ArticleMicrobiome2024
Highly accurate and sensitive absolute quantification of bacterial strains in human fecal samples.
Article in Microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Effect of Supplementation withNutrients · 2026Trial
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- The Female Reproductive Microbiome: Mechanistic Insights and Bioengineering Perspectives.Biology · 2026Review
- Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.iMeta · 2026Article
- Impact pattern of heavy metals on gut microbiota in the polluted city of Tehran.Iranian journal of microbiology · 2026Article
- Standardizing oral microbiome sampling for qPCR: methodological and exploratory insights into nutritional status.Scientific reports · 2026Article
- Gi-MAPS: a quantitative engineering framework for AI-guided pediatric gut microbiome ecological interpretation and digital-twin simulation.Frontiers in microbiology · 2026Article
- Digital Droplet PCR (ddPCR) for Absolute Quantification of 16S rRNA Copy Number in Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Rapid and low-cost detection of six major pediatric enteric pathogens using a closed-tube PCR-invasive reaction assay.Frontiers in cellular and infection microbiology · 2026Article
- Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.Nature protocols · 2025Review
- Reutericyclin, a specialized metabolite ofGut microbes · 2025Article
- Isolation of viable Mycobacterium bovis from faeces of naturally infected free-ranging rural domestic cattle (Bos taurus).Journal of applied microbiology · 2025Article
- Real-time PCR assay design and validation for Prevotella bivia, Peptostreptococcus anaerobius, and Dialister micraerophilus, bacteria associated with increased HIV susceptibility.Scientific reports · 2025Article
- Single-cell quantification of the microbiota by flow cytometry: MicFLY.bioRxiv : the preprint server for biology · 2025Article
- Harnessing flavonoids to control probiotic function:Microbiology spectrum · 2025Article
- Cooked Bean (Nutrients · 2025Article
- Exploring and evaluating microbiome resilience in the gut.FEMS microbiology ecology · 2025Review
- A blueprint for contemporary studies of microbiomes.Microbiome · 2025Article
- Acquired Bacterial Resistance to Antibiotics and Resistance Genes: From Past to Future.Antibiotics (Basel, Switzerland) · 2025Review
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext-generation sequencing (NGS) approaches have revolutionized gut microbiome research and can provide strain-level resolution, but these techniques have limitations in that they are only semi-quantitative, suffer from high detection limits, and generate data that is compositional. The present study aimed to systematically compare quantitative PCR (qPCR) and droplet digital PCR (ddPCR) for the absolute quantification of Limosilactobacillus reuteri strains in human fecal samples and to develop an optimized protocol for the absolute quantification of bacterial strains in fecal samples.
resultsUsing strain-specific PCR primers for L. reuteri 17938, ddPCR showed slightly better reproducibility, but qPCR was almost as reproducible and showed comparable sensitivity (limit of detection [LOD] around 10
conclusionsBased on our analyses, we consider qPCR with kit-based DNA extraction approaches the best approach to accurately quantify gut bacteria at the strain level in fecal samples. The provided step-by-step protocol will allow scientists to design highly sensitive strain-specific PCR systems for the accurate quantification of bacterial strains of not only L. reuteri but also other bacterial taxa in a broad range of applications and sample types. Video Abstract.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.