Journal: Cell host & microbe

Article Title: Clinical Sequelae of Gut Microbiota Development and Disruption in Hospitalized Preterm Infants

doi: 10.1016/j.chom.2024.07.027

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 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 Open in a separate window KEY RESOURCES TABLE.

Techniques: Virus, Recombinant, Software

Journal: Cell host & microbe

Article Title: Clinical Sequelae of Gut Microbiota Development and Disruption in Hospitalized Preterm Infants

doi: 10.1016/j.chom.2024.07.027

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 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 Open in a separate window KEY RESOURCES TABLE.

Techniques: Virus, Recombinant, Software