← All .science files
pmid:41227642
Foodborne Lactic Acid Bacteria Inactivate Planktonic and Sessile Escherichia coli O157:H7 in a Meat Processing Environment: A Physiological and Proteomic Study.
Lucia Cisneros · Ayelen Antonella Baillo · Diego Ploper · María Pia Valacco · Silvia Moreno · Osvaldo Yantorno · Vincenzina Fusco · Silvina Fadda
Foods (Basel, Switzerland) · 2025 doi:10.3390/foods14213670
Paper
complete
Experiment
partial
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 8 items
claims array · 2 items
[0] object · 6 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 1 field
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 1 item
data object · 3 fields
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 0 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 1 item
parameters object · 1 field
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 0 items
missing_operations array · 1 item
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 1 item
[0] object · 3 fields
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 8 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41227642", "kind": "science-record", "revision": 3, "content_hash": "sha256:86a364d8a108d99ead4136e11e472ffa9b55416931c16cd394141a45122738a9", "created_at": "2026-11-01T20:31:16Z", "updated_at": "2026-11-01T22:14:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Foodborne Lactic Acid Bacteria Inactivate Planktonic and Sessile Escherichia coli O157:H7 in a Meat Processing Environment: A Physiological and Proteomic Study.", "doi": "10.3390/foods14213670", "pmid": "41227642", "authors": ["Lucia Cisneros", "Ayelen Antonella Baillo", "Diego Ploper", "María Pia Valacco", "Silvia Moreno", "Osvaldo Yantorno", "Vincenzina Fusco", "Silvina Fadda"], "journal": "Foods (Basel, Switzerland)", "year": 2025, "abstract": "Enterohemorrhagic Escherichia coli (EHEC) forms persistent biofilms on meat processing surfaces, posing a significant cross-contamination risk. This study assessed the antagonistic capacity of lactic acid bacteria (LAB) against EHEC under meat-processing-like conditions. Three LAB strains were tested in planktonic co-culture with EHEC at 12 °C, all displaying bactericidal activity. In biofilm assays on stainless steel, LAB reduced EHEC biofilms without affecting their own viability. LAB cell-free supernatants further inhibited EHEC biofilms by 2.6-3.5 log CFU/cm2, highlighting the role of secreted antagonistic compounds. Among the tested strains, Pediococcus pentosaceus CRL 2145 showed the strongest effect and was selected for deeper analysis. Fluorescence microscopy confirmed EHEC cell death within mixed biofilms. Proteomic profiling of CRL 2145 under mixed-biofilm conditions revealed 162 differentially expressed proteins, with 156 upregulated. These proteins were mainly associated with metabolism, transcription, translation, and stress response pathways, suggesting a multifactorial inhibitory mechanism involving metabolic dominance, physical competition, and secretion of antagonistic molecules. Overall, this study deepens our understanding of the molecular and physiological aspects of LAB-EHEC interaction. P. pentosaceus CRL 2145 emerges as a promising biocontrol agent that could be applied, alone or with its supernatants, to meat processing surfaces to improve food safety. Proteomic data: ProteomeXchange PXD067300.", "claims": [{"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [27] with the dataset identifier PXD067300.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41227642", "locator": "sections[43] \"Data Availability Statement\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [27] with the dataset identifier PXD067300."}], "state": "complete"}, {"id": "claim-target-result", "statement": "LAB cell-free supernatants further inhibited EHEC biofilms by 2.6–3.5 log CFU/cm2, highlighting the role of secreted antagonistic compounds.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41227642", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "LAB cell-free supernatants further inhibited EHEC biofilms by 2.6–3.5 log CFU/cm2, highlighting the role of secreted antagonistic compounds."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "LAB cell-free supernatants further inhibited EHEC biofilms by 2.6–3.5 log CFU/cm2, highlighting the role of secreted antagonistic compounds.", "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:41227642"], "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:PXD067300"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"p_value": "Log p-value (–Log Student T-test p-"}, "inputs": ["data:geo:PXD067300"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41227642", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/foods14213670", "sha256": "sha256:4668287d7ad946e90766755868bfdb1f06b6f32e3641c3bc7f9e55e4d5d05f72", "bytes": 69520, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/foods14213670", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12607491", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD067300", "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=PXD067300", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD067300", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [27] with the dataset identifier PXD067300.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [27] with the dataset identifier PXD067300.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Foodborne Lactic Acid Bacteria Inactivate Planktonic and Ses-sile Escherichia coli O157:H7 in a meat processing environment: A Physiological and Proteomic Study", "resolution_checked_at": "2026-11-01T20:16:18Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD067300 not downloaded", "asset:data:geo:PXD067300 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {"p_value": "Log p-value (–Log Student T-test p-"}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Student T-test"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}], "targets": [], "gaps": ["method.student_t"]}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["PXD067300"], "resolved_accessions": ["PXD067300"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository [27] with the dataset identifier PXD067300."], "basis": "The paper names PXD067300 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:41227642", "data:geo:PXD067300"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD067300"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:05:35Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20250, "completion_tokens": 1619, "cached_tokens": 264}}, "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:41227642", "type": "paper", "label": "pmid:41227642"}, {"id": "source:pmid:41227642", "type": "manuscript", "label": "PMID 41227642 full text"}, {"id": "data:geo:PXD067300", "type": "dataset", "label": "GEO PXD067300"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41227642", "type": "paper", "label": "pmid:41227642"}, {"id": "source:pmid:41227642", "type": "manuscript", "label": "PMID 41227642 full text"}, {"id": "data:geo:PXD067300", "type": "dataset", "label": "GEO PXD067300"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41227642", "type": "extraction", "used": ["source:pmid:41227642"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD067300", "type": "accession_resolution", "used": ["data:geo:PXD067300"], "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:41227642", "parent_hash": "sha256:2c1414d8a15befb6e65d6f0ab75fc393d77d7fe5899b2545c4cf81bac6e8fb97", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD067300 licence not read", "asset:data:geo:PXD067300 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student T-test"], "order_basis": "analysis_only", "id": "assay:1"}]}