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barcode shrna oligonucleotide  (Qiagen)


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    Structured Review

    Qiagen barcode shrna oligonucleotide
    Barcode Shrna Oligonucleotide, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 62012 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoding+kit/QIAquick+PCR+Purification+Kit/pm42842673-239-3-14
    Average 99 stars, based on 62012 article reviews
    barcode shrna oligonucleotide - by Bioz Stars, 2026-11
    99/100 stars

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    Related Articles

    Control:

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNA was isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. .. Cells were sequenced on an R9.4.1 flow cell for 24 h. Reads were aligned to both the human genome (hg38) and the S. flexneri 2a strain 2475 T genome ( NC_004741.1 ), and BrdU content was detected as described above.

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems.
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNAwas isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. ..

    Isolation:

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNA was isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. .. Cells were sequenced on an R9.4.1 flow cell for 24 h. Reads were aligned to both the human genome (hg38) and the S. flexneri 2a strain 2475 T genome ( NC_004741.1 ), and BrdU content was detected as described above.

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems.
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNAwas isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. ..

    Article Title: The evolution of ovary-biased gene expression in Hawaiian Drosophila
    Article Snippet: .. For DNA barcoding, DNA was extracted from one or two legs from male specimens using the Qiagen DNeasy blood and tissue extraction kit, or from the DNA of females isolated during RNA extraction (see below). ..

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    Infection:

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNA was isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. .. Cells were sequenced on an R9.4.1 flow cell for 24 h. Reads were aligned to both the human genome (hg38) and the S. flexneri 2a strain 2475 T genome ( NC_004741.1 ), and BrdU content was detected as described above.

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems.
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNAwas isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. ..

    Sequencing:

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNA was isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. .. Cells were sequenced on an R9.4.1 flow cell for 24 h. Reads were aligned to both the human genome (hg38) and the S. flexneri 2a strain 2475 T genome ( NC_004741.1 ), and BrdU content was detected as described above.

    Article Title: Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems.
    Article Snippet: .. 24 h post-infection, new media containing 150 μM BrdU (or no BrdU control) was added to the cells, and cells were harvested at the following timepoints: 1 h, 4 h, and 24 h. DNAwas isolated from the infected cells using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for sequencing using a Rapid Barcoding kit. ..

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
    Article Snippet: .. DNase I 300 units/μL Invitrogen, Cat: 18047019 NA PCR H20 NA Qiagen, Cat: 17000-10 NA DNA binding beads NA Aline biosciences, Cat: C-1003-50 NA Molecular grade ethanol NA Sigmaaldrich, Cat: 51976- 500ML-F NA Qubit dsDNA BR assay Kit NA ThermoFisher, Cat: Q32853 NA Qubit assay tubes NA ThermoFisher, Cat: Q32856 NA PCR master mix NA RepliQa HiFi ToughMix, Quantabio, Cat: 95200- 500 For ultra rapid PCR amplifica on and barcoding Proteinase K NA Qiagen, Cat: RP107B-1 DNA extrac on kit NA Qiagen, Cat: 50214, with Pathogen Lysis Tubes L, Cat: 19092 Users can choose their own extrac on method as long as it is sensi ve and robust DNA/RNA Shield 1x Zymo research, Cat: R1100-50 NA Liga on Sequencing Kit NA ONT, Cat: SQK-LSK109 NA PCR Barcoding Expansion Kit NA ONT, Cat: EXP-PBC096 NA NEBNext Ultra II End Repair/dA-Tailing Module NA NEB, Cat: E7546L NA NEBNext Quick NA NEB, Cat: E6056L NA 682 683 Name Concentra on/units Commercial source Comments Liga on Module Flow Cell Priming Kit NA ONT, Cat: EXP-FLP002 Required for both protocols Flow Cell Wash Kit NA ONT, Cat: EXP-WSH004 Required for both protocols ONT Flow Cell R9.4.1 NA ONT, Cat: FLO-MIN106 or FLO-FLG001 Required for both protocols Magne c rack/plate holder NA ThermoFisher, Cat: 12331D and 12321D NA PCR plate 96 well NA Merck, Cat: BR781378 NA 1.5 ml DNA LoBind tubes NA Eppendorf, Cat: 0030108051-250EA Use LoBind tubes 2 ml round bo om tubes NA Starlab, Cat: S1620-2700C or Eppendorf, Cat: 0030120094 Avoid using LoBind tubes Pipe es and pipe e ps P2, P10, P20, P100, P200, P1000, Mul channel NA Any NA Centrifuge /Microplate centrifuge NA Any NA Hea ng block for 1.5/2 mL tubes NA Any NA Sequencing device NA Flongle, MinION Mk1B, GridION NA Device for live basecalling NA GridION or A powerful laptop A laptop with minimum 8 Gb GPU (RTX 3060 or higher), 16 GB Ram, 1 Tb M.2 NVMe SSD Disclaimer: Some parts of the following protocol has been copied directly from the manufacturer’s official website or from the kit manual. ..

