ArticlemSystems
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer.
Article in mSystems. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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
91 citing papers in PubMed, 1 synthesis or guideline pooled it, 163 citations in OpenAlex.
- Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.Nature medicine · 2022Pooled it
- Recovering anaerobic bacterial genomes in saliva, tumour and blood whole genome sequencing data from patients with prostate cancer.NPJ biofilms and microbiomes · 2026Article
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease.Cell reports. Medicine · 2026Article
- Article
- Microbe Decoder uncovers functional traits of microbes in microbiome datasets.Nucleic acids research · 2026Article
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.Cell press blue · 2026Article
- Isolation by distance promotes gut microbial strain divergence in wild mouse populations.Nature ecology & evolution · 2026Article
- Genomic and Functional Diversity of Pseudoalteromonas Associated with the Tropical Bivalve Anadara tuberculosa.Microbial ecology · 2026Article
- Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions.bioRxiv : the preprint server for biology · 2026Article
- Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.Scientific reports · 2026Article
- Genomic and phenotypic characterization of a human gutFuture microbiology · 2026Article
- Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.Genome biology · 2026Article
- Complete genome sequence and functional characterization of Bacillus amyloliquefaciens NJF-55: a sheep-derived probiotic candidate.Scientific reports · 2026Article
- Noncanonical genetic markers resolve the pre-GOE emergence of aerobic bacteria in Earth's history.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- metaTraits: a large-scale integration of microbial phenotypic trait information.Nucleic acids research · 2026Article
- Genome description of a potentially novel species of Rossellomorea sp. strain H39_3 isolated from the Hindon River, India.Access microbiology · 2026Article
- Genome description of a potentially novel species of Billgrantia sp. strain SL18_1 isolated from Sambhar Lake, India.Access microbiology · 2026Article
- Antibiotic Resistance Crisis: From Bacterial Bioprospecting to Artificial Intelligence.Environmental microbiology reports · 2025Review
- Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.Microbial genomics · 2025Article
- Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.Nature communications · 2025Article
31 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
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The number of sequenced genomes is growing exponentially, profoundly shifting the bottleneck from data generation to genome interpretation. Traits are often used to characterize and distinguish bacteria and are likely a driving factor in microbial community composition, yet little is known about the traits of most microbes. We describe Traitar, the microbial trait analyzer, which is a fully automated software package for deriving phenotypes from a genome sequence. Traitar provides phenotype classifiers to predict 67 traits related to the use of various substrates as carbon and energy sources, oxygen requirement, morphology, antibiotic susceptibility, proteolysis, and enzymatic activities. Furthermore, it suggests protein families associated with the presence of particular phenotypes. Our method uses L1-regularized L2-loss support vector machines for phenotype assignments based on phyletic patterns of protein families and their evolutionary histories across a diverse set of microbial species. We demonstrate reliable phenotype assignment for Traitar to bacterial genomes from 572 species of eight phyla, also based on incomplete single-cell genomes and simulated draft genomes. We also showcase its application in metagenomics by verifying and complementing a manual metabolic reconstruction of two novel
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.