Abstract
Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.
Highlights
There is currently a lack of consensus in the methodologies and procedures for the collection and preservation of stool samples, notably if further downstream metagenomic applications are envisaged
In this paper we present GutAlive, a stool collection kit for fecal sampling and transport that ensures the viability of the fecal microbiota, including obligate anaerobes and extreme oxygen sensitive (EOS) bacteria
Most importantly, keeping anaerobic conditions from the sampling moment is expected to have a positive impact on the recovery of obligate anerobe or EOS bacteria
Summary
There is currently a lack of consensus in the methodologies and procedures for the collection and preservation of stool samples, notably if further downstream metagenomic applications are envisaged. It seems quite difficult to envisage how the results of microbiome studies using just different sampling methods could be compared Variables such as oxygen toxicity during fecal sample collection and transport can be even more impactful if bacterial viability, notably affecting the populations of obligate anaerobes, is considered. In this paper we present GutAlive, a stool collection kit for fecal sampling and transport that ensures the viability of the fecal microbiota, including obligate anaerobes and EOS bacteria This product follows the same principle of an anaerobic system but in the form of a portable, single use device, which generates an anaerobic atmosphere just right after stool collection. The use of GutAlive in protocol normalization and downstream applications are discussed in the manuscript
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