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    DNA Extraction:

    Article Title: Biodiversity and genetic connectivity of Brachyura and Anomura (Decapoda) from artificial reefs in the Gulf of Mexico
    Article Snippet: Artificial reefs act as islands of biodiversity that provide substrate where sessile organisms can settle and mobile invertebrates and fishes can find shelter and food.. Though these structures are common and widespread in the Gulf of Mexico, their community composition is not well understood.. We aimed to ameliorate understanding of the invertebrate communities living on artificial reefs in the northeastern Gulf of Mexico by using molecular techniques and morphological examination to describe the biodiversity and genetic connectivity of crabs (Infraorders Anomura and Brachyura) living on and among artificial reefs near Pensacola, FL, USA.

    Extraction:

    Article Title: Biodiversity and genetic connectivity of Brachyura and Anomura (Decapoda) from artificial reefs in the Gulf of Mexico
    Article Snippet: Artificial reefs act as islands of biodiversity that provide substrate where sessile organisms can settle and mobile invertebrates and fishes can find shelter and food.. Though these structures are common and widespread in the Gulf of Mexico, their community composition is not well understood.. We aimed to ameliorate understanding of the invertebrate communities living on artificial reefs in the northeastern Gulf of Mexico by using molecular techniques and morphological examination to describe the biodiversity and genetic connectivity of crabs (Infraorders Anomura and Brachyura) living on and among artificial reefs near Pensacola, FL, USA.

    Article Title: The evolution of ovary-biased gene expression in Hawaiian Drosophila
    Article Snippet: .. For DNA barcoding, DNA was extracted from one or two legs from male specimens using the Qiagen DNeasy blood and tissue extraction kit, or from the DNA of females isolated during RNA extraction (see below). ..

    Polymerase Chain Reaction:

    Article Title: Characterisation of the Gut Bacteria of Cultured and Wild Spiny Lobster Panulirus ornatus
    Article Snippet: .. The primary PCR program was 95 ◦C for 3 min, 20 cycles of 95 ◦C for 15 s, 50 ◦C for 30 s, 72 ◦C for 45 s; and 72 ◦C for 3 min. One microliter of the primary PCR product was used in secondary PCR, which consisted of 25 μL of 2×MyTaq HS mix, 10 μL of 16S rRNA gene barcoded primer (16S Barcoding Kit 1-24 SQK-16S024), and 14 μL of microbial DNA-free water (Qiagen, Germantown, MD, USA). ..

