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A widely used sampling device in colorectal cancer screening programmes allows for large-scale microbiome studies
  1. Dita Gudra1,
  2. Saeed Shoaie2,3,
  3. Davids Fridmanis1,
  4. Janis Klovins1,
  5. Hugo Wefer2,4,
  6. Ivars Silamikelis1,
  7. Raitis Peculis1,
  8. Ineta Kalnina1,
  9. Ilze Elbere1,
  10. Ilze Radovica-Spalvina1,
  11. Rolf Hultcrantz2,
  12. Ģirts Šķenders5,6,
  13. Marcis Leja5,6,
  14. Lars Engstrand2,4
  1. 1 Latvian Biomedical Research and Study Centre, Riga, Latvia
  2. 2 Centre for Translational Microbiome Research, Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
  3. 3 Centre for Host–Microbiome Interactions, Dental Institute, King’s College London, London, UK
  4. 4 Science for Life Laboratory, Solna, Sweden
  5. 5 Faculty of Medicine, University of Latvia, Riga, Latvia
  6. 6 Institute of Clinical and Preventive Medicine, University of Latvia, Riga, Latvia
  1. Correspondence to Dr Davids Fridmanis, Latvian Biomedical Research and Study Centre, Ratsupites 1K-1, LV-1067, Riga, Latvia; davids{at} and Professor Lars Engstrand, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 171 77, Sweden; lars.engstrand{at}

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We read with interest the article by Passamonti et al,1 reporting the performance of two different faecal immunochemical tests (FITs) highlighting the importance of standardisation and validation of screening methodologies. Conventionally, laboratory-based FIT is the preferred approach in testing for occult blood in faeces, which includes colorectal cancer screening programmes.2–4 The potential of preserving stable faecal samples in a widely used FIT buffer for microbiome research would enable prospective microbiome studies in generally healthy subjects undergoing colorectal cancer screening.

For this purpose, we evaluated faecal sample stability in the commonly used OC-Sensor (Eiken Chemical, Tokyo, Japan) under various storage conditions. Faecal samples from five healthy adult individuals were used for the analysis and exposed to 16 different conditions: immediately frozen at −86°C (with FIT (wFIT)/without FIT (woFIT)); immediately frozen at −20°C (wFIT/woFIT); wFIT stored at 4°C for 1, 2, 7, 14 days; stored at 20°C for 1, 2, 7, 14 days; stored at 30°C for 1, 2, 7 days and lastly stored at 4°C for 2 days and at 20°C for additional 2 days. Shotgun metagenomic analysis was performed by Illumina 2500, while taxonomic compositions were determined by 16S rRNA analysis employing Illumina MiSeq and Ion Torrent PGM.

Our first attempt to extract DNA from wFIT samples failed due to low amount of DNA obtained. Thus, lyophilisation for all of the wFIT samples, except for woFIT samples, was applied, increasing the yield of DNA up to 30 times.

As shown by the figure 1, the Shannon index in both platforms displayed a clear pattern of …

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