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Updated: Oct 14, 2025

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

Published on: March 19, 2018

Building up a clinical microbiota profiling: a quality framework proposal.

Valentin Scherz¹, Gilbert Greub¹, Claire Bertelli¹

¹Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.

Critical Reviews in Microbiology

|November 9, 2021

Summary

This summary is machine-generated.

Establishing quality management for human microbiota profiling is crucial for clinical utility. This review proposes a framework to standardize methods, ensuring reliable biomarkers for health and disease research and patient care.

Keywords:

Metagenomics biomarkers microbiome microbiota profiling quality management

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Area of Science:

Microbiology
Bioinformatics
Clinical Diagnostics

Background:

Human microbiota composition is linked to health and disease, driving interest in microbiota profiling for biomarkers.
Technical challenges and inherent complexity hinder the generalization and clinical utility of current microbiota profiling methods.
A lack of standardized quality management schemes specific to microbiota profiling limits its reliability and reproducibility.

Purpose of the Study:

To review and adapt classical quality management tools for microbiota profiling.
To propose a specific quality management framework for microbiota profiling.
To enhance the clinical utility and research reproducibility of microbiota profiling.

Main Methods:

Discussion of adapting traditional quality management tools for diagnostic laboratories.
Proposal of a comprehensive quality management framework covering all profiling steps.
Adaptation of standard operating procedures for bioinformatic tools.

Main Results:

Identification of the need for multiple quality controls from sampling to data processing.
Highlighting the necessity to adapt validation and proficiency testing to account for process heterogeneity.
A proposed framework to guide the implementation of routine microbiota profiling.

Conclusions:

A robust quality management framework is essential for routine clinical microbiota profiling.
Implementing this framework will improve the reproducibility of research findings.
Standardization will facilitate the transfer of microbiota profiling methods and results from research to clinical practice.