Virus:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
Recombinant:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
Enzyme-linked Immunosorbent Assay:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
Sequencing:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
RNA Sequencing:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
Mass Spectrometry:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
Infection:Article Title: The natural product chlorotonil A preserves colonization resistance and prevents relapsing Clostridioides difficile infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains C. difficile 630 DSMZ DSM 27543 C. difficile VPI10463 ATCC ATCC43255 C. difficile 1780 DSMZ DSM 1296 C. difficile R20291 DSMZ DSM 27147 C. difficile CD-10-00484 (vancomycin resilient) PMID 26444881 N/A C. difficile CD-22-00115 (Metronidazole resistant) PMID 32001686 N/A C. difficile CD-22-00001 (Fidaxomicin resistant) Schwanbeck et al.23 N/A C. difficile CD-15-00638 (vancomycin resilient) PMID 32726198 N/A Chemicals, peptides, and recombinant proteins Chlorotonil A, B1-Epo2 Helmholtz Institute for Pharmaceutical Research Saarland N/A Menadione crystalline (vitamin K) Sigma-Aldrich Cat# M5625 Brain Heart Infusion OXOID Cat#CM1135B DMSO Carl Roth Cat#A994.2 Vancomycin HCl Carl Roth Cat# 0242.3 Metronidazole Sigma Cat# 443-48-1 Fidaxomicin MedChemExpress Cat# HY-17580 Ethanol J. T. Baker Cat# 64-17-5 Clindamycin HCl Sigma Cat# 21462-39-5 CaCl2 3 2H2O Merck N/A Glycine Carl Roth Cat# 0079.1 Triz-Base Sigma Cat# 741883 TCA sodium salt Carl Roth Cat# 8149.2 L-Cysteine L-Cysteine Cat#1693.1 Soy oil Caelo Cat#8001-22-7 Critical commercial assays Mouse lipocalin-2/NGAL DuoSet ELISA R&D Systems Cat#DY1857 Separate detection of C. difficile toxins A and B tgcBIOMICS Cat#TGC-E002-1 ZymoBIOMICS 96 MagBead DNA Kit Zymo Research Cat#D4302 Deposited data 16S rRNA gene sequencing of mice This study PRJNA809685 16S rRNA gene sequencing of piglets This study PRJNA800240 RNA sequencing data This study PRJNA949940 Mass spectrometry proteomics data This study PXD029243 Experimental models: Organisms/strains WT C57BL/6N 6-30 weeks, housed under enhanced specific pathogen free conditions at the animal facility of the Helmholtz Institute for Infection research, Germany Janvier Labs N/A Germ-free WT C57BL/6NTac mice 16 weeks, raised in gnotobiotic isolaters at the germ-free facility of the Helmholtz Institute for Infection research, Germany Raised in house N/A Piglets 4 weeks, housed at the the animal facility of the Friedrich-Loeffler-Institute, Germany Mörsdorfer Agrar GmbH N/A (Continued on next page) Cell Host & Microbe 31, 734–750.e1–e8, May 10, 2023 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides Primers for 16 S sequencing 16S_V4Seq_515F: 5’AATGA TACGGCGACCACCGAGAT CTACACTATGGTAATTGTG TGCCAGCMGCCGCGGTAA 16S_V4Seq_806R: 5’ GGACT ACNNGGGTATCTAAT Sigma Caporaso et al.55 Software and algorithms Graphpad Prism 9.4 GraphPad Software, Inc. N/A R Studio 2022.07.01 R Studio https://cran.r-project.org/ Quantitative Insights into Microbial Ecology (QIIME) v1.8.0 Caporaso et al.55 N/A FastTree Price et al.56 N/A Ribosomal Database Project (RDP) classifier Wang et al.57 N/A OTU picking with UCLUST Edgar58 N/A PyNAST alignment Price et al.56 N/A Phyloseq McMurdie and Holmes59 N/A
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