Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis
Correction(s) for this article
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Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis
- Pauline D. Scanlan,
- Fergus Shanahan,
- Yvonne Clune,
- John K. Collins,
- Gerald C. O'Sullivan,
- Micheal O'Riordan,
- Elaine Holmes,
- Yulan Wang,
- Julian R. Marchesi,
- Volume 10Issue 5Environmental Microbiology
- pages: 1382-1382
- First Published online: April 4, 2008
Pauline D. Scanlan
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
Search for more papers by this authorJohn K. Collins
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
Medicine, University College Cork, Cork, Ireland.
Search for more papers by this authorGerald C. O'Sullivan
Cork Cancer Research Centre, Mercy University Hospital, Cork, Ireland.
Search for more papers by this authorMicheal O'Riordan
The Mercy University Hospital, University College Cork, Cork, Ireland.
Search for more papers by this authorElaine Holmes
Department of Biomolecular Medicine, SORA Division, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK.
Search for more papers by this authorYulan Wang
Department of Biomolecular Medicine, SORA Division, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK.
Search for more papers by this authorCorresponding Author
Julian R. Marchesi
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
*E-mail [email protected]; Tel. +353 21 49028220; Fax +353 21 4903101.Search for more papers by this authorPauline D. Scanlan
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
Search for more papers by this authorJohn K. Collins
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
Medicine, University College Cork, Cork, Ireland.
Search for more papers by this authorGerald C. O'Sullivan
Cork Cancer Research Centre, Mercy University Hospital, Cork, Ireland.
Search for more papers by this authorMicheal O'Riordan
The Mercy University Hospital, University College Cork, Cork, Ireland.
Search for more papers by this authorElaine Holmes
Department of Biomolecular Medicine, SORA Division, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK.
Search for more papers by this authorYulan Wang
Department of Biomolecular Medicine, SORA Division, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK.
Search for more papers by this authorCorresponding Author
Julian R. Marchesi
Departments of Microbiology and
Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
*E-mail [email protected]; Tel. +353 21 49028220; Fax +353 21 4903101.Search for more papers by this authorSummary
A role for the intestinal microbiota is routinely cited as a potential aetiological factor in colorectal cancer initiation and progression. As the majority of bacteria in the gut are refractory to culture we investigated this ecosystem in subjects with colorectal cancer and with adenomatous polyposis who are at high risk of developing colorectal cancer, using culture-independent methods. Twenty colorectal cancer and 20 polypectomized volunteers were chosen for this analysis. An exploration of the diversity and temporal stability of the dominant bacteria and several bacterial subgroups was undertaken using 16S rRNA gene denaturing gradient gel electrophoresis and ribosomal intergenic spacer analysis (RISA). Metabonomic analysis of the distal gut microbiota's environment was also undertaken. A significantly reduced temporal stability and increased diversity for the microbiota of subjects with colorectal cancer and polyposis was evident. A significantly increased diversity of the Clostridium leptum and C. coccoides subgroups was also noted for both disease groups. A clear division in the metabonome was observed for the colorectal cancer and polypectomized subjects compared with control volunteers. The intestinal microbiota and their metabolites are significantly altered in both colorectal cancer and polypectomized subjects compared with controls.
Supporting Information
Fig. S1. Typical 600 MHz 1H NMR spectra of faecal extracts obtained from three subjects. The spectra were obtained using a Bruker DRX 600 NMR spectrometer operating at 600.13 MHz for 1H equipped with a 5 mm triple resonance probe with an inverse detection (Bruker, Germany). The spectra in the aromatic region (δ 6.5–8.5) were magnified four times compared with the aliphatic region. Keys: 1: butyrate; 2: leucine; 3: propionate; 4: valine; 5: isoleucine; 6: threonine; 7: alanine; 8: lysine; 9: acetate; 10: glutamate; 11: succinate; 12: aspartic acid; 13: asparagine; 14: trimethylamine; 15: cysteine; 16: proline; 17: glycerol; 18: methylamine; 19: 5-aminosalicylic acid; 20: N-acetyl-5-aminosalicylic acid; 21: tyrosine; 22: uracil.
Table S1. Patient information for the subjects used in this study. All colorectal cancer subjects are preceded by the code CC while polyp subjects are preceded by PP.
Appendix S1. 2D NMR experiment. For assignment purposes, two-dimensional (2D) correlation spectroscopy (COSY) and total correlation spectroscopy (TOCSY) NMR spectra were also acquired for a selective sample. In both cases, 64 transients per increment and 128 increments were collected into 2 k data points. The spectral width in both dimensions was 10 ppm. The TOCSY NMR spectra were acquired using the MLEV-17 (Bax and Davis, 1985) spin-lock scheme for 1H-1H transfers with a spin-lock power of 6 kHz. The COSY spectra were recorded using gradient selection. In both 2D NMR experiments, the water signal was irradiated with a weak pulse (∼50 Hz) during the recycle delay, the data were zero-filled to 2 k data points in the evolution dimension. Prior to Fourier transformation, an unshifted sine-bell and a shifted sine-bell apodisation function were applied to the free induction decays from the COSY and TOCSY spectra, respectively.
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