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Towards the human colorectal cancer microbiome.

Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H - PLoS ONE (2011)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, Cardiff University, Cardiff, United Kingdom.

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.

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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.
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pone-0020447-g002: 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.

Mentions: To define the colon tumor microbiome at a deep level, we amplified and sequenced the V1–V3 region of the bacterial 16S rRNA genes (Table S1), which resulted in a total of 193,880 ribotags of length 401–500 bp. The data showed high coverage values (>88%) and rarefaction curves indicated satisfactory sampling of the communities at 90% identity (Figure S2B; Table S2). Libshuff analysis indicated that all on- and off-tumor communities were significantly different (p<0.0001) from each other (Table S3). Importantly, both alignment-dependent and independent methods supported the observation of these altered tumor microbiomes (Figure 2, Figure S2C and D; Table S3). Moreover, while DGGE and RISA only showed minor differences for patient D, subtle, but significant, differences could be identified by the deep sequencing approach. This clearly exemplifies the superior resolution that can be obtained with the latter technology. The data showed a general tendency of more Bacteroidetes and less Firmicutes from in tumor tissue compared to matching off-tumor mucosa (Figure S3). However, as could be expected the observed microbiome shifts showed a high level of variability among patients (Figure S3A–F) and in certain cases were even contrary to the general tendency (Figure S3G). Although S. bovis or C. septicum infections have a known clinical association with CRC, only very few sequences mapped to rRNA of these two species and no dependable colonization of CRC tissue was observed. This could be explained by the fact that such opportunistic pathogens are predominantly present in the transient adenoma stage of CRC [37].


Towards the human colorectal cancer microbiome.

Marchesi JR, Dutilh BE, Hall N, Peters WH, Roelofs R, Boleij A, Tjalsma H - PLoS ONE (2011)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3101260&req=5

pone-0020447-g002: 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.
Mentions: To define the colon tumor microbiome at a deep level, we amplified and sequenced the V1–V3 region of the bacterial 16S rRNA genes (Table S1), which resulted in a total of 193,880 ribotags of length 401–500 bp. The data showed high coverage values (>88%) and rarefaction curves indicated satisfactory sampling of the communities at 90% identity (Figure S2B; Table S2). Libshuff analysis indicated that all on- and off-tumor communities were significantly different (p<0.0001) from each other (Table S3). Importantly, both alignment-dependent and independent methods supported the observation of these altered tumor microbiomes (Figure 2, Figure S2C and D; Table S3). Moreover, while DGGE and RISA only showed minor differences for patient D, subtle, but significant, differences could be identified by the deep sequencing approach. This clearly exemplifies the superior resolution that can be obtained with the latter technology. The data showed a general tendency of more Bacteroidetes and less Firmicutes from in tumor tissue compared to matching off-tumor mucosa (Figure S3). However, as could be expected the observed microbiome shifts showed a high level of variability among patients (Figure S3A–F) and in certain cases were even contrary to the general tendency (Figure S3G). Although S. bovis or C. septicum infections have a known clinical association with CRC, only very few sequences mapped to rRNA of these two species and no dependable colonization of CRC tissue was observed. This could be explained by the fact that such opportunistic pathogens are predominantly present in the transient adenoma stage of CRC [37].

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, Cardiff University, Cardiff, United Kingdom.

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.

Show MeSH
Related in: MedlinePlus