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Updated: Jun 24, 2025
Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
Published on: August 29, 2014
MIST: A microbial identification and source tracking system for next-generation sequencing data
Minghui Song1, Chang Han2, Linmeng Liu2
1Shanghai Institute for Food and Drug Control NMPA Key Laboratory for Testing Technology of Pharmaceutical Microbiology Shanghai.
Abstract:
The Professional Committee of Microbiology of the National Pharmacopoeia Commission organized the drafting of the Technical Guidelines for Microbial Whole Genome Sequencing (WGS), aiming to standardize the method process and technical indicators of microbial WGS and ensure the accuracy of sequencing and identification. On the basis of the Guidelines, we developed an integrated microbial identification and source tracking (MIST) system, which could meet the needs of microbial identification and contamination investigation in food and drug quality control. MIST integrates three analysis pipelines: 16S/18S/internal transcribed spacer amplicon-based microbial identification, WGS-based microbial identification, and single-nucleotide polymorphism-based microbial source tracking. MIST can analyze sequence data in a variety of formats, such as Fasta, base call file, and FASTQ. It can be connected to a high-throughput sequencing instrument to acquire sequencing data directly. We also developed a publicly accessible web server for MIST (http://syj.i-sanger.cn).
Insights
This study introduces the Microbial Identification and Source Tracking (MIST) system, integrating whole genome sequencing (WGS) for accurate microbial identification and contamination investigation in food and drugs. The MIST system standardizes microbial analysis, enhancing quality control.
Area of Science:
- Microbiology
- Bioinformatics
- Genomics
Background:
- Standardization of microbial whole genome sequencing (WGS) is crucial for accurate identification and contamination investigations.
- Existing methods may lack integration for comprehensive microbial analysis in quality control.
Purpose of the Study:
- To develop an integrated system for microbial identification and source tracking based on established WGS guidelines.
- To enhance microbial analysis capabilities for food and drug quality control.
Main Methods:
- Development of the Microbial Identification and Source Tracking (MIST) system.
- Integration of 16S/18S/ITS amplicon sequencing, WGS, and SNP-based source tracking pipelines.
- Support for multiple sequence data formats (Fasta, base call file, FASTQ) and direct connection to sequencing instruments.
Main Results:
- The MIST system offers integrated microbial identification and source tracking.
- The system supports diverse sequence data inputs and direct data acquisition.
- A publicly accessible web server for MIST was established (http://syj.i-sanger.cn).
Conclusions:
- The MIST system provides a standardized and integrated approach for microbial analysis.
- This system improves microbial identification and contamination investigation in food and drug safety.
- The developed MIST system and its web server facilitate broader application in quality control.
