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. 2024 Sep 6;5(9):101729. doi: 10.1016/j.xcrm.2024.101729
REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
Mother’s milk (1 mL) (O’Connor et al., 2018)59 Clinicaltrials.gov, NCT02137473
Infant stool samples (O’Connor et al., 2018)59 Clinicaltrials.gov, NCT02137473
Critical commercial assays
NucleoSpin Food DNA Isolation Kit Macherey-Nagel Cat#740945.50
DNeasy PowerSoil Kit Qiagen Cat#12855-100
KAPA2G Robust HotStart Ready Mix KAPA Biosystems Cat#KK5702
1.8X Ampure XP Magnetic Beads Agencourt Cat#A63881
MiSeq Reagent Kit V2 (150 bp x 2) Illumina Cat#MS-102-2002
TaqMan™ Gene Expression Master Mix Thermo Fisher Scientific Cat#4444964
Custom TaqMan™ Gene Expression Assay Thermo Fisher Scientific Cat#4332078
Deposited data
Milk raw sequencing data (Asbury et al., 2020)19 16S rRNA gene sequence data (NCBI) BioProject: PRJNA607284
Stool raw sequencing data (Asbury et al., 2022)20 16S rRNA sequence data (NCBI) BioProject: PRJNA723326
Oligonucleotides
16S rRNA Forward Primer for V4 region 515F: GTGCCAGCMGCCGCGGTAA (Caporaso et al., 2012)60 N/A
16S rRNA Reverse Primer for V4 region 806R: GGACTACHVGGGTWTCTAAT (Caporaso et al., 2012)60 N/A
16S rRNA Forward Primer for all bacteria: CG GTGAATACGTTCCCGG (Furet et al., 2009)61 N/A
16S rRNA Reverse Primer for all bacteria: TA CGGCTACCTTGTTACGACTT (Furet et al., 2009)61 N/A
16S rRNA Probe for all bacteria: 50-CTTGTAC ACACCGCCCGTC-30 (Furet et al., 2009)61 N/A
Software and algorithms
USEARCH version 11.0.667 (Edgar 2010, 2013, 2016)62,63,64 http://www.drive5.com/usearch/
VSEARCH version 2.10.4 (Rognes et al., 2016)65 https://github.com/torognes/vsearch
QIIME1 version 1.9.1 (Caporaso et al., 2010)66 http://qiime.org
FastTree version 2.1.11 (Price et al., 2009)67 http://www.microbesonline.org/fasttree/
R version 4.3.1 (R Core Team, 2017)68 https://www.r-project.org
Phyloseq version 1.44.0 (McMurdie et al., 2013)69 https://joey711.github.io/phyloseq/
Decontam version 1.13.0 (Davis et al., 2018)70 https://benjjneb.github.io/decontam/
SAS University Edition SAS Institute Inc N/A
Vegan version 2.6.4 (Oksanen et al., 2022)71 https://github.com/vegandevs/vegan
ggplot2 version 3.4.3 (Wickham et al., 2016)72 https://ggplot2.tidyverse.org
forestplot version 3.1.3 (Gordon et al., 2023)73 https://rdrr.io/cran/forestplot/
ggalluvial version 0.12.5 (Brunson et al., 2018)74 https://corybrunson.github.io/ggalluvial/
pheatmap version 1.0.12 (Kolde et al., 2018)75 https://github.com/raivokolde/pheatmap
circlize version 0.4.15 (Gu et al., 2014)76 https://jokergoo.github.io/circlize_book/book/
Other
ZymoBIOMICS Mock Community Standard Zymo Research Cat#D6300
ZymoBIOMICS Mock Community DNA Standard Zymo Research Cat#D6306