ArticleFEMS microbiology ecology2019
Issues and current standards of controls in microbiome research.
Article in FEMS microbiology ecology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 129 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
129 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Impact of Electronic Cigarette Use on the Oral Microbiota: A Systematic Review.Journal of clinical periodontology · 2026Pooled it
- Pooled it
- Improvements to postprandial glucose control in subjects with type 2 diabetes: a multicenter, double blind, randomized placebo-controlled trial of a novel probiotic formulation.BMJ open diabetes research & care · 2020Trial
- Beyond the gut microbe: Rethinking infection, microbiome harmony, and the one-health continuum.World journal of gastrointestinal pharmacology and therapeutics · 2026Review
- Differentiation of the Foliar Microbiomes From Co-Occurring Grass Species Reflects Their Recency of Invasion.Ecology and evolution · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Limited impact of schistosome infection on Biomphalaria glabrata snail microbiomes.Parasites & vectors · 2026Article
- Spatial and temporal patterns of public transit aerobiomes.Microbiome · 2026Article
- Metagenomic Data Preprocessing and Quality Control.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- Host Genetics and the Skin Microbiome Independently Predict Parasite Resistance.Ecology and evolution · 2026Article
- Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- Respiratory bacteriome and its predicted functional profiles in blue whales (Balaenoptera musculus).Scientific reports · 2025Article
- STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies.Nature microbiology · 2025Review
- Next-Generation Sequencing for Bloodstream Infections: Shaping the Future of Rapid Diagnostics and Precision Medicine.Diagnostics (Basel, Switzerland) · 2025Review
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.Microbiology spectrum · 2025Article
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.Molecular ecology resources · 2025Article
69 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Good scientific practice is important in all areas of science. In recent years this has gained more and more attention, especially considering the 'scientific reproducibility crisis'. While most researchers are aware of the issues with good scientific practice, not all of these issues are necessarily clear, and the details can be very complicated. For many years it has been accepted to perform and publish sequencing based microbiome studies without including proper controls. Although in recent years more scientists realize the necessity of implementing controls, this poses a problem due to the complexity of the field. Another concern is the inability to properly interpret the information gained from controls in microbiome studies. Here, we will discuss these issues and provide a comprehensive overview of problematic points regarding controls in microbiome research, and of the current standards in this area.
Indexed as
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What OpenQuestion holds
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.