ArticleNature biotechnology2024
Quantifying bias introduced by sample collection in relative and absolute microbiome measurements.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 60 papers, 1 of them a synthesis that pooled it.
What it found
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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
60 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A gut microbial signature for combination immune checkpoint blockade across cancer types.Nature medicine · 2024Pooled it
- The calf holobiont under challenge: longitudinal microbiota-pathogen dynamics and respiratory health.Veterinary research · 2026Article
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
- Review
- Bacterial Community Expansion and Nutrient Activation Underlie Yield Improvement Following Diazotrophic Inoculant Application in Paddy Soil.Microorganisms · 2026Article
- The human breast milk microbiome: a landscape review of its composition, origins, and impact on infant health.Archives of microbiology · 2026Review
- Disentangling host identity and storage time effects on gut microbiota composition in captive migratory birds using absolute and relative quantification.Current zoology · 2026Article
- Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.iMeta · 2026Article
- Article
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Evaluating preservation effects on honeybee gut microbiota inocula.Microbiology spectrum · 2026Article
- Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.BMC microbiology · 2026Article
- Article
- Effects of succinate supplementation on rumen fermentation, microbiota, and propionate-associated metabolismFrontiers in microbiology · 2026Article
- Sampling method influences hemolymph bacterial communities in the eastern oyster,Frontiers in microbiology · 2026Article
- Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control.Microbiome research reports · 2026Article
- Decoding the dynamics of calves' respiratory and gut microbiota: exploring stability, resistance, and individual patterns.Animal microbiome · 2025Article
- Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR.Nature protocols · 2025Review
- Pharmacomicrobiomics.Clinical pharmacology and therapeutics · 2025Review
- Quantifying the relative contributions of bacterial and fungal communities to carcass decomposition using a quantitative microbiome profiling approach.NPJ biofilms and microbiomes · 2025Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.
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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.