ArticleApplied and environmental microbiology2019
Towards Quantitative Microbiome Community Profiling Using Internal Standards.
Article in Applied and environmental microbiology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 78 citations in OpenAlex.
- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- The dynamic mesoscale sink and source niches for eukaryotic phytoplankton in a subtropical gyre.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Molecular and physiological acclimation to low light and iron scarcity in a globally abundant oceanic pelagophyte.Nature communications · 2026Article
- Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.Current protocols · 2026Article
- Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.ISME communications · 2026Article
- A novel internal reference microorganism-based method reveals wild-enrichedFrontiers in microbiology · 2026Article
- Impact of animal socioecology on gut microbial communities: Insights from wild meerkats in the Kalahari.The Journal of animal ecology · 2025Article
- Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.Nature communications · 2025Article
- Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.bioRxiv : the preprint server for biology · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies.Frontiers in microbiology · 2025Article
- Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.ISME communications · 2025Article
- Mapping total microbial communities and waterborne pathogens in household drinking water in China by citizen science and metabarcoding.Frontiers in microbiology · 2025Article
- Article
- Multi-factor analysis of the quality of cellar mud of Luzhou-flavor liquor in Yibin production area.Food science & nutrition · 2024Article
- Three steps towards comparability and standardization among molecular methods for characterizing insect communities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Article
- Amplicon sequencing with internal standards yields accurate picocyanobacteria cell abundances as validated with flow cytometry.ISME communications · 2024Article
- A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes.Environmental microbiology reports · 2023Article
- Synechococcus nitrogen gene loss in iron-limited ocean regions.ISME communications · 2023Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An inherent issue in high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations, making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxon cooccurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In
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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.