ArticleFrontiers in microbiology2021
Equivolumetric Protocol Generates Library Sizes Proportional to Total Microbial Load in 16S Amplicon Sequencing.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Bifidogenic Effect of 2'-Fucosyllactose (2'-FL) on the Gut Microbiome of Healthy Formula-Fed Infants: A Randomized Clinical Trial.Nutrients · 2025Trial
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- Organosilane for surface cleaning in intensive care units: protocol for a cluster randomized controlled trial with crossover.Critical care science · 2025Article
- Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses.mSphere · 2024Article
- Oral microbiome test as an alternative diagnostic tool for gastric alterations: A prospective, bicentric cross-sectional study.PloS one · 2024Article
- 16S rRNA amplicon sequencing and antimicrobial resistance profile of intensive care units environment in 41 Brazilian hospitals.Frontiers in public health · 2024Observational
- Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.Nature communications · 2022Article
- Reduced gut microbiota diversity in patients with congenital generalized lipodystrophy.Diabetology & metabolic syndrome · 2022Article
- Detection of Intestinal Dysbiosis in Post-COVID-19 Patients One to Eight Months after Acute Disease Resolution.International journal of environmental research and public health · 2022Article
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- Sampling the fish gill microbiome: a comparison of tissue biopsies and swabs.BMC microbiology · 2021Article
- SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment.Microbiome · 2021Article
- Article
- Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital.Frontiers in microbiology · 2021Article
- Nicotine Changes Airway Epithelial Phenotype and May Increase the SARS-COV-2 Infection Severity.Molecules (Basel, Switzerland) · 2020Article
- Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment.medRxiv : the preprint server for health sciences · 2020Article
- SQMtools: automated processing and visual analysis of 'omics data with R and anvi'o.BMC bioinformatics · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing of 16S rRNA amplicon has been extensively employed to perform microbiome characterization worldwide. As a culture-independent methodology, it has allowed high-level profiling of sample bacterial composition directly from samples. However, most studies are limited to information regarding relative bacterial abundances (sample proportions), ignoring scenarios in which sample microbe biomass can vary widely. Here, we use an equivolumetric protocol for 16S rRNA amplicon library preparation capable of generating Illumina sequencing data responsive to input DNA, recovering proportionality between observed read counts and absolute bacterial abundances within each sample. Under specified conditions, we show that the estimation of colony-forming units (CFU), the most common unit of bacterial abundance in classical microbiology, is challenged mostly by resolution and taxon-to-taxon variation. We propose Bayesian cumulative probability models to address such issues. Our results indicate that predictive errors vary consistently below one order of magnitude for total microbial load and abundance of observed bacteria. We also demonstrate our approach has the potential to generalize to previously unseen bacteria, but predictive performance is hampered by specific taxa of uncommon profile. Finally, it remains clear that high-throughput sequencing data are not inherently restricted to sample proportions only, and such technologies bear the potential to meet the working scales of traditional microbiology.
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