Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation

The gut microbiome in CRC showed reproducibly higher richness than controls (P <0.01), in part due to the expansion of species typically derived from the oral cavity. A meta-analysis of the functional potential of the microbiome identified gluconeogenesis and putrefaction, and fermentation pathways as associated with CRC. In contrast, stachyose and starch degradation pathways were associated with controls. In addition, pooled analysis of raw metagenomes indicated that the choline trimethylamine lyase gene was abundant in CRC (P = 0.001), identifying a relationship between microbial choline metabolism and CRC.

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