The Dr Dorothea Sandars Churchill Fellowship to improve the effectiveness of bowel cancer screening in Australia using next generation testing

Recommendations: Large, population-based cohort studies are required to provide meaningful insight into the complex relationships between the host, the gut microbiome and the environment.  Collection of relevant data on extrinsic host or environmental factors that may alter the gut microbiome will be crucial.  Longitudinal studies with repeated sample and data collection will be required to investigate pathophysiology and causality.  Australia’s National Bowel Cancer Screening Program represents a unique opportunity to derive information from a large population-based resource to facilitate further research in interactions between the gut microbiome and colorectal cancer. Quality control during stool collection, transport, processing and storage is essential for ensuring the integrity of the collected microbiome specimens.  The ‘gold standard’ for faecal sample collection used in microbial-associated analysis is to freeze freshly collected faecal samples at -80°C without any additives.  Key measures used in evaluating faecal sample collection methods for feasibility in large cohort studies include technical reproducibility, stability at ambient temperature and accuracy when compared with the ‘gold standard’ When compared with the ‘gold standard’, faecal sample collection methods of RNAlater, 95% ethanol, gFOBT and iFOBT have good reproducibility and stability over 4 days at ambient temperature for microbiome analysis using 16s rRNA sequencing and shotgun metagenomic sequencing. There was also good correlation on microbial diversity measures, but each of the faecal collection methods showed variability in the relative abundance of various bacteria.  Most studies on the faecal microbiome have used 16s rRNA sequencing but future studies are likely to adopt a combination of shotgun metagenomics and metabolomics. Therefore, faecal collection methods will need to accommodate a wide range of analyses.  Significant differences exist between the different faecal sample collection methods which can impact technical reproducibility, stability and accuracy. It would be ideal to collect samples using more than one preservation method if this were economically feasible. Implementing a dual collection approach (using at least one common collection method), even on only a subset of participants, would allow for comparisons across cohorts. If possible, the faecal sample for gut microbiome research should be collected in sufficient amounts that would allow for aliquoting at the storage facility. Aliquoting may provide opportunities for further researches of gut microbiota with multi-omic approaches.  The ability to accumulate data from health-relevant records will be essential in collecting the necessary clinical data to facilitate interpretation of microbiome-associated analysis findings.  Researchers will likely need to combine data from multiple studies in the future. Therefore, it is important for future studies to coordinate and collect faecal samples using at least one common method in addition to their method of choice.  Keywords: Gut microbiome, colorectal cancer screening, National Bowel Cancer Screening Program, bioinformatics