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Updated: Jan 28, 2026
Author Spotlight: Exploring the Fermentation Microbiome Through Next-Generation Sequencing
Published on: December 1, 2023
Investigating the bacterial microbiota of traditional fermented dairy products using propidium monoazide with
1Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, P. R. China.
Abstract:
Traditional fermented dairy foods have been the major components of the Mongolian diet for millennia. In this study, we used propidium monoazide (PMA; binds to DNA of nonviable cells so that only viable cells are enumerated) and single-molecule real-time sequencing (SMRT) technology to investigate the total and viable bacterial compositions of 19 traditional fermented dairy foods, including koumiss from Inner Mongolia (KIM), koumiss from Mongolia (KM), and fermented cow milk from Mongolia (CM); sample groups treated with PMA were designated PKIM, PKM, and PCM. Full-length 16S rRNA sequencing identified 195 bacterial species in 121 genera and 13 phyla in PMA-treated and untreated samples. The PMA-treated and untreated samples differed significantly in their bacterial community composition and α-diversity values. The predominant species in KM, KIM, and CM were Lactobacillus helveticus, Streptococcus parauberis, and Lactobacillus delbrueckii, whereas the predominant species in PKM, PKIM, and PCM were Enterobacter xiangfangensis, Lactobacillus helveticus, and E. xiangfangensis, respectively. Weighted and unweighted principal coordinate analyses showed a clear clustering pattern with good separation and only minor overlapping. In addition, a pure culture method was performed to obtain lactic acid bacteria resources in dairy samples according to the results of SMRT sequencing. A total of 102 LAB strains were identified and Lb. helveticus (68.63%) was the most abundant, in agreement with SMRT sequencing results. Our results revealed that the bacterial communities of traditional dairy foods are complex and vary by type of fermented dairy product. The PMA treatment induced significant changes in bacterial community structure.
Insights
This study reveals complex bacterial communities in traditional Mongolian fermented dairy foods using propidium monoazide (PMA) and single-molecule real-time sequencing (SMRT). PMA treatment significantly altered bacterial composition, highlighting viable microbial diversity.
Area of Science:
- Microbiology
- Food Science
- Genomics
Background:
- Traditional fermented dairy foods are integral to the Mongolian diet.
- Understanding their microbial ecosystems is crucial for food safety and quality.
Purpose of the Study:
- To investigate the total and viable bacterial composition of Mongolian fermented dairy products.
- To assess the impact of propidium monoazide (PMA) treatment on bacterial community analysis.
- To identify key bacterial species and lactic acid bacteria (LAB) resources.
Main Methods:
- Utilized propidium monoazide (PMA) combined with single-molecule real-time sequencing (SMRT) for full-length 16S rRNA sequencing.
- Analyzed 19 traditional fermented dairy food samples, including koumiss and fermented cow milk.
- Employed pure culture methods for LAB isolation and identification.
Main Results:
- Identified 195 bacterial species across 121 genera and 13 phyla.
- PMA treatment significantly altered bacterial community structure and alpha-diversity.
- Lactobacillus helveticus was identified as a predominant species in both PMA-treated and untreated samples, and as the most abundant LAB strain.
Conclusions:
- The bacterial communities in traditional Mongolian fermented dairy foods are complex and diverse.
- PMA treatment is effective in differentiating viable bacterial communities.
- The study identified key bacterial players and potential LAB resources for future applications.
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