The raw 16S rRNA gene sequencing reads were demultiplexed, quality-filtered by fastp version 0.20.0 (Chen et al., 2018 (link)), and merged by FLASH version 1.2.7 (Magoc and Salzberg, 2011 (link)). Operational taxonomic units (OTUs) with 97% similarity cutoff (Edgar, 2013 (link)) were clustered using UPARSE version 7.1 [3], and chimeric sequences were identified and removed. The taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.2 (Wang et al., 2007 (link)) against the 16S rRNA database using a confidence threshold of 70% (PRJNA889391).
Intestinal Microbiome Profiling by 16S rRNA Sequencing
The raw 16S rRNA gene sequencing reads were demultiplexed, quality-filtered by fastp version 0.20.0 (Chen et al., 2018 (link)), and merged by FLASH version 1.2.7 (Magoc and Salzberg, 2011 (link)). Operational taxonomic units (OTUs) with 97% similarity cutoff (Edgar, 2013 (link)) were clustered using UPARSE version 7.1 [3], and chimeric sequences were identified and removed. The taxonomy of each OTU representative sequence was analyzed by RDP Classifier version 2.2 (Wang et al., 2007 (link)) against the 16S rRNA database using a confidence threshold of 70% (PRJNA889391).
Corresponding Organization : Chinese Academy of Agricultural Sciences
Other organizations : Gembloux Agro-Bio Tech
Variable analysis
- Bacterial DNA extraction method (EZNA Soil DNA kit)
- Primers used for 16S rRNA gene amplification (338F and 806R)
- Sequencing platform (Illumina MiSeq PE300)
- Bacterial community composition and diversity as measured by 16S rRNA gene sequencing
- Intestinal chyme and mucosa samples from the same source
- Sequence processing and analysis pipeline (fastp, FLASH, UPARSE, RDP Classifier)
- None specified
- None specified
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