Normalization of the microbiota in patients after treatment for colonic lesions

Abstract

Background: Colorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26).

Results: There were small changes to the bacterial community associated with adenoma or advanced adenoma and large changes associated with carcinoma. The communities from patients with carcinomas changed significantly more than those with adenoma following treatment (P value < 0.001). Although treatment was associated with intrapersonal changes, the change in the abundance of individual OTUs in response to treatment was not consistent within diagnosis groups (P value > 0.05). Because the distribution of OTUs across patients and diagnosis groups was irregular, we used the random forest machine learning algorithm to identify groups of OTUs that could be used to classify pre and post-treatment samples for each of the diagnosis groups. Although the adenoma and carcinoma models could reliably differentiate between the pre- and post-treatment samples (P value < 0.001), the advanced-adenoma model could not (P value = 0.61). Furthermore, there was little overlap between the OTUs that were indicative of each treatment. To determine whether individuals who underwent treatment were more likely to have OTUs associated with normal colons we used a larger cohort that contained individuals with normal colons and those with adenomas, advanced adenomas, and carcinomas. We again built random forest models and measured the change in the positive probability of having one of the three diagnoses to assess whether the post-treatment samples received the same classification as the pre-treatment samples. Samples from patients who had carcinomas changed toward a microbial milieu that resembles the normal colon after treatment (P value < 0.001). Finally, we were unable to detect any significant differences in the microbiota of individuals treated with surgery alone and those treated with chemotherapy or chemotherapy and radiation (P value > 0.05).

Conclusions: By better understanding the response of the microbiota to treatment for adenomas and carcinomas, it is likely that biomarkers will eventually be validated that can be used to quantify the risk of recurrence and the likelihood of survival. Although it was difficult to identify significant differences between pre- and post-treatment samples from patients with adenoma and advanced adenoma, this was not the case for carcinomas. Not only were there large changes in pre- versus post-treatment samples for those with carcinoma, but also these changes were toward a more normal microbiota.

Keywords: Colorectal cancer; Microbiota; Polyps; Risk factor; Treatment.

Fig. 1

General differences between adenoma, advanced adenoma, and carcinoma groups after treatment. a (θ)_YC distances from pre- versus post-sample within each individual. A significant difference was found between the adenoma and carcinoma group (P value = 5.36e–05). Solid black points represent the median value for each diagnosis group. b NMDS of the pre- and post-treatment samples for the adenoma group. c NMDS of the pre- and post-treatment samples for the advanced adenoma group. d NMDS of the pre- and post-treatment samples for the carcinoma group

Fig. 2

The top 10 most important OTUs used to classify treatment for adenoma, advanced adenoma, and carcinoma. a Adenoma OTUs. b Advanced Adenoma OTUs. c Carcinoma OTUs. The darker circle highlights the median log10 MDA value obtained from 100 different 80/20 splits while the lighter colored circles represents the value obtained for a specific run

Fig. 3

Top 10% most important OTUs common to those models used to differentiate between patients with normal colons and those with adenoma, advanced adenoma, and carcinoma. a Venn diagram showing the OTU overlap between each model. b For each common OTU the lowest taxonomic identification and importance rank for each model run is shown

Fig. 4

Treatment response based on models built for adenoma, advanced adenoma, or carcinoma. a Positive probability change from initial to follow-up sample in those with adenoma. b Positive probability change from initial to follow-up sample in those with advanced adenoma. c Positive probability change from initial to follow-up sample in those with carcinoma