Decontamination Reveals a Convergent Microbiome-Functional Signature of Gut-Lymph-Lung Translocation in Sepsis - Processed 16S rRNA Data

Dataset: Decontamination Reveals a Convergent Microbiome-Functional Signature of Gut-Lymph-Lung Translocation in Sepsis Description: Processed 16S rRNA gene (V4 region) sequencing data from a rat cecal ligation and puncture (CLP) sepsis model. Mesenteric lymph, fecal, and bronchoalveolar lavage fluid (BALF) samples were collected at 0, 4, 8, 12, and 24 hours post-CLP (n=5 per time point). Six negative extraction controls were included. Sequencing: Platform: Illumina MiSeq (2x300 bp paired-end) Primers: 515F / 806R (V4 region) DNA extraction: E.Z.N.A. Soil DNA Kit (Omega Bio-tek) Sequencing provider: Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China) Bioinformatics: Quality filtering: Trimmomatic (Phred >= 20) Read merging: FLASH Chimera detection: UCHIME OTU clustering: UPARSE (97% similarity) Taxonomy: SILVA 138 database File descriptions: otu_table.xls - OTU count table (8042 OTUs x 66 samples) otu_reps.fasta - Representative sequences for each OTU taxonomy_assignments.txt - SILVA 138 taxonomy assignments per OTU merged_sequences.fasta.gz - Quality-filtered merged sequences (all samples) phylogenetic_tree.tre - Phylogenetic tree of OTU representative sequences alpha_diversity_estimators.xls - Alpha diversity indices per sample family_level_abundance.xls - Family-level aggregated abundance table genus_level_abundance.xls - Genus-level aggregated abundance table samples_info.txt - Per-sample sequencing statistics Sample naming convention: [rat_id]_[timepoint]LB = Mesenteric lymph (e.g., 1_0hLB, 5_4hLB) [rat_id]_FB = Fecal sample (e.g., 1_FB, 3_FB) [rat_id]_FP = Bronchoalveolar lavage fluid (e.g., 1_FP, 3_FP) con_1 to con_5 = Negative extraction controls water = Water blank control LB_1 to LB_5 = Additional lymph controls Ethics: Approved by Institutional Animal Care and Use Committee of Shanghai (Approval No. A2015035) License: CC BY 4.0