16S rRNA sequencing raw data related to the pre-print "The Critical Period Microbiota Shape Brain Plasticity"

The dataset reports 16S rRNA sequencing (16S rRNA-seq) raw data obtained from bacterial DNA extracted from fecal samples of Mus musculus. The experiments were performed on female C57BL/6J (JAX #00064), housed (2-3 per cage) in individually ventilated cages to safely maintain the microbiota composition. Weaning was performed on P21–23. Animals were kept in rooms at 22°C with a standard 12 h light–dark cycle. Food (standard diet, 4RF25 GLP Certificate, Mucedola) and water were available ad libitum and replaced weekly. Fresh fecal samples were collected from mice, snap-frozen in liquid nitrogen and stored at −80°C until processing. Bacterial DNA was extracted using the QIAamp PowerFecal DNA kit (Qiagen, cat # 12830-50), and DNA concentration was quantified by NanoDrop 2000 C Spectrophotometer (ThermoFisher Scientific). The 16S rRNA sequencing and analysis was performed by Novogene UK Company Ltd. Targeted regions were amplified using specific primers connected with barcodes, followed by selection of PCR products of appropriate size through agarose gel electrophoresis. Equal amounts of PCR products from each sample were pooled, end-repaired, A-tailed, and ligated with Illumina adapters. The prepared libraries were sequenced on a paired-end Illumina platform. The library was checked with Qubit and real-time PCR for quantification, while a bioanalyzer was used for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms according to the effective library concentration and data amount required. Antibiotic cocktail (ABX) experiment Dataset experimental groups 16S rRNA-seq data were generated from fecal DNA of the following groups: ABX DON.YOUNG P21 mice were weaned and subjected to an antibiotic cocktail (ABX, vancomycin (Duchefa Biochemie Cat# V0155.0005) (0.5 g/L), ampicillin (Sigma-Aldrich Cat#A9518) (1 g/L), and neomycin (Gibco-Life technologies Cat#21810-031) (1 g/L)). dissolved in drinking water for 1 week, while control mice (called young donors in the data-set, DON.YOUNG) drank regular water. Fecal transplantation (FT) experiment Dataset experimental groups 16S rRNA-seq data were generated from fecal DNA of the following groups: DON.YOUNG – juvenile donor mice DON.ADULT – adult donor mice PRE.YOUNG – adult recipient mice before FT from juvenile donors POST.YOUNG – adult recipient mice after FT from juvenile donors PRE.AD – adult recipient mice before FT from adult donors POST.AD – adult recipient mice after FT from adult donors Adult female C57BL/6J recipient mice (P120), housed 2–3 per cage after weaning (P21), were randomly assigned to receive (i) fecal microbiota transplantation (FT) from juvenile female C57BL/6J donors (P28), (ii) FT from adult female donor mice, or (iii) sterile PBS as vehicle control. Before transplantation, recipient mice were treated with an antibiotic cocktail consisting of vancomycin (0.5 g/L), ampicillin (1 g/L), neomycin (1 g/L), and metronidazole (Merck Sigma-Aldrich, Cat# M3761; 1 g/L) in the drinking water for one week. After a two-day washout period, FT was performed by oral gavage once daily for a total of five administrations. For FT, freshly collected donor fecal pellets were suspended in sterile PBS, vortexed for 10 min to obtain a homogeneous suspension, and filtered through a cell strainer to remove large debris. Each recipient mouse received 200 µL of the freshly prepared fecal suspension by oral gavage. Following transplantation, recipient mice were housed in separate autoclaved cages according to treatment group for four weeks to allow microbiota engraftment. Fecal samples were collected immediately before antibiotic treatment and four weeks after FT to assess microbiota composition by 16S rRNA sequencing.