Profiling Gut Microbiome Diversity

Total bacterial DNA was extracted from fecal samples using the DNA extraction kit (TIANGEN, China). For analysis of the taxonomic composition of gut microbiota, the hypervariable regions V3-V4 region of 16S rRNA genes was pooled and sequenced at the Illumina MiSeq 2500 platform (Illumina MiSeq, USA). Reads were trimmed and classified using QIIME (V 1.8.0).^{46 (link)} After quality filtering and chimera removal, these sequences were assigned to operational taxonomic units (OTUs) with ≥ 97% similarity using UPARSE^{47 (link)} and RDP classifier^{48 (link)} was used to classify OTUs at a given taxonomic rank. The gut microbial signature was identified using selbal,^{49 (link)} a greedy stepwise algorithm for balance selection, and unsupervised RandomForest classification analysis.

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Zhang S.L., Han B., Mao Y.Q., Zhang Z.Y., Li Z.M., Kong C.Y., Wu Y., Chen G.Q, & Wang L.S. (2022). Lacticaseibacillus paracasei sh2020 induced antitumor immunity and synergized with anti-programmed cell death 1 to reduce tumor burden in mice. Gut Microbes, 14(1), 2046246.

Publication 2022

DNA extraction kit MiSeq 2500

Bacterial dna Chimera Fecal Gut microbiota Quality Rrna genes

Corresponding Organization : Chinese Academy of Medical Sciences & Peking Union Medical College

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Taxonomic composition of gut microbiota

control variables

None explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

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