{"id":"b06e748b-3d6a-532e-9ac5-6972019e69ca","stable_key":"7484635e-cc8f-5cd6-a978-6dc5775a7db5:berberine-microbial-genes","predicate":"alters","statement":"Metagenomics identified altered cutC/cntA abundance alongside changes in microbial composition after berberine.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"context_dependent","is_public":true,"mechanism_event_id":"399b8e9a-2602-5ec2-8a72-6e1200966cf2","mechanism_event_label":"The community abundance of metabolic genes changed; direct inhibition of each encoded enzyme was not established.","subject":{"id":"7bbe0633-b2f1-510f-adc0-3c4d0ddad05d","slug":"berberine","display_name":"Berberine","entity_type_key":"small_molecule"},"object":{"id":"b10445de-1264-5a5b-a1f6-ec11709b696e","slug":"microbial-cutc-cnta-abundance","display_name":"Gut microbial cutC and cntA gene abundance","entity_type_key":"cellular_process"},"evidence_count":1,"mechanism_event":{"id":"399b8e9a-2602-5ec2-8a72-6e1200966cf2","stable_key":"7484635e-cc8f-5cd6-a978-6dc5775a7db5:berberine-microbial-genes-event","event_type":"biochemical_relationship","label":"The community abundance of metabolic genes changed; direct inhibition of each encoded enzyme was not established.","description":"Metagenomics identified altered cutC/cntA abundance alongside changes in microbial composition after berberine.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"7bbe0633-b2f1-510f-adc0-3c4d0ddad05d","slug":"berberine","display_name":"Berberine","entity_type_key":"small_molecule"},"role":"subject","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"b10445de-1264-5a5b-a1f6-ec11709b696e","slug":"microbial-cutc-cnta-abundance","display_name":"Gut microbial cutC and cntA gene abundance","entity_type_key":"cellular_process"},"role":"target","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""}]},"contexts":[{"dimension":"evidence_span","value_text":"{\"source_cache\": \"artifacts/berberine-research/33863898.abstract.txt\", \"locator\": \"Primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"a81ea95bbf1d7f7f1e924998b9e02bc29d908d759dd575ffdf9c56bf4deb9b77\", \"start_char\": 0, \"end_char\": 1309, \"text_sha256\": \"a81ea95bbf1d7f7f1e924998b9e02bc29d908d759dd575ffdf9c56bf4deb9b77\"}","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"experimental_model","value_text":"Choline tracer, microbial culture, microbiome transfer and atherosclerosis models","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"Choline-supplemented chow and berberine; deuterated choline tracing","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Human fecal culture is not a human treatment trial. Reduced TMAO in mice does not establish fewer human cardiovascular events or justify reducing essential choline intake.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Berberine research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"berberine","display_name":"Berberine","entity_type_key":"small_molecule"}},{"dimension":"organism","value_text":"C57BL/6J and ApoE-knockout mice; bacterial cultures and human fecal consortia","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"The community abundance of metabolic genes changed; direct inhibition of each encoded enzyme was not established.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[berberine-p33863898] Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome. (2021). https://pubmed.ncbi.nlm.nih.gov/33863898/ DOI: 10.1038/s41522-021-00205-8","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Microbial choline metabolism","comparator":null,"unit":null,"notes":"","entity":null}],"evidence":[{"id":"40e9a1a8-522b-5b54-af07-a615f657ba8d","evidence_kind":"source_excerpt","locator":"Lines 1104-1115","start_line":1104,"end_line":1115,"excerpt":"### berberine-microbial-genes\nMetagenomics identified altered cutC/cntA abundance alongside changes in microbial composition after berberine.\nCondition category: normal\nnutrient_topic: Berberine research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: The community abundance of metabolic genes changed; direct inhibition of each encoded enzyme was not established.\norganism: C57BL/6J and ApoE-knockout mice; bacterial cultures and human fecal consortia\ntissue_or_cell_type: Microbial choline metabolism\nexperimental_model: Choline tracer, microbial culture, microbiome transfer and atherosclerosis models\nlimitations: Human fecal culture is not a human treatment trial. Reduced TMAO in mice does not establish fewer human cardiovascular events or justify reducing essential choline intake.\nexposure: Choline-supplemented chow and berberine; deuterated choline tracing\nevidence_span: {\"source_cache\": \"artifacts/berberine-research/33863898.abstract.txt\", \"locator\": \"Primary indexed abstract; zero-based, end-exclusive Unicode character offsets\", \"file_sha256\": \"a81ea95bbf1d7f7f1e924998b9e02bc29d908d759dd575ffdf9c56bf4deb9b77\", \"start_char\": 0, \"end_char\": 1309, \"text_sha256\": \"a81ea95bbf1d7f7f1e924998b9e02bc29d908d759dd575ffdf9c56bf4deb9b77\"}\n[berberine-p33863898] Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome. (2021). https://pubmed.ncbi.nlm.nih.gov/33863898/ DOI: 10.1038/s41522-021-00205-8","model_system":"Choline tracer, microbial culture, microbiome transfer and atherosclerosis models","directness":"author_interpretation","verification_status":"source_derived_draft","notes":"Exact curation-document quotation, not publisher quotation. Study references: [berberine-p33863898] Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome. (2021). https://pubmed.ncbi.nlm.nih.gov/33863898/ DOI: 10.1038/s41522-021-00205-8","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"9bb61e1d-e5cf-5b05-a9ca-409291f7a313","stable_key":"import-7484635e-cc8f-5cd6-a978-6dc5775a7db5","title":"Berberine: metabolism, nutrient connections and drug interactions (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. Not publisher full text.","file_path":"","sha256":"2f376a035ae79c93e62e2ea4a8d5385643bf16553f108d12b6a80c89e6d41f4c","revision_id":"2a099429-1c4a-55be-aa2c-0565d08bda80","review_status":"unverified_draft","notes":""}}],"relations":[],"conflicts":[],"corrections":[],"research":null}