ArticleNucleic acids research2025
BacDive in 2025: the core database for prokaryotic strain data.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut microbiota signatures in mild cognitive impairment: a scoping review of microbial taxa and clinical implications.Frontiers in microbiology · 2026Pooled it
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- Comparative Metabolomics Reveals the Production of Sulfated Metabolites by Human Gut Bacteria.Journal of the American Chemical Society · 2026Article
- Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.BMC genomics · 2026Article
- Comparing optimal transport and machine learning approaches for databases merging in scenarios involving missing data in covariates. Application to medical research.Bioinformatics (Oxford, England) · 2026Article
- Phylogenetic analysis of the bacterial intracellular R-body killer proteins indicates extensive horizontal gene transfer and signature Reb sequence motifs.BMC genomics · 2026Article
- Comparative assessment of large language models for microbial phenotype assignment.Genome biology · 2026Article
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- Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation.Communications biology · 2026Review
- SigMine and OPathDb: a literature-mining pipeline and database of potential opportunistic pathogens.Archives of microbiology · 2026Article
- Microbe Decoder uncovers functional traits of microbes in microbiome datasets.Nucleic acids research · 2026Article
- A high-throughput heterologous expression platform for plant synthetic biology based on Arabidopsis suspension cells.Journal of experimental botany · 2026Article
- Zeaxanthin-Producing Winogradskyella schleiferi Strains.Journal of basic microbiology · 2026Article
- Hybrid genome assembly and phenotypic assays reveal carbohydrate metabolism diversity in Lacticaseibacillus strains.Applied microbiology and biotechnology · 2026Article
- Enhanced identification of key bacterial motility genes via a cross-species genomic hybrid feature machine learning approach.BMC genomics · 2026Article
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- Biocalorimetry for the biotechnological use of natural and synthetic macromolecules.Applied microbiology and biotechnology · 2026Review
- Deep-learning deconvolution and segmentation of fluorescent membranes for high-precision bacterial cell-size profiling.Communications biology · 2026Article
19 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
11 authors.
Funding
Abstract
In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is increasingly being used for the training of artificial intelligence models and resulting genome-based predictions with high confidence are now used to fill content gaps in the database.
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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.