Towards the human colorectal cancer microbiome

Abstract

Multiple factors drive the progression from healthy mucosa towards sporadic colorectal carcinomas and accumulating evidence associates intestinal bacteria with disease initiation and progression. Therefore, the aim of this study was to provide a first high-resolution map of colonic dysbiosis that is associated with human colorectal cancer (CRC). To this purpose, the microbiomes colonizing colon tumor tissue and adjacent non-malignant mucosa were compared by deep rRNA sequencing. The results revealed striking differences in microbial colonization patterns between these two sites. Although inter-individual colonization in CRC patients was variable, tumors consistently formed a niche for Coriobacteria and other proposed probiotic bacterial species, while potentially pathogenic Enterobacteria were underrepresented in tumor tissue. As the intestinal microbiota is generally stable during adult life, these findings suggest that CRC-associated physiological and metabolic changes recruit tumor-foraging commensal-like bacteria. These microbes thus have an apparent competitive advantage in the tumor microenvironment and thereby seem to replace pathogenic bacteria that may be implicated in CRC etiology. This first glimpse of the CRC microbiome provides an important step towards full understanding of the dynamic interplay between intestinal microbial ecology and sporadic CRC, which may provide important leads towards novel microbiome-related diagnostic tools and therapeutic interventions.

Figure 1. DGGE Fingerprinting of CRC Tissue and Non-malignant Adjacent Mucosa.

An internal fragment (∼450 bps) of the bacterial 16S rRNA gene was amplified from colon tissue-extracted DNA by a broad-range PCR approach after which these amplicon mixtures were applied to DGGE. Patient characteristics can be found in Table 1; off, non-malignant tissue; on, tumor tissue.

Figure 2. Phylogenetic Analysis of Altered Microbiomes.

The 454 sequencing data were normalized in MEGAN (Huson et al. 2009) and parsed through the RDP pyropipeline classifier tool (Cole et al. 2009) to generate a csv file of taxonomic abundance. This file was used as input for MEGAN to visualize in which families differences between non-malignant tissue (off-tumor) and CRC tissue (on-tumor) communities are present. A high-resolution image of this Figure for “zoom-in” purposes can be downloaded from Figure S2E .

Figure 3. Consistent Biases in Microbiota CRC Tissue and Non-malignant Adjacent Mucosa.

Relative distribution of selected CRC over/under represented taxa was calculated as the fraction annotated sequences of the total number of reads in that specific sample. Consistency score for the indicated taxon (see Table 2) is given between brackets and reflects how consistently clades were enriched across patients A–F; green bars indicate the fraction in off-tumor and red bars indicate fraction of this taxon on-tumor.