Intestinal microbiome studies from faecal samples involve complex logistics of shipping and maintaining the samples, which can result in high cost and low quality results.
In this entry we analyze 7 critical aspects in stool microbiome studies that should be taken into account when selecting the best sample collection protocol to optimize the quality of the results.
7 CRITICAL ASPECTS IN STOOL MICROBIOME STUDIES
Donor involvement is the critical first step in selecting the best sample collection protocol for stool microbiome studies.
It is essential that this collection system is easy to use and comfortable for correct collection. Furthermore, it is essential that the collection system stabilizes the sample at the same time of collection to avoid alterations and / or degradations of the same, introducing biases when analyzing it.
2.- STABILITY OF THE SAMPLE
The second critical aspect is to ensure the stability of the sample in relatively extreme environments (temperatures between -20ºC and 50ºC) from its collection to its arrival at the laboratory.
It may take days from when the donor collects the sample at home until it arrives at the analysis laboratory. Furthermore, the environmental conditions to which the sample is exposed during that time can contribute to its degradation. In the event of resorting to freezing for better stability over time, it is important to assess how freeze-thaw cycles will affect you .
The collection protocol must also guarantee the homogeneity of the sample, that is, the comparability of the results when analyzing different aliquots of the same stool sample on multiple occasions.
The composition of the sample at the time of analysis should be as accurate as possible to that of the freshly collected and processed fresh sample (or immediately deep-frozen at -80ºC) to avoid bias in the results. This metric, known as neutrality, consists of knowing the degree to which a sample provides a snapshot of the in vivo state at the time of collection.
Neutrality is critical in stool microbiome studies as biases can be introduced within a minimal time frame from sample collection, for example, the time it takes for an FOBT or FTA card to dry or the time it takes in freezing the sample in a conventional freezer.
5.- DONOR EXPERIENCE
The donor’s experience for a given sample collection protocol has a more than significant impact on compliance and commitment ratios, especially in those studies that require the collection of samples from the same donor over time.
Therefore, the collection system and protocol must be simple, comfortable and easy to carry out.
6.- SCALABILITY AND PERFORMANCE
In selecting the sample collection protocol, it is also important to consider whether it allows for the scaling option for a potential larger multiple study in the future.
On the other hand, performance is a critical parameter in human microbiome studies, especially in those deeper sequencing projects. The amount of microbial DNA that can be obtained from the stool sample is also a relevant aspect when selecting the collection system.
Another consideration that is sometimes not given much attention in the initial stages of a study, and which undoubtedly has a great impact when analyzing their cost-benefit, is the capacity of the collection protocol. samples to lend themselves to high-performance automation in the laboratory.
7.- PERFORMANCE METRICS
Finally, we must not forget to study the sample collection kits offered by the different manufacturers based on the relevant scientific publications and articles in which they are referenced.
In conclusion , to effectively capture a snapshot of the in vivo state at the time of sample collection, all aliquots obtained from the same stool sample must be equivalent to the fresh sample freshly collected and processed immediately (or immediately deep-frozen at -80ºC), regardless of where or who collected it, and the ” journey ” of it to the laboratory. All this without forgetting the performance and the donor experience generated.
Therefore, when comparing the costs and benefits of the different sample collection protocols for stool microbiome studies , all these parameters should be assessed as a whole, evaluating the cost per donor, but without losing sight of the value of the analysis of the microbiological profile in vivo , without bias.