Metagenomic comparative analysis of fecal samples from colorectal cancer patients from Argentina

MAYORDOMO, ANDREA CONSTANZA; WOOD, HENRY M.; YOUNG, CAROLINE; ARGUERO, M.JULIETA; BALAGUER, ALBA FUENTES; BURGOS, VALERIA; ETCHEVERRY, JOSEFINA FUHR; PAVICIC, WALTER HERNÁN; RISK, MARCELO; QUIRKE, PHIL; VACCARO C.A.; PIÑERO T.A.

Conferencia; 2nd Women in Bioinformatics & Data Science LA Conference Fostering collaboration among women; 2021

Women Bioinformatics Network LA

Research investigating the CRC-associated microbiome has been almost entirelyconducted in 'Western' countries. The aim of this pilot study was to characterize theCRC-associated microbiome profile in Argentinian patients and make a comparisonbetween two alternative methods of fecal sample collection and sequencingapproaches. To determine the effect of storage in gFOBT and frozen to -80°C DNAextraction were performed using a similar methodology. gFOBT were collected fromten CRC patients and ten healthy volunteers and replicates of samples were conservedat -80°C. All gFOBT were stored at ambient temperature. V4 16SrRNA sequencing wasperformed in gFOBT samples and V3-V4 16SrRNA sequencing by Illumina platformHiSeq and miSeq respectively. Bioinformatics analysis was performed by Qiime2 anddata was exported to determine taxa which differed significantly between groups usingLEfSe. Alpha diversity was calculated and significance was assessed by the Kruskal-Wallis test. Weighted/Unweighted Unifrac and Bray-curtis distance were calculatedand the significance of differences between groups was assessed by PERMANOVAanalysis. No significant differences were found in alpha diversity and the compositionof the microbiome of both methods of storage was similar. However, in beta diversitydistances were observed by unweighted unifrac and Bray-curtis distance amongsamples from each experiment. The relevant genus taxa for this pathology wereobtained in both types of analysis such as Escherichia-Shigella, Alistipes, Porphyromonas,Parvimonas, Peptostreptococcus, and Gemella.This study demonstrates that both methods represent suitable protocols of fecalsample analysis for 16SrRNA microbiome research in CRC patients. gFBOT cards haveproven to be useful when a freezer storage method is not available and allows longtermstorage and preservation of samples at room temperature. Conservation at -80°Crepresents the most economical and accessible method for the adequate long-termpreservation of the samples avoiding their degradation and concomitant loss of speciespresent in them.