Quantification and characterization of mouse and human tissue-resident microbiota by qPCR and 16S sequencing

Bingqing Yao; Tingting Dong; Aikun Fu; Hang Li; Chuhan Jiang; Nan Li; Shang Cai

doi:10.1016/j.xpro.2022.101765

Quantification and characterization of mouse and human tissue-resident microbiota by qPCR and 16S sequencing

STAR Protoc. 2022 Dec 16;3(4):101765. doi: 10.1016/j.xpro.2022.101765. Epub 2022 Oct 7.

Authors

Bingqing Yao¹, Tingting Dong², Aikun Fu³, Hang Li⁴, Chuhan Jiang³, Nan Li⁴, Shang Cai⁵

Affiliations

¹ Fudan University, Shanghai 200000, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China. Electronic address: yaobingqing@westlake.edu.cn.
² Fudan University, Shanghai 200000, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.
³ Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China.
⁴ Westlake University High-Performance Computing Center, Westlake University, Hangzhou, Zhejiang 310024, China.
⁵ Fudan University, Shanghai 200000, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China. Electronic address: caishang@westlake.edu.cn.

Abstract

The tissue-resident microbiota is an integral component of multiple tumor types, but it remains challenging to characterize its abundance and composition due to its low biomass. Here, we describe an optimized protocol for quantification and profiling of tissue-resident microbiota. The major optimized steps include DNA extraction, qPCR, 16S library construction, and bioinformatics analysis. This protocol enables robust and accurate characterization of the dynamics of normal and tumor tissue-resident microbiota at its physiological abundance from both mouse and human origins. For complete details on the use and execution of this protocol, please refer to Fu et al. (2022).

Keywords: Bioinformatics; Cancer; Microbiology; Molecular Biology; Sequence analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Humans
Microbiota*
Neoplasms*
RNA, Ribosomal, 16S / genetics
Sequence Analysis, DNA

Substances

RNA, Ribosomal, 16S