characteristics.text: Cells were maintained over the duration of the experiment within mice until ex vivo sampling occurred. Immediately after collection, cecal samples were subjected to flash-freezing and stored at -80C until total community DNA extractions could be performed. Microbial DNA was extracted using a MagAttract HMW DNA Kit (Qiagen, Hilden, Germany). The 16S rRNA V4 region was amplified and sequenced on Illumina Iseq 100 platform following the manufacturer’s instructions. Raw 16S amplicon sequence (forward reads only) and metadata were demultiplexed using the split_libraries_fastq.py script implemented in QIIME1.9.1. The demultiplexed fastq file was split into sample-specific fastq files using split_sequence_file_on_sample_ids.py script from Qiime1.9.1. Individual fastq files without nonbiological nucleotides were processed using Divisive Amplicon Denoising Algorithm pipeline. The output of the dada2 pipeline (feature table of amplicon sequence variants) was processed for alpha and beta diversity analysis using phyloseq and microbiomeSeq (http://www.github.com/umerijaz/microbiomeSeq) packages in R. Alpha diversity estimates were analysed within group categories using estimate_richness function of the phyloseq package. Nonmultidimensional scaling (NMDS) was performed using Bray-Curtis dissimilarity matrix between groups and visualized by using ggplot2 package. We assessed the statistical significance (P<0.05) throughout and whenever necessary adjusted P values for multiple comparisons according to the Benjamini and Hochberg method to control False Discovery Rate, while performing multiple testing on taxa abundance according to sample categories. We performed an ANOVA among sample categories while measuring α-diversity using the plot_anova_diversity function in microbiomeSeq package (http://www.github.com/umerijaz/microbiomeSeq). Permutational multivariate ANOVA with 999 permutations was performed to test the statistical significance of the non-multidimensional scaling patterns with the ordination function of the microbiomeSeq package. Linear regression was performed on taxa abundances against metadata variables using “lm” function implemented in dplyr package in R.
characteristics.characteristic: Design_Description
characteristics.text: SAMN17209846
characteristics.characteristic: External Id
characteristics.text: fastq
characteristics.characteristic: File_Type
characteristics.text: MW-95_S23_L001_R1_001.fastq
characteristics.characteristic: Filename 1
characteristics.text: MW-95_S23_L001_R2_001.fastq
characteristics.characteristic: Filename 2
characteristics.text: Cleveland Clinic
characteristics.characteristic: INSDC center name
characteristics.text: 2022-02-01T00:51:22.757Z
characteristics.characteristic: INSDC first public
characteristics.text: 2022-02-01T00:51:22.757Z
characteristics.characteristic: INSDC last update
characteristics.text: SRS7962017
characteristics.characteristic: INSDC secondary accession
characteristics.text: live
characteristics.characteristic: INSDC status
characteristics.text: PCR
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/OBI_0000415
characteristics.characteristic: Library_Selection
characteristics.text: Metagenomic
characteristics.characteristic: Library_Source
characteristics.text: Amplicon
characteristics.characteristic: Library_Strategy
characteristics.text: Paired
characteristics.characteristic: Libray_Layout
characteristics.text: Model organism or animal
characteristics.characteristic: NCBI submission model
characteristics.text: Model.organism.animal.1.0
characteristics.characteristic: NCBI submission package
characteristics.text: SRS7962017
characteristics.characteristic: SRA accession
characteristics.text: 14 wks
characteristics.characteristic: age
characteristics.text: 3
characteristics.characteristic: biological replicate
characteristics.text: Conventional
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000624
characteristics.characteristic: breeding_history
characteristics.text: iSeq 100
characteristics.characteristic: instrument model
characteristics.text: TF3
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0007937
characteristics.characteristic: library id
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: Illumina
characteristics.characteristic: platform
characteristics.text: female
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000383
characteristics.characteristic: sex
characteristics.text: C57BL/6J
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000606
characteristics.characteristic: strain
characteristics.text: Cecum
characteristics.characteristic: tissue
characteristics.text: Model organism or animal sample from Mus musculus
characteristics.characteristic: title
characteristics.text: minimal choline diet 10d
characteristics.characteristic: treatment