Changes in microbiota profiles after prolonged frozen storage of stool suspensions

Article Article scientifique Article Changes in microbiota profiles after prolonged frozen storage of stool suspensions eng 2020 author Dorsaz Stéphane 540643 author Charretier Yannick 814451 author Girard Myriam 666631 author Gaia Nadia 800637 author Leo Stefano 876581 author Schrenzel Jacques 29184 author Harbarth Stéphan Juergen 0000-0002-3551-1025 93885 author Huttner Benedikt 0000-0002-1749-9464 666500 author Lazarevic Vladimir 0000-0002-6839-2536 684594 10.3389/fcimb.2020.00077 32185143 2235-2988 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7058979/ Fecal microbiota transplantation (FMT) is recommended as safe and effective treatment for recurrent Clostridioides difficile infections. Freezing the FMT preparation simplifies the process, allowing a single stool sample to be used for multiple receivers and over an extended period of time. We aimed to assess the effect of long-term frozen storage on bacterial taxonomic profiles of a stool suspension prepared for FMT. Methods: DNA was extracted from a stool suspension before freezing and sequentially during the 18-month storage period at -80°C. Two different protocols were used for DNA extraction. The first relied on a classical mechanical and chemical cell disruption to extract both intra- and extracellular DNA; the second included specific pre-treatments aimed at removing free DNA and DNA from human and damaged bacterial cells. Taxonomic profiling of bacterial communities was performed by sequencing of V3-V4 16S rRNA gene amplicons. Results: Microbiota profiles obtained by whole DNA extraction procedure remained relatively stable during frozen storage. When DNA extraction procedure included specific pre-treatments, microbiota similarity between fresh and frozen samples progressively decreased with longer frozen storage times; notably, the abundance of Bacteroidetes decreased in a storage duration-dependent manner. The abundance of Firmicutes, the main butyrate producers in the colon, were not much affected by frozen storage for up to 1 year. DNA extraction Fecal microbiota transplantation Long-term frozen storage Microbiota Stool Taxonomic profiling Dewey 616 European Commission Resistance in Gram-Negative Organisms: Studying Intervention Strategies 282512 R-GNOSIS EU FP7 56 Département de médecine 221 false 338 Génomique et microbiote 604 526 Résistance aux antibiotiques 866 https://www.ebi.ac.uk/ena/browser/view/PRJEB33794 Frontiers in Cellular and Infection Microbiology 10 77 d4486d27-0144-4fab-9cd2-0aae549897d5 Article (Published version) Public CHANGES.pdf 1754391 application/pdf CC BY openAccess Faculté de médecine / Section de médecine clinique / Département de médecine

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Changes in microbiota profiles after prolonged frozen storage of stool suspensions	Frontiers in Cellular and Infection Microbiology			2020	404	271

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Dorsaz, Stéphane