Abstract 3589: Microbiomic analysis of colon cancer tumors and their matched normal reveals distinct gut floras

• Published in: Cancer research (Chicago, Ill.) Ill.), 2013-04, Vol.73 (8_Supplement), p.3589-3589
• Main Authors: Brim, Hassan, Yooseph, Shibu, Torralba, Manolito, Lee, Edward, Nelson, Karen, Ashktorab, Hassan
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2013-3589

Background: The gut flora has long been suspected to play a role in colon carcinogenesis either through their secreted toxins or through their processing of ingested nutrients leading to the production of carcinogenic products. We previously have shown that stool samples flora from patients with pre-neoplastic colon lesions differ from those from healthy individuals. However, bacteria in stool samples are not representative of the colon adherent bacteria that are more prone to affect colon mucosa homeostasis. Here we analyzed the microbiota composition in 10 colon tumors and their matched normal tissue from 10 African American patients. Materials & Methods: DNA extracts from 10 pairs of colon tumors and matched normal tissue, was used to amplify the V1-V3 regions of the 16S rRNA gene. The PCR primers included the A and B adaptor sequences for 454 pyrosequencing as well as a unique 12 bp barcode incorporated onto the reverse primer such that each sample receives its own unique barcode. The amplicons were purified, quantified, normalized, and then pooled in preparation for emulsion PCR followed by 454 sequencing using Titanium chemistry. After deconvolution and trimming, the sequences were put through chimera checking (using chimera slayer). Those sequences of length >=100 bp that were not labeled as chimeras were then processed using RDP's classifier. Results: Overall, each tumor sample microbiota was the closest to its matched normal based on the general bacterial profile. Bacteroidetes and Firmicutes were the dominant bacterial groups in all analyzed samples. Using a Principal Component Analysis at the genus level with bacterial genera that are represented at least 5% in one sample revealed two distinctly separated healthy tissue groups, one defined primarily by Bacteroides and the second defined by Prevotella bacteria. No tumor sample was within these two groups. It is noteworthy that Fusobacteria, that was shown by other similar studies as primarily abundant in tumors, was not defining any tumor group in our study. Conclusion: Our study reveals the presence of significant microbiota changes between tumor samples and matched normal tissue even though our analysis were done only at the genus level. Further analysis at the Operational Taxonomic Units (sub-genus level) for each pair of samples are underway and will further dissect the observed differences. Citation Format: Hassan Brim, Shibu Yooseph, Manolito Torralba, Edward Lee, Karen Nelson, Hassan Ashkt