Background: Colibactin-producing Escherichia coli containing polyketide synthase (pks+ E. coli) has been shown involved in colorectal cancer (CRC) development through gut microbiota analysis in animal models. Stool status has been associated with potentially adverse gut microbiome profiles from fecal analysis in adults. We examined the association between stool patterns and the prevalence of pks+ E. coli isolated from microbiota in fecal samples of 224 healthy Japanese individuals. Results: Stool patterns were determined by factorial analysis using a previously validated questionnaire including stool frequency, volume, color, shape, and odor. Factor scores were classified by tertile. The prevalence of pks+ E. coli was determined using specific primers for pks+ E. coli in fecal samples. Plasma and fecal fatty acids were measured via gas chromatography-mass spectrometry. The prevalence of pks+ E. coli was 26.8%. Three stool patterns contributed 70.1 % of all patterns seen (factor 1: lower frequency, darker color, and softer shape, factor 2: higher volume and harder shape, and factor 3: darker color and stronger odor). Multivariable adjusted odds ratios (95% confidence intervals) of the prevalence of pks+ E. coli for the highest versus the lowest third of the factor 1 score was 3.16 (1.38 to 7.24; P for trend = 0.006). This stool pattern correlated with some plasma and fecal fatty acids. No other stool patterns were significant. Conclusions: These results suggest that stool pattern may be useful for evaluating gut microbiota, including the presence of tumorigenic bacteria and fecal fatty acids. It may provide useful insight for effective early discovery strategies for CRC.