In:
Frontiers in Microbiology, Frontiers Media SA, Vol. 14 ( 2023-5-22)
Abstract:
Colorectal cancer (CRC) is linked to distinct gut microbiome patterns. The efficacy of gut bacteria as diagnostic biomarkers for CRC has been confirmed. Despite the potential to influence microbiome physiology and evolution, the set of plasmids in the gut microbiome remains understudied. Methods We investigated the essential features of gut plasmid using metagenomic data of 1,242 samples from eight distinct geographic cohorts. We identified 198 plasmid-related sequences that differed in abundance between CRC patients and controls and screened 21 markers for the CRC diagnosis model. We utilize these plasmid markers combined with bacteria to construct a random forest classifier model to diagnose CRC. Results The plasmid markers were able to distinguish between the CRC patients and controls [mean area under the receiver operating characteristic curve (AUC = 0.70)] and maintained accuracy in two independent cohorts. In comparison to the bacteria-only model, the performance of the composite panel created by combining plasmid and bacteria features was significantly improved in all training cohorts (mean AUC composite = 0.804 and mean AUC bacteria = 0.787) and maintained high accuracy in all independent cohorts (mean AUC composite = 0.839 and mean AUC bacteria = 0.821). In comparison to controls, we found that the bacteria-plasmid correlation strength was weaker in CRC patients. Additionally, the KEGG orthology (KO) genes in plasmids that are independent of bacteria or plasmids significantly correlated with CRC. Conclusion We identified plasmid features associated with CRC and showed how plasmid and bacterial markers could be combined to further enhance CRC diagnosis accuracy.
Type of Medium:
Online Resource
ISSN:
1664-302X
DOI:
10.3389/fmicb.2023.1130446
DOI:
10.3389/fmicb.2023.1130446.s001
DOI:
10.3389/fmicb.2023.1130446.s002
DOI:
10.3389/fmicb.2023.1130446.s003
DOI:
10.3389/fmicb.2023.1130446.s004
DOI:
10.3389/fmicb.2023.1130446.s005
DOI:
10.3389/fmicb.2023.1130446.s006
DOI:
10.3389/fmicb.2023.1130446.s007
DOI:
10.3389/fmicb.2023.1130446.s008
Language:
Unknown
Publisher:
Frontiers Media SA
Publication Date:
2023
detail.hit.zdb_id:
2587354-4