The time between the collection of a (stool) sample and its processing in a laboratory has a major impact on the quality and reliability of research results. Our analysis shows that samples for research using the FISH analysis method (such as that of NL-Lab) remain reliable significantly longer and are more economical to transport than samples for other analytical techniques such as polymerase chain reaction (PCR), next generation sequencing (NGS) and selective culture.
Why fecal samples for NL-Lab's gut microbiome research have a longer shelf life and more reliable results.
Fecal samples are subject to biological decay, therefore they should be analyzed as soon as possible. Travel time is affected by several factors, such as distance, type of transport, weekend and seasonal crowds. Added to this is the fact that temperature has a major influence on sample quality.
In addition, the conditions for (optimal) transport differ by analytical technique:
Selective Breeding
Samples for culture should preferably be kept refrigerated and analyzed within 1-3 days of production. Within that period, the reliability of the measurement result decreases rapidly.
PCR and NGS
Fecal samples suffer from so-called DNA polymerase inhibitors, which are always present in feces and inhibit the "motor" of the PCR reaction in its function. Samples for PCR and NGS no longer provide reliable results after 3-4 days.
A common solution is to use a preservative (fixative), but this in turn has the disadvantage of being an additional step in making the sample, where errors can easily occur. In addition, the ratios between fixative and sample are not ideal and proper mixing is very difficult. Therefore, the effectiveness of these agents in gut microbiome studies has not yet been convincingly demonstrated.
FISH
Samples analyzed by the FISH method are not unusable until the cell wall structure of the microbiome bacteria and their ribosomal cell contents are degraded. Bacterial cells remain structurally intact for a long time and thus analyzable by FISH-based methods. We have tested this extensively at NL-Lab and samples for FISH have a shelf life of at least 7 days and can then still be reliably examined.
Other benefits FISH
The FISH method is not only superior in terms of sample preservation, there are more advantages: FISH also offers much higher analytical coverage (96% of the microbiome) and is the only one that can measure the microbial activity of bacterial groups.
Our patented and automated C-FISH method ensures that this superior method has now become affordable for complex analyses such as gut microbiome studies.
Interested or questions?
If you are interested in NL-Lab's gut microbiome research or have questions following this article, we warmly encourage you to contact us.
