Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:23840181", "kind": "science-record", "revision": 7, "content_hash": "sha256:f08b3e109adb14b64aeac49e3419d7d4922f87d8ee217e52a901d39c427e2902", "created_at": "2026-11-01T15:40:03Z", "updated_at": "2026-11-01T21:58:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples.", "doi": "10.1371/journal.pcbi.1003107", "pmid": "23840181", "authors": ["David R Riley", "Karsten B Sieber", "Kelly M Robinson", "James Robert White", "Ashwinkumar Ganesan", "Syrus Nourbakhsh", "Julie C Dunning Hotopp"], "journal": "PLoS computational biology", "year": 2013, "abstract": "There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5'-UTR and 3'-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome.", "claims": [{"id": "claim-method", "statement": "Reads supporting bacterial DNA integration were detected more frequently in the human mitochondrial genome (Figure 6A, 41,852 reads in 16.6 kbp) than in the human nuclear genome (48,874 reads in 2.86 Gbp; p<2×10−16, Chi-squared test).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23840181", "locator": "sections[11] \"Acute myeloid leukemia\" paragraph 6", "quote": "Reads supporting bacterial DNA integration were detected more frequently in the human mitochondrial genome (Figure 6A, 41,852 reads in 16.6 kbp) than in the human nuclear genome (48,874 reads in 2.86 Gbp; p<2×10−16, Chi-squared test)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Illumina sequences were downloaded from the 1000 Genomes Project that were in the NCBI Short Read Archive as of November 2010 and from the TCGA in the NCBI dbGap between September 18, 2011, and September 20, 2011.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:23840181", "locator": "sections[23] \"Analysis of Illumina data from the TCGA\" paragraph 2", "quote": "Illumina sequences were downloaded from the 1000 Genomes Project that were in the NCBI Short Read Archive as of November 2010 and from the TCGA in the NCBI dbGap between September 18, 2011, and September 20, 2011."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:23840181"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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