ArticleNucleic acids research2018
fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- The Diverse Mycorrizal Morphology ofJournal of fungi (Basel, Switzerland) · 2024Article
- Learning from the unknown: exploring the range of bacterial functionality.Nucleic acids research · 2023Article
- Functional comparison of metabolic networks across species.Nature communications · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- CDEMI: Characterizing differences in microbial composition and function in microbiome data.Computational and structural biotechnology journal · 2023Article
- Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer.Science advances · 2022Article
- Biodiversity-based development and evolution: the emerging research systems in model and non-model organisms.Science China. Life sciences · 2021Review
- Functional prediction of environmental variables using metabolic networks.Scientific reports · 2021Article
- Codon usage bias and environmental adaptation in microbial organisms.Molecular genetics and genomics : MGG · 2021Article
- Impact of vitamin A transport and storage on intestinal retinoid homeostasis and functions.Journal of lipid research · 2021Article
- Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds.MicrobiologyOpen · 2020Article
- Genomic Analysis ofInternational journal of genomics · 2020Article
- