The human intestinal microbiota contains a vast community of microorganisms increasingly studied using high-throughput DNA sequencing. Standardized protocols for storage and DNA extraction from fecal samples have been established mostly for bacterial microbiota analysis. Here, we investigated the impact of storage and DNA extraction on bacterial and fungal community structures detected concomitantly.. Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols.

Three feces from healthy adults were stored at -80°C as such or diluted in RNAlater® and subjected to 2 extraction protocols with mechanical lysis: the Powersoil® MoBio kit or the International Human Microbiota Standard Protocol Q. Libraries targeting the V3-V4 16S and the ITS1 regions were prepared using Metabiote® (Genoscreen, France) and sequenced on GSFLX-454. Sequencing data were analysed using SHAMAN (http://shaman.c3bi.pasteur.fr/). For each storage and extraction conditions, the bacterial and fungal microbiota were compared in terms of diversity and relative abundance.