Concentration Assay:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
RNA Sequencing:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Microscopy:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Amplification:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Sequencing:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Recombinant:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Plasmid Preparation:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
Software:Article Title: Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019 .. REAGENT or RESOURCE SOURCE IDENTIFIER 1 40,6-diamidino-2-phenylindole (DAPI) Roth Cat# 6335.1 Lot# 31087560 ezDNase Thermo Fisher Cat# 11766051 lipocalin-2 standard R&D Cat# 1857-LC-050 HRP-streptavidin BioLegend Cat# 405210 ABTS Chromophore Diammonium Salt Calbiochem Cat# 194430 Soybean trypsin inhibitor Sigma-Aldrich Cat# T6522 Critical Commercial Assays QIAamp Fast DNA Stool Mini Kit Qiagen Cat# 51604 Ribo-Zero bacterial kit Illumina Cat# MRZMB126 Experion RNA HighSens kit Bio-Rad Cat# 7007105 NEBNext Ultra RNA library prep for Illumina New England Biolabs Cat# E7530S GeneJET RNA cleanup and Concentration Micro Kit Thermo Fisher Cat# K0841 Quant-iT RiboGreen RNA Assay Kit Thermo Fisher Cat# R11490 NucleoSpin gDNA clean-up kit Macherey-Nagel, Cat# 740230 Deposited Data RNA sequencing raw data This paper ENA: PRJNA504618 S. Tm 1344 genome PRJNA50407 MicroScope platform SALTS.1 M. schaedleri genome PRJNA213740 MicroScope platform NZ_AYGZ.1 M. schaedleri raw reads without S. Tm. (Loy et al., 2017) ENA: PRJEB13534 Amplicon sequencing data This paper SRA: SRP164745 Experimental Models: Cell Lines HuTu80 cells ATCC HTB-40 Experimental Models: Organisms/Strains Agr2tm1.2Erle (Park et al., 2009) N/A Agr2tm1.2Erle C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A C57BL/6J germfree A. Bleich; M. Basic (MHH) N/A Oligonucleotides See Table S5 N/A Recombinant DNA Plasmid pM974 (Ackermann et al., 2008) N/A Plasmid pM973 (Hapfelmeier et al., 2005) N/A Plasmid pM1419 (Stecher et al., 2008) N/A Plasmid pWKS30 (Wang and Kushner, 1991) N/A Plasmid pKD3 (Datsenko and Wanner, 2000) N/A Plasmid pKD4 (Datsenko and Wanner, 2000) N/A Plasmid pKD46 (Datsenko and Wanner, 2000) N/A Plasmid pCP20 (Cherepanov, and Wackernagel, 1995) N/A pBluescript SKII+ GENBANK: X52328.1 Stratagene N/A pLB02 (Gunn et al., 1995) N/A pM1471 (pLB02 insertion of PsicA before luc) W. D. Hardt N/A Software and Algorithms GraphPad Prism version 5.01 for Windows GraphPad Software, San Diego, California, USA www.graphpad.com ImageJ 1.48v (Schneider et al., 2012) https://imagej.nih.gov/ij/ Trimmomatic (Bolger et al., 2014) http://www.usadellab.org/cms/?page= trimmomatic BWA (Li and Durbin, 2009) http://bio-bwa.sourceforge.net/ (Continued on next page) e2 Cell Host & Microbe 25, 1–14.e1–e8, May 8, 2019
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ATCC is a verified supplier 
ATCC manufactures this product 