Fecal microbiome of Rattus norvegicus
Rat fecal material was used to inoculate fresh LB medium with or without single addition of probiotic bacteria. Following 24 h or 48 h incubation cells were pelleted by centrifugation, and total DNA was isolated using the QIAamp Fast DNA Stool Mini Kit (Qiagen, Germany) and purified with using Monarch PCR & DNA Cleanup Kit (New England Biolabs, USA). The sequence of 16S rRNA gene was amplified in a 50 l reaction volume from fecal sample-derived total DNA with high-fidelity Q5 DNA polymerase (New England Biolabs, USA) on a Veriti device (Thermo Fisher Scientific, USA). The obtained amplicons were purified and used for preparation of sequencing libraries with Ligation Sequencing Kit LSK-SQK109 (Oxford Nanopore Technologies, UK) and barcode sets Native Barcoding Expansion 1-12 and 13-24 (Oxford Nanopore Technologies, UK) on FLO-MIN106D flow cells (Oxford Nanopore Technologies, UK).