ArticleNucleic acids research2016
The landscape of microbial phenotypic traits and associated genes.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 130 citations in OpenAlex.
- MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.BMC bioinformatics · 2019Pooled it
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- Primary tumor microbiomes predict distant metastasis of colorectal cancer.NPJ precision oncology · 2025Article
- Experimental mapping of bacterial fitness landscapes reveals eco-evolutionary fingerprints.Scientific reports · 2025Article
- Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
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- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- From genotype to phenotype: computational approaches for inferring microbial traits relevant to the food industry.FEMS microbiology reviews · 2023Review
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- Application and Challenge of 3rd Generation Sequencing for Clinical Bacterial Studies.International journal of molecular sciences · 2022Review
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- Function-based classification of hazardous biological sequences: Demonstration of a new paradigm for biohazard assessments.Frontiers in bioengineering and biotechnology · 2022Article
- PPA-GCN: A Efficient GCN Framework for Prokaryotic Pathways Assignment.Frontiers in genetics · 2022Article
- Multisubstrate DNA stable isotope probing reveals guild structure of bacteria that mediate soil carbon cycling.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Exploring the functional composition of the human microbiome using a hand-curated microbial trait database.BMC bioinformatics · 2021Article
- gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.Genome biology · 2021Article
- Discovering microbe-disease associations from the literature using a hierarchical long short-term memory network and an ensemble parser model.Scientific reports · 2021Article
- A synthesis of bacterial and archaeal phenotypic trait data.Scientific data · 2020Article
- Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.Scientific reports · 2019Article
- Linking high GC content to the repair of double strand breaks in prokaryotic genomes.PLoS genetics · 2019Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text. Moreover, the ProTraits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in metagenomes. Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability. A global analysis of trait interrelatedness outlined clusters in the microbial phenotype network, suggesting common genetic underpinnings. Our extended set of phenotype annotations allows detection of 57 088 high confidence gene-trait links, which recover many known associations involving sporulation, flagella, catalase activity, aerobicity, photosynthesis and other traits. Over 99% of the commonly occurring gene families are involved in genetic interactions conditional on at least one phenotype, suggesting that epistasis has a major role in shaping microbial gene content.
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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.