A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28883813", "kind": "science-record", "revision": 6, "content_hash": "sha256:de847a1c7bb5914da8bae61ab49285c4405efbc0b7b80e88699911f1597db197", "created_at": "2026-11-01T15:40:28Z", "updated_at": "2026-11-01T21:21:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Structural and Functional Elucidation of the Rumen Microbiome Influenced by Various Diets and Microenvironments.", "doi": "10.3389/fmicb.2017.01605", "pmid": "28883813", "authors": ["Simon Deusch", "Amélia Camarinha-Silva", "Jürgen Conrad", "Uwe Beifuss", "Markus Rodehutscord", "Jana Seifert"], "journal": "Frontiers in microbiology", "year": 2017, "abstract": "The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal's feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology, and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or grass hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, particle-associated rumen liquid, and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500 MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Data are available via ProteomeXchange with the identifier PXD006070. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of microbial adaptation in the rumen.", "claims": [{"id": "claim-method", "statement": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data are available via ProteomeXchange with the identifier PXD006070.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are available via ProteomeXchange with the identifier PXD006070."}], "state": "complete"}, {"id": "claim-target-result", "statement": "ANOSIM showed that bacterial protein abundance differed significantly between corn silage and grass silage diets (R = 0.600, P = 0.0001) and between corn silage and hay diets (R = 0.442, P = 0.0001); the underlying sequencing and mass-spectrometry data are available through the European Nucleotide Archive under accession PRJEB19491 and ProteomeXchange under identifier PXD006070.", "kind": "quantitative", "target": {"value": 0.0001, "unit": "p-value", "tolerance": null, "source": "ANOSIM verified significant differences in bacterial protein abundances regarding the diets with an R-value of 0.600 (P = 0.0001) for the corn silage- and grass silage-based samples and 0.442 (P = 0.0001) for the corn silage- and hay-derived samples."}, "evidence": [{"asset": "source:pmid:28883813", "locator": "sections[13] \"Metaproteomics and amplicon sequencing of the rumen microbiome\" paragraph 2", "quote": "ANOSIM verified significant differences in bacterial protein abundances regarding the diets with an R-value of 0.600 (P = 0.0001) for the corn silage- and grass silage-based samples and 0.442 (P = 0.0001) for the corn silage- and hay-derived samples."}, {"asset": "source:pmid:28883813", "locator": "sections[11] \"Statistical analyses\" paragraph 2", "quote": "One-way analysis of similarities (ANOSIM) was used to determine statistical differences in protein and OTU abundance between diets, sample fractions and host animals (Clarke and Warwick, 2001)."}, {"asset": "source:pmid:28883813", "locator": "sections[6] \"Illumina amplicon sequencing\" paragraph 2", "quote": "Sequences were submitted to European Nucleotide Archive under the study accession number PRJEB19491."}, {"asset": "source:pmid:28883813", "locator": "sections[9] \"Bioinformatic data analysis\" paragraph 2", "quote": "The mass spectrometry data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaino et al., 2016) with the dataset identifier PXD006070."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "ANOSIM showed that bacterial protein abundance differed significantly between corn silage and grass silage diets (R = 0.600, P = 0.0001) and between corn silage and hay diets (R = 0.442, P = 0.0001); the underlying sequencing and mass-spectrometry data are available through the European Nucleotide Archive under accession PRJEB19491 and ProteomeXchange under identifier PXD006070.", "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:28883813"], "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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