Proteomic profiling of dysbiosis-challenged broilers reveals potential blood biomarkers for intestinal health.

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In broilers, dysbiosis disrupts the microbiota-host balance, often without obvious clinical symptoms but with intestinal inflammation, and leads to impaired animal performance. This study aimed to identify host blood-based protein biomarkers that indicate intestinal inflammation and intestinal barrier dysfunction. Using mass spectrometry-based proteomics, blood plasma samples from broilers derived from an in vivo dysbiosis model were analyzed and compared to healthy controls. Microscopic histologic changes in the gut (shortened villi, increased crypt depth) were observed in the duodenal and jejunal tissue of 25-days old challenged birds. Elevated levels of permeability markers faecal ovotransferrin and serum iohexol additionally indicated increased intestinal leakage in the challenged group. The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups. The challenge was marked by activation of immune and signaling pathways, and response to bacteria, while proteins related to cellular physiology, cell-cell communication, and extracellular matrix (ECM) processes were suppressed. Protein-protein interaction analysis revealed two clusters of downregulated proteins involved in ECM organization and cell adhesion. Intestinal dysbiosis in broilers demonstrated that the host prioritizes immune defense over structural maintenance. The activation of immune processes and suppression of ECM pathways highlight potential biomarkers and therapeutic targets. Data are available via ProteomeXchange with identifier PXD056546.", "claims": [{"id": "claim-method", "statement": "Pairwise comparisons between experimental groups were conducted using the limma package [24], followed by Benjamini–Hochberg method for multiple hypothesis testing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40629482", "locator": "sections[8] \"LC–MS/MS and data analysis\" paragraph 4", "quote": "Pairwise comparisons between experimental groups were conducted using the limma package [24], followed by Benjamini–Hochberg method for multiple hypothesis testing."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [74] partner repository with the dataset identifier PXD056546 (Username: reviewer_pxd056546@ebi.ac.uk and Password: DV2LINNIyVsS).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40629482", "locator": "sections[22] \"Data availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [74] partner repository with the dataset identifier PXD056546 (Username: reviewer_pxd056546@ebi.ac.uk and Password: DV2LINNIyVsS)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40629482", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The blood plasma proteome analysis enabled quantification of 388 proteins, 25 of which were significantly different between the tested groups.", "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:40629482"], "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. 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