Functional amplification and preservation of human gut microbiota

Nadia Gaci (1) , Prem Prashant Chaudhary (1) , William Tottey (1) , Monique Alric (1, 2) , Jean-François Brugère (1)

1 CIDAM - Conception, Ingénierie et Développement de l'Aliment et du Médicament
2 MEDIS - Microbiologie Environnement Digestif Santé

Background: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. Objective: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. Design: Taking advantage of in vitro gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations. Preservation efficiencies were determined after 3 and 6 months and compared with the fresh initial microbiota diversity and metabolic activity, using the chemostat-based Environmental Control System for Intestinal Microbiota (ECSIM) in vitro model of the gut environment. Microbial populations were tested for fermentation gas, short-chain fatty acids, and composition of amplified and resuscitated microbiota, encompassing methanogenic archaea. Results: Amplification of the microbial repertoire from a fresh fecal sample was achieved with high fidelity. Dimethylsulfoxide, alone or mixed with other CPAs, showed the best efficiency for functional preservation, and the duration of preservation had little effect. Conclusions: The amplification and resuscitation of fecal microbiota can be performed using specialized in vitro gut models. Correct amplification of the initial microbes should ease the sharing of clinical samples and improve the safety of fecal microbiota transplantation.

Mots clés: cryoprotective agent (CPA); dimethylsulfoxide; glycerol; gut microbiota preservation; polyethylene glycol; environmental control system for intestinal microbiota (ECSIM)

Mots clés: fecal microbiota transplantation (FMT)

Domaines: Alimentation et Nutrition; Bactériologie

Nadia Gaci, Prem Prashant Chaudhary, William Tottey, Monique Alric, Jean-François Brugère. Functional amplification and preservation of human gut microbiota. Microbial Ecology in Health and Disease, 2017, 28 (1), pp.1308070. ⟨10.1080/16512235.2017.1308070⟩. ⟨hal-01612774⟩