    Article Title: MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
    Article Snippet: .. DNase I 300 units/μL Invitrogen, Cat: 18047019 NA PCR H20 NA Qiagen, Cat: 17000-10 NA DNA binding beads NA Aline biosciences, Cat: C-1003-50 NA Molecular grade ethanol NA Sigmaaldrich, Cat: 51976- 500ML-F NA Qubit dsDNA BR assay Kit NA ThermoFisher, Cat: Q32853 NA Qubit assay tubes NA ThermoFisher, Cat: Q32856 NA PCR master mix NA RepliQa HiFi ToughMix, Quantabio, Cat: 95200- 500 For ultra rapid PCR amplifica on and barcoding Proteinase K NA Qiagen, Cat: RP107B-1 DNA extrac on kit NA Qiagen, Cat: 50214, with Pathogen Lysis Tubes L, Cat: 19092 Users can choose their own extrac on method as long as it is sensi ve and robust DNA/RNA Shield 1x Zymo research, Cat: R1100-50 NA Liga on Sequencing Kit NA ONT, Cat: SQK-LSK109 NA PCR Barcoding Expansion Kit NA ONT, Cat: EXP-PBC096 NA NEBNext Ultra II End Repair/dA-Tailing Module NA NEB, Cat: E7546L NA NEBNext Quick NA NEB, Cat: E6056L NA 682 683 Name Concentra on/units Commercial source Comments Liga on Module Flow Cell Priming Kit NA ONT, Cat: EXP-FLP002 Required for both protocols Flow Cell Wash Kit NA ONT, Cat: EXP-WSH004 Required for both protocols ONT Flow Cell R9.4.1 NA ONT, Cat: FLO-MIN106 or FLO-FLG001 Required for both protocols Magne c rack/plate holder NA ThermoFisher, Cat: 12331D and 12321D NA PCR plate 96 well NA Merck, Cat: BR781378 NA 1.5 ml DNA LoBind tubes NA Eppendorf, Cat: 0030108051-250EA Use LoBind tubes 2 ml round bo om tubes NA Starlab, Cat: S1620-2700C or Eppendorf, Cat: 0030120094 Avoid using LoBind tubes Pipe es and pipe e ps P2, P10, P20, P100, P200, P1000, Mul channel NA Any NA Centrifuge /Microplate centrifuge NA Any NA Hea ng block for 1.5/2 mL tubes NA Any NA Sequencing device NA Flongle, MinION Mk1B, GridION NA Device for live basecalling NA GridION or A powerful laptop A laptop with minimum 8 Gb GPU (RTX 3060 or higher), 16 GB Ram, 1 Tb M.2 NVMe SSD Disclaimer: Some parts of the following protocol has been copied directly from the manufacturer’s official website or from the kit manual. ..

    RNA Extraction:

    Article Title: The evolution of ovary-biased gene expression in Hawaiian Drosophila
    Article Snippet: .. For DNA barcoding, DNA was extracted from one or two legs from male specimens using the Qiagen DNeasy blood and tissue extraction kit, or from the DNA of females isolated during RNA extraction (see below). ..

    Virus:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    Recombinant:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    cDNA Synthesis:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    SYBR Green Assay:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    Sample Prep:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    Amplification:

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15 Article ll OPEN ACCESS

    Article Title: Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains Lactobacillus crispatus 1 Isolated from Isala participant (Lebeer et al.2) AMBV-815 Lactobacillus crispatus 2 Isolated from Isala participant (Lebeer et al.2) AMBV-961 Lactobacillus jensenii 1 Isolated from Isala participant (Lebeer et al.2) AMBV-494 Lactobacillus jensenii 2 Isolated from Isala participant (Lebeer et al.2) AMBV-805 Limosilactobacillus reuteri 1 Isolated from Isala participant (Lebeer et al.2) AMBV-339 Limosilactobacillus reuteri 2 Isolated from Isala participant (Lebeer et al.2) AMBV-532 Biological samples Vaginal samples Isala project, University of Antwerp ClinicalTrials.gov: NCT04319536 Chemicals, peptides, and recombinant proteins ReadyScript cDNA Synthesis Mix Sigma Aldrich UNSPSC: 12352200 Power Up SYBR Green Thermo Fisher Scientific Cat no. A25743 Critical commercial assays Illumina DNA Prep (M) Tagmentation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/library-prepkits/illumina-dna-prep.html; "RRID:SCR_010233" NovaSeq 6000 S4 Reagent Kit v1.5 Illumina https://www.illumina.com/products/ by-type/sequencing-kits/cluster-gensequencing-reagents/novaseqreagent-kits.html; "RRID:SCR_010233" NexteraXT DNA Sample Preparation kit Illumina https://www.illumina.com/products/ by-type/sequencing-kits/libraryprep-kits/nextera-xt-dna.html; "RRID:SCR_010233" RNeasy Mini Kit Qiagen Cat no. 74106 16S Barcoding Kit 24 V14 Oxford Nanopore Technologies SQK-16S114.24; "RRID:SCR_003756" Flongle flow cell (R10.4.1) Oxford Nanopore Technologies FLO-MIN114; "RRID:SCR_003756" Deposited data 16S rRNA amplicon sequencing data, Isala project Lebeer et al.,2 European Nucleotide Archive PRJEB50407 Metagenomic sequencing data, VIRGO Ma et al.88 http://virgo.igs.umaryland.edu. .. Metagenomic sequencing data, Isala project This paper, European Nucleotide Archive PRJEB87999 Top-down SynCom sequencing data This paper, European Nucleotide Archive PRJEB87999 Genome-scale metabolic models This paper, European Bioinformatics Institute BioModels repository41 MODEL250707000, https://github.com/ LebeerLab/2025_GEMS_syncom_vagina Oligonucleotides 27F (5′-AGAGTTTGATCCTGGCTCAG-3′) and 1492R (5′- CTACGGCTACCTTGTTACGA-3′) universal 16S primers This paper N/A Strain-specific primers for bottom-up SynComs, see Table S2 This paper N/A (Continued on next page) Cell Reports 44, 116171, September 23, 2025 15

