ArticlePeerJ2018
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data.
Article in PeerJ, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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
105 citing papers in PubMed.
- Predicting the absence of World Health Organization fungal priority pathogens in agricultural soils using machine learning and ITS metabarcoding.Die Naturwissenschaften · 2026Article
- Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum.Molecular ecology · 2026Article
- Opportunistic fungi in tropical beaches: Diversity, WHO fungal priority pathogens, and antifungal resistance case study.Scientific reports · 2026Article
- Predictors and consequences of diet composition in a declining generalist aerial insectivore.Oecologia · 2026Article
- Sporecasting Biogeography Across Scales: Continental Patterns and Local Constraints on Macrofungal Dispersal.Molecular ecology · 2026Article
- Hydroxytyrosol Mitigates Anxiety-Like Behaviors After a Traumatic Experience in Aged Mice in Parallel With Increased Neurogenesis in the Ventral and Dorsal Dentate Gyrus, and Preservation of Gut Microbiota Composition.Journal of neurochemistry · 2026Article
- Interannual Bacterial Diversity Variability in Antarctic Snow/Ice Samples in the Vicinity of Concordia Station.Life (Basel, Switzerland) · 2026Article
- Complex landscapes, complex diets: DNA metabarcoding reveals lady beetle prey richness increases with landcover diversity.Ecological applications : a publication of the Ecological Society of America · 2026Article
- MitoNGS: an online platform to analyze fish metabarcoding data in high resolution.Molecular biology and evolution · 2026Article
- Microbiota and horizontal microbial transmission dynamics associated with bramble (Rubus spp.) flowers.Environmental microbiome · 2026Article
- Seasonal Turnover and Functional Structure of the Foliar Mycobiota in a Gondwanan Temperate Forest Keystone Tree.Journal of fungi (Basel, Switzerland) · 2025Article
- Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.Microorganisms · 2025Article
- Warming and Reduced Rainfall Alter Fungal Necromass Decomposition Rates and Associated Microbial Community Composition and Functioning at a Temperate-Boreal Forest Ecotone.Global change biology · 2025Article
- Observation Bias in Metabarcoding.Molecular ecology resources · 2025Article
- Secondary Decomposers Meet Their Predators: Decomposition Stage and Substrate Quality Jointly Structure Microbial Brown Food Webs During Fungal Necromass Decay.Molecular ecology · 2025Article
- Abundance and Diversity of Endolithic Fungal Assemblages in Granite and Sandstone from Victoria Land, Antarctica.Life (Basel, Switzerland) · 2025Article
- Population Persistence and Soil Microbial Communities of a Serpentine Endemic Plant Outside Its Historic Elevation Range.Ecology and evolution · 2025Article
- Intrathalline Fungal and Bacterial Diversity Is Uncovered in Antarctic Lichen Symbioses.Environmental microbiology reports · 2025Article
- A blueprint for contemporary studies of microbiomes.Microbiome · 2025Article
- Exploring Fungal Abundance and WHO Fungal Priority Pathogens in Agricultural Fields: A One Health Perspective in Northeast Thailand.Life (Basel, Switzerland) · 2025Article
45 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput amplicon sequencing (HTAS) of conserved DNA regions is a powerful technique to characterize microbial communities. Recently, spike-in mock communities have been used to measure accuracy of sequencing platforms and data analysis pipelines. To assess the ability of sequencing platforms and data processing pipelines using fungal internal transcribed spacer (ITS) amplicons, we created two ITS spike-in control mock communities composed of cloned DNA in plasmids: a biological mock community, consisting of ITS sequences from fungal taxa, and a synthetic mock community (SynMock), consisting of non-biological ITS-like sequences. Using these spike-in controls we show that: (1) a non-biological synthetic control (e.g., SynMock) is the best solution for parameterizing bioinformatics pipelines, (2) pre-clustering steps for variable length amplicons are critically important, (3) a major source of bias is attributed to the initial polymerase chain reaction (PCR) and thus HTAS read abundances are typically not representative of starting values. We developed AMPtk, a versatile software solution equipped to deal with variable length amplicons and quality filter HTAS data based on spike-in controls. While we describe herein a non-biological SynMock community for ITS sequences, the concept and AMPtk software can be widely applied to any HTAS dataset to improve data quality.
Indexed as
Identifiers
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.