SynthesisMicrobiology spectrum2022
Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes.
Synthesis in Microbiology spectrum, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 2 of them syntheses that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 2 syntheses or guidelines pooled it, 40 citations in OpenAlex.
- Pancreatic microbiota composition and diversity in pancreatitis-associated infection: a systematic review with focus on infected pancreatic necrosis.Frontiers in microbiology · 2026Pooled it
- Associations of the gut, cervical, and vaginal microbiota with cervical cancer: a systematic review and meta-analysis.BMC women's health · 2025Pooled it
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
- Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.Molecular ecology resources · 2025Article
- Toxicological and Functional Assessment of Minicell-Encapsulated dsRNA on Biocontrol Agents in Agriculture.ACS environmental Au · 2025Article
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).PLoS computational biology · 2025Article
- Beyond clinical genomics: addressing critical gaps in One Health AMR surveillance.Frontiers in microbiology · 2025Article
- Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.Frontiers in microbiology · 2025Article
- Impact of sample multiplexing on detection of bacteria and antimicrobial resistance genes in pig microbiomes using long-read sequencing.Frontiers in microbiology · 2025Article
- From Tradition to Innovation: Diverse Molecular Techniques in the Fight Against Infectious Diseases.Diagnostics (Basel, Switzerland) · 2024Review
- Chinese expert consensus on standard technical specifications for a gut microecomics laboratory (Review).Experimental and therapeutic medicine · 2024Review
- Article
- Single-Cell Sequencing Technology and Its Application in the Study of Central Nervous System Diseases.Cell biochemistry and biophysics · 2024Review
- Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.International journal of molecular sciences · 2024Review
- Microbiota-gut-brain axis and its therapeutic applications in neurodegenerative diseases.Signal transduction and targeted therapy · 2024Review
- Integrated overview of stramenopile ecology, taxonomy, and heterotrophic origin.The ISME journal · 2024Review
- A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.Microorganisms · 2023Article
- A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences.NAR genomics and bioinformatics · 2023Article
- RAPIDViruses · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics is increasingly used to describe microbial communities in biological specimens. Ideally, the steps involved in the processing of the biological specimens should not change the microbiome composition in a way that it could lead to false interpretations of inferred microbial community composition. Common steps in sample preparation include sample collection, storage, DNA isolation, library preparation, and DNA sequencing. Here, we assess the effect of three library preparation kits and two DNA sequencing platforms. Of the library preparation kits, one involved a PCR step (Nextera), and two were PCR free (NEXTflex and KAPA). We sequenced the libraries on Illumina HiSeq and NextSeq platforms. As example microbiomes, two pig fecal samples and two sewage samples of which aliquots were stored at different storage conditions (immediate processing and storage at -80°C) were assessed. All DNA isolations were performed in duplicate, totaling 80 samples, excluding controls. We found that both library preparation and sequencing platform had systematic effects on the inferred microbial community composition. The different sequencing platforms introduced more variation than library preparation and freezing the samples. The results highlight that all sample processing steps need to be considered when comparing studies. Standardization of sample processing is key to generating comparable data within a study, and comparisons of differently generated data, such as in a meta-analysis, should be performed cautiously.
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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.