

Fastq files from 16S rRNA gene sequencing	This paper	Accession number: NCBI SRA under BioProject ID: PRJNA690658

Software and algorithms

PediTools version 1.1.1	Chou et al.²⁵	https://www.peditools.org/fenton2013/
R version 3.6.1	The R Project for Statistical Computing	https://www.r-project.org/
Vegan R package version 2.5-7	CRAN R project	https://cran.r-project.org/web/packages/vegan/index.html
Phyloseq R package version 1.30.0	McMurdie and Holmes⁵⁰	https://joey711.github.io/phyloseq/
Microbiome R package version 1.8.0	Lahti and Shetty⁵¹	https://microbiome.github.io/tutorials/
Splinectome R package version 0.1.0	Shields-Cutler et al.⁵²	https://rrshieldscutler.github.io/splinectomeR/
ComplexHeatMap R package version 2.2.0	Gu et al.⁵³	https://jokergoo.github.io/ComplexHeatmap-reference/book/
MaAsLin2 R package version 1.5.2	Mallick et al.⁵⁴	https://github.com/biobakery/Maaslin2
HIT DB version 1.0	Ritari et al.⁵⁵	https://github.com/openresearchlabs/HITdb
DADA2 R package version 1.14.1	Callahan et al.⁵⁶	https://benjjneb.github.io/dada2/tutorial.html
Decontam R package version 1.6.0	Davis et al.⁵⁷	https://benjjneb.github.io/decontam/vignettes/decontam_intro.html
ggplot2 R package version 3.3.3	Tidyverse project R	https://ggplot2.tidyverse.org/