Pronounced metabolic changes in adaptation to biofilm growth by Streptococcus pneumoniae.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25188255", "kind": "science-record", "revision": 3, "content_hash": "sha256:3c98843a6e85e2fe0ccea85570e961c8d4d560edab277ed595808f6d1f4d8316", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:19:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pronounced metabolic changes in adaptation to biofilm growth by Streptococcus pneumoniae.", "doi": "10.1371/journal.pone.0107015", "pmid": "25188255", "authors": ["Raymond N Allan", "Paul Skipp", "Johanna Jefferies", "Stuart C Clarke", "Saul N Faust", "Luanne Hall-Stoodley", "Jeremy Webb"], "journal": "PloS one", "year": 2014, "abstract": "Streptococcus pneumoniae accounts for a significant global burden of morbidity and mortality and biofilm development is increasingly recognised as important for colonization and infection. Analysis of protein expression patterns during biofilm development may therefore provide valuable insights to the understanding of pneumococcal persistence strategies and to improve vaccines. iTRAQ (isobaric tagging for relative and absolute quantification), a high-throughput gel-free proteomic approach which allows high resolution quantitative comparisons of protein profiles between multiple phenotypes, was used to interrogate planktonic and biofilm growth in a clinical serotype 14 strain. Comparative analyses of protein expression between log-phase planktonic and 1-day and 7-day biofilm cultures representing nascent and late phase biofilm growth were carried out. Overall, 244 proteins were identified, of which >80% were differentially expressed during biofilm development. Quantitatively and qualitatively, metabolic regulation appeared to play a central role in the adaptation from the planktonic to biofilm phenotype. Pneumococci adapted to biofilm growth by decreasing enzymes involved in the glycolytic pathway, as well as proteins involved in translation, transcription, and virulence. In contrast, proteins with a role in pyruvate, carbohydrate, and arginine metabolism were significantly increased during biofilm development. Downregulation of glycolytic and translational proteins suggests that pneumococcus adopts a covert phenotype whilst adapting to an adherent lifestyle, while utilization of alternative metabolic pathways highlights the resourcefulness of pneumococcus to facilitate survival in diverse environmental conditions. These metabolic proteins, conserved across both the planktonic and biofilm phenotypes, may also represent target candidates for future vaccine development and treatment strategies. Data are available via ProteomeXchange with identifier PXD001182.", "claims": [{"id": "claim-method", "statement": "The protein ratios were calculated using MASCOT version 2.2.1, where the peptide ratios were weighted and median normalisation was performed, automatic outlier removal was chosen and the peptide threshold was set to ‘at least homology’.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25188255", "locator": "sections[11] \"Peak list generation and database searching\" paragraph 3", "quote": "The protein ratios were calculated using MASCOT version 2.2.1, where the peptide ratios were weighted and median normalisation was performed, automatic outlier removal was chosen and the peptide threshold was set to ‘at least homology’."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The authors confirm that all data underlying the findings are fully available without restriction. All mass spectrometry data files are available from the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001182.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25188255", "locator": "sections[20] \"Data Availability\" paragraph 2", "quote": "The authors confirm that all data underlying the findings are fully available without restriction. All mass spectrometry data files are available from the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001182."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used iTRAQ-based quantitative proteomics to compare planktonic, nascent 1-day biofilm, and late-phase 7-day biofilm cultures, identifying 244 proteins with more than 80% differentially expressed during biofilm development; the underlying mass-spectrometry data are available through ProteomeXchange under identifier PXD001182.", "kind": "quantitative", "target": {"value": 80.0, "unit": "per cent", "tolerance": null, "source": "Overall, 244 proteins were identified, of which >80% were differentially expressed during biofilm development."}, "evidence": [{"asset": "source:pmid:25188255", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "iTRAQ (isobaric tagging for relative and absolute quantification), a high-throughput gel-free proteomic approach which allows high resolution quantitative comparisons of protein profiles between multiple phenotypes, was used to interrogate planktonic and biofilm growth in a clinical serotype 14 strain."}, {"asset": "source:pmid:25188255", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Overall, 244 proteins were identified, of which >80% were differentially expressed during biofilm development."}, {"asset": "source:pmid:25188255", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with identifier PXD001182."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used iTRAQ-based quantitative proteomics to compare planktonic, nascent 1-day biofilm, and late-phase 7-day biofilm cultures, identifying 244 proteins with more than 80% differentially expressed during biofilm development; the underlying mass-spectrometry data are available through ProteomeXchange under identifier PXD001182.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25188255"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD001182"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD001182"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25188255", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0107015", "sha256": "sha256:d20b8c5c7ece8a955293dc9aa7b3fe9340356d1231aee365b31bc70606a2b036", "bytes": 54186, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0107015", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4154835", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD001182", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD001182", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD001182", "version": null, "note": "The authors confirm that all data underlying the findings are fully available without restriction. All mass spectrometry data files are available from the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001182.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The authors confirm that all data underlying the findings are fully available without restriction. All mass spectrometry data files are available from the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001182.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Metabolic changes in adaptation to biofilm growth by streptococcus pneumoniae", "resolution_checked_at": "2026-10-31T18:35:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD001182 not downloaded", "asset:data:geo:PXD001182 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "median normalisation", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The protein ratios were calculated using MASCOT version 2.2.1, where the peptide ratios were weighted and median normalisation was performed, automatic outlier removal was chosen and the peptide threshold was set to ‘at least homology’."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 80.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (median normalisation), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD001182"], "resolved_accessions": ["PXD001182"], "statements": ["The authors confirm that all data underlying the findings are fully available without restriction. All mass spectrometry data files are available from the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset identifier PXD001182."], "basis": "The paper names PXD001182 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:25188255", "data:geo:PXD001182"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD001182"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:41Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 102357, "completion_tokens": 3252, "cached_tokens": 51852}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:25188255", "type": "paper", "label": "pmid:25188255"}, {"id": "source:pmid:25188255", "type": "manuscript", "label": "PMID 25188255 full text"}, {"id": "data:geo:PXD001182", "type": "dataset", "label": "GEO PXD001182"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:25188255", "type": "paper", "label": "pmid:25188255"}, {"id": "source:pmid:25188255", "type": "manuscript", "label": "PMID 25188255 full text"}, {"id": "data:geo:PXD001182", "type": "dataset", "label": "GEO PXD001182"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-25188255", "type": "extraction", "used": ["source:pmid:25188255"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD001182", "type": "accession_resolution", "used": ["data:geo:PXD001182"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:25188255", "parent_hash": "sha256:66024e332b275c7404a8dafce6eef7bdb00ae7e131308a7c2dfb5438b5edd3ee", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD001182 licence not read", "asset:data:geo:PXD001182 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"]}