ArticlemSystems2023
A standardized quantitative analysis strategy for stable isotope probing metagenomics.
Article in mSystems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 11 citations in OpenAlex.
- Problems With GO Enrichment as an Endpoint for Ecological Omics Interpretation.Molecular ecology · 2026Article
- Virome DNA stable isotope probing reveals diverse active soil virus communities across ecosystem contexts.mSystems · 2026Article
- Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics.mSystems · 2026Article
- Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.Nature communications · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- SIPdb: a stable isotope probing database and analytical dashboard for linking amplicon sequences to microbial activity using reverse ecology.ISME communications · 2026Article
- Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Fitting soil extracellular enzyme activity into the complex network of abiotic and biotic soil properties often associated with soil health.Frontiers in microbiology · 2025Review
- Microbial function in food fermentations: Current research and future directions.Current research in microbial sciences · 2025Article
- Review
- MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment.GigaScience · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present
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Registered trials
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.