IMTIB   27019
INSTITUTO DE MEDICINA TRASLACIONAL E INGENIERIA BIOMEDICA
Unidad Ejecutora - UE
congresos y reuniones científicas
Título:
A PILOT CASE-CONTROL STUDY: COMPARISON OF METHODOLOGIES IN MICROBIOME ANALYSIS IN SAMPLES FROM COLORECTAL CANCER (CRC) IN ARGENTINA
Autor/es:
WOOD, HENRY; FUENTES BALAGUER, ALBA; QUIRKE, PHIL; PIÑERO T.A.; MAYORDOMO, CONSTANZA; ARGUERO, M.JULIETA; RISK, MARCELO; VACCARO, CARLOS ALBERTO; YOUNG, CAROLINE; PAVICIC, WALTER HERNÁN; RIVERA POMAR, ROLANDO
Lugar:
CABA
Reunión:
Simposio; 5SAJIB - 2020; 2020
Resumen:
Colorectal cancer (CCR) is the third cause of cancer (12,2%) and the second commonest cause of cancer-related deaths (10,8%) in Argentina. The association between CRC and an altered faecal microbiome is growing, with the potential to determine novel biomarkers, applicable to screening, prognostic factors or therapeutic treatments. The main objective of this work was to compare the microbiome composition of samples from healthy volunteers and CRC patients in a pilot study. This same set of samples from both groups were analyzed to study the composition of the microbiome in a reference laboratory (Leeds University, UK) and the Hospital Italiano from Buenos Aires. In the reference laboratory, the samples were stored in gFBOT and the 16SrRNA library was prepared with V4 primers using Illumina HiSeq 3000 equipment; and at the local level, the samples were stored at -80°C and the 16SrRNA library was prepared with V3-V4 primers using Illumina miSeq. Bioinformatics analysis of V3-V4 and V4 sequences was performed using qiime2 (2020.2) separately. No differences in alpha and beta diversity were found between healthy and CRC groups, but differences were detected among higher taxonomic level from the microbiome community in both groups, regardless of methodology. To determine the reason for these differences, a new analysis was performed. On one hand, the aforementioned results of the control samples and on the other hand, a merged analysis of sequences of both groups was carried out in order to keep the shared V4 region between both sequencing results. Our results indicate that the analysis of only the V4 region carried out with all the samples produces a huge decrease in the number of OTU obtained in the local samples. Then, we compared the taxa at the level of phylum from both types of analysis, using LefSe tool, and no differences in the relative abundance of Bacteroidetes, Firmicutes, Proteobacteria and Virrumicrobia, were detected but in the samples obtained locally, Actinobacteria, showed a decrease in relative abundance. To validate these preliminary results, extra samples need to be evaluated. In this study, we were able to obtain results comparable to a reference laboratory by modifying the sample storage method and the construction of the 16SrRNA library using V3-V4 primers that allowed a greater coverage of NGS results.