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Updated: Jun 25, 2026

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
Development of Faecalibacterium 16S rRNA gene marker for identification of human faeces
G Zheng1, H Yampara-Iquise, J E Jones
1Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA.
Aims:
The focus of this study was to identify a bacterial 16S rRNA gene sequence, unique to microbiota in the human gut, for use in development of a dependable PCR assay to detect human faecal pollution in water.
Methods And Results:
Suppression subtractive hybridization (SSH) and bioinformatics were used to identify a genetic marker, within the 16S rRNA gene of Faecalibacterium, for the detection of human faeces. DNA sequencing analysis demonstrated that a majority (16) of 74 clones of the SSH library contained insertion sequences identified as Faecalibacterium 16S rRNA genes. Human faeces-specific sequences were derived and six PCR primer sets designed and tested against faecal DNA samples from human and nonhuman sources. One PCR primer set, HFB-F3 and HFB-R5, was exclusively associated with human faeces. These primers generated a human faeces-specific amplicon of 399 bp from 60.2% of human faecal samples and 100% of sewage samples.
Conclusions:
The subject Faecalibacterium marker is specific for sewage.
Significance And Impact Of The Study:
This study represents the initial report of a Faecalibacterium marker for human faeces, which may prove useful for microbial source tracking.
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