Reproducible profiling of the gut microbiota using surplus clinical faecal immunochemical test samples

Background. Numerous countries use the EXTEL HEMO-AUTO MC quantitative faecal immunochemical test (qFIT) to screen for faecal haemoglobin. We aimed to determine if bacterial 16S rRNA gene sequencing results from the leftover qFIT cassettes would be stable over time and comparable with larger volume faecal collection protocols. Methods. Four qFIT probe samples were taken from each of sixteen fresh healthy volunteer stool samples, and sequencing results were compared after 0, 4, 7 and 14 days to provide a baseline control and mimic postage and sample processing conditions in cancer screening programmes. qFIT results were then compared to those of standard laboratory processing of larger whole-stool samples. DNA was extracted from 100 NHS surplus qFIT samples from symptomatic patients reporting rectal bleeding and quantified to assess suitability for 16S rRNA gene sequencing. Results. Bacterial composition and diversity from healthy volunteer qFITs remained stable over 14 days with only minor differences compared to baseline (day 0) and larger stool control samples; at least 75% of the symptomatic qFITs yielded sufficient DNA for 16S rRNA gene sequencing. Conclusion. qFIT samples were almost identical to control samples and stable over 14 days, allowing them to be used for large-scale, low-cost population-based intestinal microbiota studies. Clinical Trial Registration. The study was registered on clinicaltrials.gov (NCT06100549).