ArticleBMC biology2023
Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.
Article in BMC biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 18 citations in OpenAlex.
- Decoding the reproductive microbiome: enabling clinical and biological insights through machine and deep learning.Frontiers in endocrinology · 2026Review
- Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.Microbial genomics · 2026Article
- Skin microbiome analysis of a junctional epidermolysis bullosa patient treated with genetically modified stem cells.Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG · 2025Article
- Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2025Article
- Impact of microbiological molecular methodologies on adaptive sampling using nanopore sequencing in metagenomic studies.Environmental microbiome · 2025Article
- Bacterial DNA Contamination of Commercial PCR Enzymes: Considerations for Microbiome Protocols and Analysis.Microorganisms · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.Microbiome · 2025Article
- micRoclean: an R package for decontaminating low-biomass 16S-rRNA microbiome data.Frontiers in bioinformatics · 2025Article
- Standardization of gut microbiome analysis in sports.Cell reports. Medicine · 2024Review
- Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges.Nature metabolism · 2024Review
- The Role of Microbial Mats in the Biostabilization of Sediment Through Trapping and Binding.GeobiologyArticle
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicrobiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.
resultsWe benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (10
conclusionsMicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
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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.