    Binding Assay:

    Article Title: MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
    Article Snippet: .. DNase I 300 units/μL Invitrogen, Cat: 18047019 NA PCR H20 NA Qiagen, Cat: 17000-10 NA DNA binding beads NA Aline biosciences, Cat: C-1003-50 NA Molecular grade ethanol NA Sigmaaldrich, Cat: 51976- 500ML-F NA Qubit dsDNA BR assay Kit NA ThermoFisher, Cat: Q32853 NA Qubit assay tubes NA ThermoFisher, Cat: Q32856 NA PCR master mix NA RepliQa HiFi ToughMix, Quantabio, Cat: 95200- 500 For ultra rapid PCR amplifica on and barcoding Proteinase K NA Qiagen, Cat: RP107B-1 DNA extrac on kit NA Qiagen, Cat: 50214, with Pathogen Lysis Tubes L, Cat: 19092 Users can choose their own extrac on method as long as it is sensi ve and robust DNA/RNA Shield 1x Zymo research, Cat: R1100-50 NA Liga on Sequencing Kit NA ONT, Cat: SQK-LSK109 NA PCR Barcoding Expansion Kit NA ONT, Cat: EXP-PBC096 NA NEBNext Ultra II End Repair/dA-Tailing Module NA NEB, Cat: E7546L NA NEBNext Quick NA NEB, Cat: E6056L NA 682 683 Name Concentra on/units Commercial source Comments Liga on Module Flow Cell Priming Kit NA ONT, Cat: EXP-FLP002 Required for both protocols Flow Cell Wash Kit NA ONT, Cat: EXP-WSH004 Required for both protocols ONT Flow Cell R9.4.1 NA ONT, Cat: FLO-MIN106 or FLO-FLG001 Required for both protocols Magne c rack/plate holder NA ThermoFisher, Cat: 12331D and 12321D NA PCR plate 96 well NA Merck, Cat: BR781378 NA 1.5 ml DNA LoBind tubes NA Eppendorf, Cat: 0030108051-250EA Use LoBind tubes 2 ml round bo om tubes NA Starlab, Cat: S1620-2700C or Eppendorf, Cat: 0030120094 Avoid using LoBind tubes Pipe es and pipe e ps P2, P10, P20, P100, P200, P1000, Mul channel NA Any NA Centrifuge /Microplate centrifuge NA Any NA Hea ng block for 1.5/2 mL tubes NA Any NA Sequencing device NA Flongle, MinION Mk1B, GridION NA Device for live basecalling NA GridION or A powerful laptop A laptop with minimum 8 Gb GPU (RTX 3060 or higher), 16 GB Ram, 1 Tb M.2 NVMe SSD Disclaimer: Some parts of the following protocol has been copied directly from the manufacturer’s official website or from the kit manual. ..

    Lysis:

