Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank
The role of gut microbiota in colorectal cancer is subject to extensive research. Before usage of biorepositories for microbiome studies, it is crucial to evaluate technical feasibility of microbiome profiling from various biospecimens. The aim of this study was to assess the feasibility of DNA-extr...
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| Format: | Article |
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MDPI AG
2020-12-01
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| Series: | Cancers |
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| Online Access: | https://www.mdpi.com/2072-6694/12/12/3702 |
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| author | Ulrich Wirth Debora Garzetti Lara M. Jochum Stefanie Spriewald Florian Kühn Matthias Ilmer Serene M. L. Lee Hanno Niess Alexandr V. Bazhin Joachim Andrassy Jens Werner Barbara Stecher Tobias S. Schiergens |
| author_facet | Ulrich Wirth Debora Garzetti Lara M. Jochum Stefanie Spriewald Florian Kühn Matthias Ilmer Serene M. L. Lee Hanno Niess Alexandr V. Bazhin Joachim Andrassy Jens Werner Barbara Stecher Tobias S. Schiergens |
| author_sort | Ulrich Wirth |
| collection | DOAJ |
| description | The role of gut microbiota in colorectal cancer is subject to extensive research. Before usage of biorepositories for microbiome studies, it is crucial to evaluate technical feasibility of microbiome profiling from various biospecimens. The aim of this study was to assess the feasibility of DNA-extraction and microbiome profiling of samples from different sample sites, tissue sites and storage duration of a colorectal cancer biobank. Mucosa samples, mucosal scrapings and feces as well as different tissue sites (tumor, normal mucosa) were analyzed. 16S rRNA gene-based microbiome profiling with taxonomic assignment was performed on the Illumina MiSeq (Illumina, San Diego, USA) platform from stored snap frozen samples. For statistical analysis, α- and β-diversity measures, PCoA, permutational multivariate analysis of variance and graphical representation were performed. Microbiome analysis could be successfully performed in most of the samples (overall 93.3%) with sufficient numbers of high-quality reads. There were no differences between sample sites, while in some measures significant differences were found between tumor and normal mucosa (α-diversity, Shannon/Simpson Indices <i>p </i>= 0.028/0.027, respectively). Samples stored for up to eight years were used and storage conditions had no significant influence on the results. Tumor and tissue samples of a biobank stored long term can be successfully used for microbiome analysis. As large sample sizes are needed for association studies to evaluate microbial impact on tumorigenesis or progression of colorectal cancer, an already established biorepository may be a useful alternative to prospective clinical studies. |
| first_indexed | 2024-03-10T14:12:20Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2072-6694 |
| language | English |
| last_indexed | 2024-03-10T14:12:20Z |
| publishDate | 2020-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cancers |
| spelling | doaj.art-11426210703d4481922329f4c720f3842023-11-21T00:03:58ZengMDPI AGCancers2072-66942020-12-011212370210.3390/cancers12123702Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer BiobankUlrich Wirth0Debora Garzetti1Lara M. Jochum2Stefanie Spriewald3Florian Kühn4Matthias Ilmer5Serene M. L. Lee6Hanno Niess7Alexandr V. Bazhin8Joachim Andrassy9Jens Werner10Barbara Stecher11Tobias S. Schiergens12Department of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyMax-Von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Pettenkoferstr. 9A, D-80336 Munich, GermanyMax-Von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Pettenkoferstr. 9A, D-80336 Munich, GermanyMax-Von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Pettenkoferstr. 9A, D-80336 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyMax-Von-Pettenkofer Institute, Ludwig-Maximilians-University Munich, Pettenkoferstr. 9A, D-80336 Munich, GermanyDepartment of General, Visceral and Transplant Surgery, Ludwig-Maximilians-University Munich, Marchioninistr. 15, D-81377 Munich, GermanyThe role of gut microbiota in colorectal cancer is subject to extensive research. Before usage of biorepositories for microbiome studies, it is crucial to evaluate technical feasibility of microbiome profiling from various biospecimens. The aim of this study was to assess the feasibility of DNA-extraction and microbiome profiling of samples from different sample sites, tissue sites and storage duration of a colorectal cancer biobank. Mucosa samples, mucosal scrapings and feces as well as different tissue sites (tumor, normal mucosa) were analyzed. 16S rRNA gene-based microbiome profiling with taxonomic assignment was performed on the Illumina MiSeq (Illumina, San Diego, USA) platform from stored snap frozen samples. For statistical analysis, α- and β-diversity measures, PCoA, permutational multivariate analysis of variance and graphical representation were performed. Microbiome analysis could be successfully performed in most of the samples (overall 93.3%) with sufficient numbers of high-quality reads. There were no differences between sample sites, while in some measures significant differences were found between tumor and normal mucosa (α-diversity, Shannon/Simpson Indices <i>p </i>= 0.028/0.027, respectively). Samples stored for up to eight years were used and storage conditions had no significant influence on the results. Tumor and tissue samples of a biobank stored long term can be successfully used for microbiome analysis. As large sample sizes are needed for association studies to evaluate microbial impact on tumorigenesis or progression of colorectal cancer, an already established biorepository may be a useful alternative to prospective clinical studies.https://www.mdpi.com/2072-6694/12/12/3702gut microbiome16S rRNAcolorectal cancerbiobankbiorepository |
| spellingShingle | Ulrich Wirth Debora Garzetti Lara M. Jochum Stefanie Spriewald Florian Kühn Matthias Ilmer Serene M. L. Lee Hanno Niess Alexandr V. Bazhin Joachim Andrassy Jens Werner Barbara Stecher Tobias S. Schiergens Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank Cancers gut microbiome 16S rRNA colorectal cancer biobank biorepository |
| title | Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank |
| title_full | Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank |
| title_fullStr | Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank |
| title_full_unstemmed | Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank |
| title_short | Microbiome Analysis from Paired Mucosal and Fecal Samples of a Colorectal Cancer Biobank |
| title_sort | microbiome analysis from paired mucosal and fecal samples of a colorectal cancer biobank |
| topic | gut microbiome 16S rRNA colorectal cancer biobank biorepository |
| url | https://www.mdpi.com/2072-6694/12/12/3702 |
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