Using fecal immunochemical tubes for the analysis of the gut microbiome has the potential to improve colorectal cancer screening

Abstract

Colorectal cancer (CRC) is a challenging public health problem which successful treatment depends on the stage at diagnosis. Recently, CRC-specific microbiome signatures have been proposed as a marker for CRC detection. Since many countries have initiated CRC screening programs, it would be useful to analyze the microbiome in the samples collected in fecal immunochemical test (FIT) tubes for fecal occult blood testing. Therefore, we investigated the impact of FIT tubes and stabilization buffer on the microbial community structure evaluated in stool samples from 30 volunteers and compared the detected communities to those of fresh-frozen samples, highlighting previously published cancer-specific communities. Altogether, 214 samples were analyzed by 16S rRNA gene sequencing, including positive and negative controls. Our results indicated that the variation between individuals was greater than the differences introduced by the collection strategy. The vast majority of the genera were stable for up to 7 days. None of the changes observed between fresh-frozen samples and FIT tube specimens were related to previously identified CRC-specific bacteria. Overall, we show that FIT tubes can be used for profiling the microbiota in CRC screening programs. This circumvents the need to collect additional samples and can possibly improve the sensitivity of CRC detection.

Microbiome Profiling from Fecal Immunochemical Test Reveals Microbial Signatures with Potential for Colorectal Cancer Screening

“…Bacteroidetes and Firmicutes were the most represented phyla, and the ten most abundant genera were, in this order: Bacteroides, Faecalibacterium, Prevotella, Blautia, F.Lachnospiraceae.UCG, Ruminococcus, Agathobacter, Bifidobacterium, Alistipes and Akkermansia (Figure S1). These results are consistent with previous studies using stool samples [39][40][41][42][43], and with earlier analyses showing a high correspondence between stool and FIT samples from the same individuals [36,37]. We compared our data with that of a recent Spanish population gut microbiome study [27].…”

“…To validate our strategy we built a model training with all the CRIPREV samples and tested it in two independent datasets: a cohort from the USA [36,37] and 100 extra samples from the same Catalan screening. For the USA cohort, we applied the Catalan hemoglobin threshold (>20 µg of hemoglobin/g of feces) to select the FIT-positive samples to include in the validation.…”

Microbiome and Colorectal Cancer Management

“…Subsequently, the gut microbiome could serve as a screening tool for CRC detection [ 72 ]. By combining microbial biomarker tests with the FITs, sensitivity for CRC detection and accuracy of treatment outcomes prediction might increase [ 73 ].…”

443: Colorectal Cancer-Associated Bacterial Genes Are Widely Encoded in Human Microbiomes

“…Of note, all 3 fecal samples tested negative when run on a fecal immunochemical testing (FIT) analyzer, thus contributing to the body of literature demonstrating the potential for microbiomebased profiling to offer insights complementing established non-invasive screening tests such as FIT. 37,38 To test real-world temperature and time limits beyond which CRC-associated scoring of residual stool from a FIT kit may be unreliable, we modeled FIT-based sampling of 4 fecal microbiomes (including sampleIDs 2119T1 and 2006T2, which were used in the preclinical study above) in the laboratory by preparing "mock FIT kits" comprised of 50 mg aliquots of stool in 2 mL HEPES buffer. We then subjected fecal samples to varying temperatures (-80°C, -20°C, 4°C, 25°C, or 37°C) for various time intervals (0, 1, 3, 7, or 14 days) and generated shotgun metagenomic sequencing data.…”