Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis

Curr Protoc Immunol. 2014 Nov 3:107:7.41.1-7.41.11. doi: 10.1002/0471142735.im0741s107.

Abstract

Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.

Keywords: 16S rRNA; Illumina sequencing; intestinal microbiota; lavage; mucosal microbiota.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Gastrointestinal Microbiome / genetics*
  • Gastrointestinal Microbiome / immunology
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Mice
  • Nucleic Acid Amplification Techniques / methods*
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / immunology
  • RNA, Ribosomal, 16S / genetics*
  • RNA, Ribosomal, 16S / immunology

Substances

  • RNA, Bacterial
  • RNA, Ribosomal, 16S