ArticleCurrent research in food science2023
Absolute quantification of viable bacteria abundances in food by next-generation sequencing: Quantitative NGS of viable microbes.
Article in Current research in food science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Spoilage-Associated Bacteria in Fresh Cow Cheeses: Diversity, Spoilage-Related Changes, Quantification and Identification Approaches-A Scoping Review.Microorganisms · 2026Review
- Development of PMAxx-droplet digital PCR method for the absolute quantification of viableFrontiers in microbiology · 2026Article
- Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control.Microbiome research reports · 2026Article
- Polyphasic Characterisation of Microbiota Associated with Sant'Agostino Table Olives Flavoured withFoods (Basel, Switzerland) · 2025Article
- Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.bioRxiv : the preprint server for biology · 2025Article
- Microbial succession and interaction in vacuum-packed beef: a longitudinal study of bacterial and fungal dynamics.NPJ science of food · 2025Article
- Current Progress and Future Trends of Genomics-Based Techniques for Food Adulteration Identification.Foods (Basel, Switzerland) · 2025Review
- Chemistry, manufacturing, and controls for live microbial products: addressing classification challenges and enhancing process validation.Frontiers in microbiomes · 2025Review
- Predicting ventilator-associated lower respiratory tract infection outcomes using sequencing-based early microbiological response: a proof-of-concept prospective study.Frontiers in cellular and infection microbiology · 2025Observational
- Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.ISME communications · 2025Article
- Microbiota in tumors: new factor influencing cancer development.Cancer gene therapy · 2024Review
- Application of PCR-Based Techniques for the Identification of Genetic Fingerprint Diversity of Dominant Bacteria in Fecal Samples of Children with Diarrhea in Vietnam.Infectious disease reports · 2024Article
- Novel delivery systems for controlled release of bacterial therapeutics.Trends in biotechnology · 2024Review
- Assessing probiotic viability in mixed species yogurt using a novel propidium monoazide (PMAxx)-quantitative PCR method.Frontiers in microbiology · 2024Article
- Review
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing (NGS) is an important tool for taxonomical bacteria identification. Recent technological developments have led to its improvement and availability. Despite the undeniable advantages of this approach, it has several limitations and shortcomings. The usual outcome of microbiota sequencing is a relative abundance of bacterial taxa. The information about bacteria viability or enumeration is missing. However, this knowledge is crucial for many applications. In the current study, we elaborated the complete workflow for the absolute quantification of living bacteria based on 16S rRNA gene amplicon sequencing. A fluorescent PMAxx reagent penetrating a damaged cell membrane was used to discriminate between the total and viable bacterial population. Bacteria enumeration was estimated by the spike-in technique or qPCR quantification. For method optimization, twenty bacterial species were taken, and the results of the workflow were validated by widely accepted methodologies: flow cytometry, microbiological plating, and viability-qPCR. Despite the minor discrepancy between all methods used, they all showed compatible results. Finally, we tested the workflow with actual food samples and received a good correlation between the methods regarding the estimation of the number of viable bacteria. Overall, the elaborated and integrated NGS approach could be the next step in perceiving a holistic picture of a sample microbiota.
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