ArticleBMC genomics2019
DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 65 citations in OpenAlex.
- Bacterial metataxonomic analysis of the Algerian traditional dried-salted meat 'El Kaddid' and characterization of its lactic acid bacteria.Antonie van Leeuwenhoek · 2026Article
- Microbial and Biochemical Analyses of High-Quality, Long-Ripened, Blue-Veined Cabrales Cheese.Foods (Basel, Switzerland) · 2025Article
- A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset.Scientific data · 2025Article
- Analytical Mapping of Swiss Hard Cheese to Highlight the Distribution of Volatile Compounds, Aroma, and Microbiota.Journal of agricultural and food chemistry · 2025Article
- Microbial dynamics in the ripening process of Vorarlberger Alpkäse: farm-specific variations at two Austrian alpine farms.Frontiers in microbiology · 2025Article
- Metataxonomic profiling of microbial communities and metabolic analyses of the traditional Spanish raw cow's milk cheese 'Casín' from manufacture to ripening.Frontiers in microbiology · 2025Article
- Antilisterial Properties of Selected Strains from the Autochthonous Microbiota of a Swiss Artisan Soft Smear Cheese.Foods (Basel, Switzerland) · 2024Article
- A comprehensive, large-scale analysis of "terroir" cheese and milk microbiota reveals profiles strongly shaped by both geographical and human factors.ISME communications · 2024Article
- Microbial Dynamics during labneh Ambaris Production in Earthenware Jars.Foods (Basel, Switzerland) · 2023Article
- Dietary Live Yeast Supplementation Influence on Cow's Milk, Teat and Bedding Microbiota in a Grass-Diet Dairy System.Microorganisms · 2023Article
- Selective enrichment of the raw milk microbiota in cheese production: Concept of a natural adjunct milk culture.Frontiers in microbiology · 2023Article
- Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study.Foods (Basel, Switzerland) · 2022Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
- High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota.BMC microbiology · 2022Article
- Integration of Multiomic Data to Characterize the Influence of Milk Fat Composition onMicroorganisms · 2022Article
- Contribution of omics to biopreservation: Toward food microbiome engineering.Frontiers in microbiology · 2022Review
- Identification of isolated or mixed strains from long reads: a challenge met onMicrobial genomics · 2021Article
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese.mSystems · 2021Article
- BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities.mSystems · 2021Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReads assignment to taxonomic units is a key step in microbiome analysis pipelines. To date, accurate taxonomy annotation of 16S reads, particularly at species rank, is still challenging due to the short size of read sequences and differently curated classification databases. The close phylogenetic relationship between species encountered in dairy products, however, makes it crucial to annotate species accurately to achieve sufficient phylogenetic resolution for further downstream ecological studies or for food diagnostics. Curated databases dedicated to the environment of interest are expected to improve the accuracy and resolution of taxonomy annotation.
resultsWe provide a manually curated database composed of 10'290 full-length 16S rRNA gene sequences from prokaryotes tailored for dairy products analysis ( https://github.com/marcomeola/DAIRYdb ). The performance of the DAIRYdb was compared with the universal databases Silva, LTP, RDP and Greengenes. The DAIRYdb significantly outperformed all other databases independently of the classification algorithm by enabling higher accurate taxonomy annotation down to the species rank. The DAIRYdb accurately annotates over 90% of the sequences of either single or paired hypervariable regions automatically. The manually curated DAIRYdb strongly improves taxonomic annotation accuracy for microbiome studies in dairy environments. The DAIRYdb is a practical solution that enables automatization of this key step, thus facilitating the routine application of NGS microbiome analyses for microbial ecology studies and diagnostics in dairy products.
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