Evidence claim

control_signal_and_optimisation: dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance

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'

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-7b8f80935f90
Property and statement	Original source and location	Review and provenance
attributes.field control_signal_and_optimisation Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.source_locator Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.value BLAST was the only software that detected viridans group streptococci in all five culture-positive samples, but it also gave signal in the negative blood and no-template control. Lowering the BLAST e-value to 10E-13 removed reads from both controls while all culture-positive samples stayed positive (Figure 1). Removing human reads first did not change viridans streptococci abundances (p = 0.15). Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.value` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
description Descriptive fact transcribed from the pinned source. Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `links:subject:dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
name control_signal_and_optimisation: dna-pathogen-20261009-protocol-song2025-bsi-vgs-abundance Context-only references	Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection Original source ↗ Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2 Version: MicrobiologyOpen 14(6):e70158, published online 2025-12-15; PMC12705909 full-text XML Retrieved: 2026-10-09T19:48:48Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` Source artifact SHA-256: `7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-10-7b8f80935f90 · Record review: source checked

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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-claim-song2025-blast-controls

field: control_signal_and_optimisation
value: BLAST was the only software that detected viridans group streptococci in all five culture-positive samples, but it also gave signal in the negative blood and no-template control. Lowering the BLAST e-value to 10E-13 removed reads from both controls while all culture-positive samples stayed positive (Figure 1). Removing human reads first did not change viridans streptococci abundances (p = 0.15).
source locator: Results paragraph 2; 'Reduction of False-Positive Signals' paragraphs 1-2
review: method: source-hash-verification; ai-assisted-source-review; reviewer: claude; reviewer note: Separate Claude review agent, independent of the extractor; no human review claimed; date: 2026-10-09; artifact sha256: 7b122b551b2155b43c26f5a15e7382a0662d859520d2939dc91e04d88e5656ef; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12705909/fullTextXML; method note: Compared the claim text with the cited paragraphs and table cells of the re-downloaded article XML.; note: Transcribed from the pinned article XML text. Pending independent review. Independent review 2026-10-09: wording matches the cited locator.

Related records

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

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