Michael Harrop
Active member
There was a criticism made about Steve Baskin's https://lastplace.org.au, regarding him using a non-frozen shipping method that takes as long as a week https://web.archive.org/web/20210414080155/https://lastplace.org.au/product/fmt/
It would be nice if shipping fresh stool by ground (5 days) were possible. And ever since I had seen him say he was doing non-frozen shipping I had in mind to go through the studies I had seen to refresh my memory. So I went through the dozen or so studies I've saved on this.
I would say there is some evidence that a stool sample may be safe at fridge temps for a week, but it definitely doesn't seem conclusive. And thus it does seem to carry some risk. The safest recommendation seems to be to keep it under 72 hours for fridge temperatures.
For c. diff the evidence shows that frozen is fine https://humanmicrobiome.info/fmt/#freezing. And there's even some evidence that frozen is fine for other conditions like IBD. So it seems wise to opt for frozen unless some substantial evidence arises that demonstrates fresh is significantly superior to frozen for efficacy in one or more conditions.
Fridge temperature = 4C, 39F. Freezing = 0C, 32F.
48 hours at room temp was "fine":
I find this result surprising and I'm skeptical, but it does suggest that a week at fridge temps would be fine too.
Not completely "fine":
Another "mostly fine" after 72 hours room temp:
"Lauber et al. reported stability of the microbiota even for up to 14 days at 4°C and 20°C":
This seems hard to believe, and I assumed they must have purified the sample (IE: extracted only the microbes, thus removing any substrate they can feed on), but it doesn't appear that they did.
Major caveat:
72 hours at 4c (39f) seems to be ok:
An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants (Feb 2021) https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02104-6 - they used a special storage device (OMNImet.GUT tube), and stored at room temp for 3-4 days.
Probably the strictest recommendations I've seen:
Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool (2015) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134802
(22 comments on /r/HumanMicrobiome).
It would be nice if shipping fresh stool by ground (5 days) were possible. And ever since I had seen him say he was doing non-frozen shipping I had in mind to go through the studies I had seen to refresh my memory. So I went through the dozen or so studies I've saved on this.
I would say there is some evidence that a stool sample may be safe at fridge temps for a week, but it definitely doesn't seem conclusive. And thus it does seem to carry some risk. The safest recommendation seems to be to keep it under 72 hours for fridge temperatures.
For c. diff the evidence shows that frozen is fine https://humanmicrobiome.info/fmt/#freezing. And there's even some evidence that frozen is fine for other conditions like IBD. So it seems wise to opt for frozen unless some substantial evidence arises that demonstrates fresh is significantly superior to frozen for efficacy in one or more conditions.
Fridge temperature = 4C, 39F. Freezing = 0C, 32F.
48 hours at room temp was "fine":
Impact of time and temperature on gut microbiota and SCFA composition in stool samples (2020) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0236944
I find this result surprising and I'm skeptical, but it does suggest that a week at fridge temps would be fine too.
Not completely "fine":
The absolute levels of acetate, propionate and butyrate increased dramatically within 24 hours, indicating general metabolic activities. Even storage at 4°C could not completely suppress metabolic activities, but proved to be clearly beneficial. Interestingly enough, the effect of time and temperature was strongly diminished when looking at ratios instead of absolute values.
Another "mostly fine" after 72 hours room temp:
Influence of Fecal Sample Storage on Bacterial Community Diversity (2009) https://benthamopen.com/FULLTEXT/TOMICROJ-3-40 - minimal (10%) differences in community composition and relative taxon abundances after 72 hours at room temp.
"Lauber et al. reported stability of the microbiota even for up to 14 days at 4°C and 20°C":
Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples (2010) https://academic.oup.com/femsle/article/307/1/80/472147
This seems hard to believe, and I assumed they must have purified the sample (IE: extracted only the microbes, thus removing any substrate they can feed on), but it doesn't appear that they did.
"even though we did observe shifts in the abundance of some taxa in our small sample set under different storage conditions, this did not mask interpersonal differences in the overall fecal bacterial community composition, and did not affect our ability to differentiate the host origin of the two fecal samples"
Major caveat:
it is not currently possible to resolve changes in bacteria at the species or the strain level
72 hours at 4c (39f) seems to be ok:
A Guide for Ex Vivo Handling and Storage of Stool Samples Intended for Fecal Microbiota Transplantation (2019) https://www.nature.com/articles/s41598-019-45173-4
An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants (Feb 2021) https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02104-6 - they used a special storage device (OMNImet.GUT tube), and stored at room temp for 3-4 days.
While the optimal method for metabolic profiling of stool is likely extraction within 1 h of collection [17], this method is out of reach in the vast majority of circumstances. It is therefore accepted that the next best method and more practical “gold standard” is flash-freezing of stool below − 20 °C [18].
Probably the strictest recommendations I've seen:
Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool (2015) https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0134802
We experimentally determined that the bacterial taxa varied with room temperature storage beyond 15 minutes and beyond three days storage in a domestic frost-free freezer. While freeze thawing only had an effect on bacterial taxa abundance beyond four cycles
We recommend that stool is frozen within 15 minutes of being defecated, stored in a domestic frost-free freezer for less than three days
(22 comments on /r/HumanMicrobiome).
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