    Article Title: MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
    Article Snippet: .. DNase I 300 units/μL Invitrogen, Cat: 18047019 NA PCR H20 NA Qiagen, Cat: 17000-10 NA DNA binding beads NA Aline biosciences, Cat: C-1003-50 NA Molecular grade ethanol NA Sigmaaldrich, Cat: 51976- 500ML-F NA Qubit dsDNA BR assay Kit NA ThermoFisher, Cat: Q32853 NA Qubit assay tubes NA ThermoFisher, Cat: Q32856 NA PCR master mix NA RepliQa HiFi ToughMix, Quantabio, Cat: 95200- 500 For ultra rapid PCR amplifica on and barcoding Proteinase K NA Qiagen, Cat: RP107B-1 DNA extrac on kit NA Qiagen, Cat: 50214, with Pathogen Lysis Tubes L, Cat: 19092 Users can choose their own extrac on method as long as it is sensi ve and robust DNA/RNA Shield 1x Zymo research, Cat: R1100-50 NA Liga on Sequencing Kit NA ONT, Cat: SQK-LSK109 NA PCR Barcoding Expansion Kit NA ONT, Cat: EXP-PBC096 NA NEBNext Ultra II End Repair/dA-Tailing Module NA NEB, Cat: E7546L NA NEBNext Quick NA NEB, Cat: E6056L NA 682 683 Name Concentra on/units Commercial source Comments Liga on Module Flow Cell Priming Kit NA ONT, Cat: EXP-FLP002 Required for both protocols Flow Cell Wash Kit NA ONT, Cat: EXP-WSH004 Required for both protocols ONT Flow Cell R9.4.1 NA ONT, Cat: FLO-MIN106 or FLO-FLG001 Required for both protocols Magne c rack/plate holder NA ThermoFisher, Cat: 12331D and 12321D NA PCR plate 96 well NA Merck, Cat: BR781378 NA 1.5 ml DNA LoBind tubes NA Eppendorf, Cat: 0030108051-250EA Use LoBind tubes 2 ml round bo om tubes NA Starlab, Cat: S1620-2700C or Eppendorf, Cat: 0030120094 Avoid using LoBind tubes Pipe es and pipe e ps P2, P10, P20, P100, P200, P1000, Mul channel NA Any NA Centrifuge /Microplate centrifuge NA Any NA Hea ng block for 1.5/2 mL tubes NA Any NA Sequencing device NA Flongle, MinION Mk1B, GridION NA Device for live basecalling NA GridION or A powerful laptop A laptop with minimum 8 Gb GPU (RTX 3060 or higher), 16 GB Ram, 1 Tb M.2 NVMe SSD Disclaimer: Some parts of the following protocol has been copied directly from the manufacturer’s official website or from the kit manual. ..

    Blocking Assay:

    Article Title: MultiSeq-AMR: a modular amplicon-sequencing workflow for rapid detection of bloodstream infection and antimicrobial resistance markers
    Article Snippet: .. DNase I 300 units/μL Invitrogen, Cat: 18047019 NA PCR H20 NA Qiagen, Cat: 17000-10 NA DNA binding beads NA Aline biosciences, Cat: C-1003-50 NA Molecular grade ethanol NA Sigmaaldrich, Cat: 51976- 500ML-F NA Qubit dsDNA BR assay Kit NA ThermoFisher, Cat: Q32853 NA Qubit assay tubes NA ThermoFisher, Cat: Q32856 NA PCR master mix NA RepliQa HiFi ToughMix, Quantabio, Cat: 95200- 500 For ultra rapid PCR amplifica on and barcoding Proteinase K NA Qiagen, Cat: RP107B-1 DNA extrac on kit NA Qiagen, Cat: 50214, with Pathogen Lysis Tubes L, Cat: 19092 Users can choose their own extrac on method as long as it is sensi ve and robust DNA/RNA Shield 1x Zymo research, Cat: R1100-50 NA Liga on Sequencing Kit NA ONT, Cat: SQK-LSK109 NA PCR Barcoding Expansion Kit NA ONT, Cat: EXP-PBC096 NA NEBNext Ultra II End Repair/dA-Tailing Module NA NEB, Cat: E7546L NA NEBNext Quick NA NEB, Cat: E6056L NA 682 683 Name Concentra on/units Commercial source Comments Liga on Module Flow Cell Priming Kit NA ONT, Cat: EXP-FLP002 Required for both protocols Flow Cell Wash Kit NA ONT, Cat: EXP-WSH004 Required for both protocols ONT Flow Cell R9.4.1 NA ONT, Cat: FLO-MIN106 or FLO-FLG001 Required for both protocols Magne c rack/plate holder NA ThermoFisher, Cat: 12331D and 12321D NA PCR plate 96 well NA Merck, Cat: BR781378 NA 1.5 ml DNA LoBind tubes NA Eppendorf, Cat: 0030108051-250EA Use LoBind tubes 2 ml round bo om tubes NA Starlab, Cat: S1620-2700C or Eppendorf, Cat: 0030120094 Avoid using LoBind tubes Pipe es and pipe e ps P2, P10, P20, P100, P200, P1000, Mul channel NA Any NA Centrifuge /Microplate centrifuge NA Any NA Hea ng block for 1.5/2 mL tubes NA Any NA Sequencing device NA Flongle, MinION Mk1B, GridION NA Device for live basecalling NA GridION or A powerful laptop A laptop with minimum 8 Gb GPU (RTX 3060 or higher), 16 GB Ram, 1 Tb M.2 NVMe SSD Disclaimer: Some parts of the following protocol has been copied directly from the manufacturer’s official website or from the kit manual. ..



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