Protocol

Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2)

Evidence concern: excluded from comparisons

Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing'

Each pipeline's relative abundance of viridans group streptococci in five culture-positive blood metagenomes and in negative blood and no-template controls.

4 evaluations · 28 results

Overview

Each pipeline's relative abundance of viridans group streptococci in five culture-positive blood metagenomes and in negative blood and no-template controls.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

4 recorded evaluations, 28 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

4 evaluations · 28 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	1.03E‐1 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Negative blood', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	2.59E‐1 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'No template control', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	1.21E‐1 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 1', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	2.87E‐2 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 2', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	6.49E‐1 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 3', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	4.39E‐2 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 4', column 'Blast'
Configuration: BLAST (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	2.39E‐2 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Blast on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 5', column 'Blast'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Negative blood', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'No template control', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	1.74E‐5 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 1', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 2', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	2.03E‐2 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 3', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	1.69E‐5 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 4', column 'Kraken'
Configuration: Kraken (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Kraken on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 5', column 'Kraken'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Negative blood', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'No template control', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 1', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 2', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	2.30E‐2 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 3', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 4', column 'Metaphlan'
Configuration: Metaphlan (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source Metaphlan on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 5', column 'Metaphlan'
Configuration: RTG Core (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source RTG on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Negative blood', column 'RTG'
Configuration: RTG Core (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source RTG on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'No template control', column 'RTG'
Configuration: RTG Core (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source RTG on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 1', column 'RTG'
Configuration: RTG Core (Song et al. 2025)	Protocol: Relative abundance of viridans group streptococci in culture-positive patient blood and negative controls (Song et al. 2025 Table 2) Dataset: Blood shotgun metagenomes from five culture-positive patients with haematological malignancy, plus negative blood and no-template controls (Song et al. 2025)	0 proportion fraction · unknown Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Evidence concern: excluded from comparisons Table 1 prints Kraken relative abundances of 5.17E‐10 (Salmonella enterica and Escherichia coli), 5.17E‐11 (Lactobacillus fermentum) and 5.17E‐12 (Enterococcus faecalis): one mantissa over three orders of magnitude. As read fractions these need at least about 2 billion to 190 billion reads per assigned read, far above the study's libraries (patient samples average 33.5 M reads after QC; the control library size is not given). The values are probably a computation or formatting artefact, so the Kraken column of Table 1 and its eta squared (3.20E‐2) should not be compared. Values are kept as printed. Table 2 values are not affected by this finding.Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 1, column 'Kraken', rows 'Salmonella enterica' to 'Enterococcus faecalis' and 'η 2'; Methods 'Sample Collection and Processing' Methods, coverage and source RTG on culture-positive blood and controls (Song et al. 2025) dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Aggregation: Not reported Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Table 2, row 'Sample 2', column 'RTG'

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Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection · Original source · MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML

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Stable ID: dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance

areas: microbes-communities
contexts: clinical_research
protocol: Blood culture is the reference. For each sample, report the relative abundance of viridans group streptococci assigned by each pipeline; the same read-out in negative blood and no-template control shows contamination or false-positive signal. The study counts a detection as valid only if absent from both negative controls.
version: Table 2 (pipelines at the settings in Methods 'Data Analysis'; before the BLAST e-value optimisation shown in Figure 1)
source locator: Methods 'Data Analysis' paragraph 1; Results paragraph 2; Table 2
limitations: Five culture-positive samples, all viridans group streptococci; no culture-negative patient samples analysed.; Table 2 prints relative abundances, not detection calls; the study's validity rule (absent from both controls) is applied in the text.; BLAST e-value optimisation that removed control signal is reported only in Figure 1, not in a table.
denominator: 5
missing metadata: uncertainty: reason: unreported

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