ArticleEnvironmental microbiome2024
MIMt: a curated 16S rRNA reference database with less redundancy and higher accuracy at species-level identification.
Article in Environmental microbiome, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- seqLens: Optimizing Language Models for Genomic Predictions.Molecular biology and evolution · 2026Article
- WGS reveals high-risk clones of Pseudomonas aeruginosa harbouring extensive antimicrobial and predicted anti-phage defense systems recovered from diabetic foot ulcer patients in Egypt.BMC microbiology · 2026Article
- User Guided Selection and Alignment of Sequence Data by GeneMatrix.Journal of molecular evolution · 2026Article
- Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.Microbiology spectrum · 2026Article
- Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: a comprehensive review.Frontiers in microbiology · 2026Review
- Distinct gut and oral microbiome patterns associated with dyslexia in a family-based cohort: A preliminary exploratory study.PloS one · 2026Article
- Review
- NaMeco - Nanopore full-length 16S rRNA gene reads clustering and annotation.BMC genomics · 2025Article
- Article
- Article
- First molecular phylogenetic and serological insights intoVeterinary world · 2025Article
- Exploring pigment-producing Streptomyces as an alternative source to synthetic pigments: diversity, biosynthesis, and biotechnological applications. A review.World journal of microbiology & biotechnology · 2025Review
- SpeSpeNet: an interactive and user-friendly tool to create and explore microbial correlation networks.ISME communications · 2025Article
- Unveiling the impact of 16S rRNA gene intergenomic variation on primer design and gut microbiome profiling.Frontiers in microbiology · 2025Article
- Lymphocystis viral disease impacts the diversity and functional profiles of the skin microbiome in gilthead seabream.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationAccurate determination and quantification of the taxonomic composition of microbial communities, especially at the species level, is one of the major issues in metagenomics. This is primarily due to the limitations of commonly used 16S rRNA reference databases, which either contain a lot of redundancy or a high percentage of sequences with missing taxonomic information. This may lead to erroneous identifications and, thus, to inaccurate conclusions regarding the ecological role and importance of those microorganisms in the ecosystem.
resultsThe current study presents MIMt, a new 16S rRNA database for archaea and bacteria's identification, encompassing 47 001 sequences, all precisely identified at species level. In addition, a MIMt2.0 version was created with only curated sequences from RefSeq Targeted loci with 32 086 sequences. MIMt aims to be updated twice a year to include all newly sequenced species. We evaluated MIMt against Greengenes, RDP, GTDB and SILVA in terms of sequence distribution and taxonomic assignments accuracy. Our results showed that MIMt contains less redundancy, and despite being 20 to 500 times smaller than existing databases, outperforms them in completeness and taxonomic accuracy, enabling more precise assignments at lower taxonomic ranks and thus, significantly improving species-level identification.
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Registered trials
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