ArticleBiotechnology letters2022
Influence of 16S rRNA reference databases in amplicon-based environmental microbiome research.
Article in Biotechnology letters, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Reference Database Selection Influences Both Taxonomic Annotation and Ecological Inference in Arbuscular Mycorrhizal Fungal Communities.Journal of fungi (Basel, Switzerland) · 2026Article
- The Effects of Breeding Methods on Cecal Microflora and Production Traits of Yimeng Black Goats.Animals : an open access journal from MDPI · 2026Article
- Dual-Action Grouper Bone and Wakame Hydrolysates Supplement Enhances Exercise Performance and Modulates Gut Microbiota in Mice.Nutrients · 2025Article
- Toward standardized methods in canine vaginal microbiome research: evaluation of storage, host DNA depletion, and database selection.Microbiology spectrum · 2025Article
- 16S rRNA metabarcoding applied to the microbiome of insect products (novel food): a comparative analysis of three reference databases.Italian journal of food safety · 2025Article
- Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges.Frontiers in microbiology · 2025Review
- Host genotype-driven shifts in theFrontiers in microbiology · 2025Article
- Antimony resistant bacteria isolated from Budúcnosť adit (Pezinok-Kolársky vrch deposit) in western Slovakia.Heliyon · 2024Article
- Don't let valuable microbiome data go to waste: combined usage of merging and direct-joining of sequencing reads for low-quality paired-end amplicon data.Biotechnology letters · 2024Article
- Existence of rare actinobacterial forms in the Indian sector of Southern Ocean: 16 S rRNA based metabarcoding study.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- A how-to guide for code sharing in biology.PLoS biology · 2024Review
- Searching for bacterial plastitrophs in modified Winogradsky columns.Frontiers in microbiomes · 2024Article
- Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies.Methods and protocols · 2023Article
- Bile acid metabolism and signaling: Emerging pharmacological targets of dietary polyphenols.Pharmacology & therapeutics · 2023Review
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Abstract
purposeThe reference databases play a pivotal role in amplicon microbiome research, however these databases differ in the sequence content and taxonomic information available. Studies on mock community and human health microbiome have revealed the problems associated with the choice of reference database on the outcome. Nonetheless, the influence of reference databases in environmental microbiome studies is not explicitly illustrated.
methodsThis study analyzed the amplicon (V1V3, V3V4, V4V5 and V6V8) data of 128 soil samples and evaluated the impact of 16S rRNA databases, Genome Taxonomy Database (GTDB), Ribosomal Database Project (RDP), SILVA and Consensus Taxonomy (ConTax), on microbiome inference.
resultsThe analyses showed that the distribution of observed amplicon sequence variants was significantly different (P-value < 2.647e-12) across four datasets, generated using different databases for each amplicon region. In addition, the beta diversity was also found to be altered by different databases. Further investigation revealed that the microbiome composition inferred by various databases differ significantly (P-value = 0.001), irrespective of amplicon regions. This study, found that the core-microbiome structure in environmental studies is influenced by the type of reference database used.
conclusionIn summary, this present study illustrates that the choice of reference database could influence the outcome of environmental microbiome research.
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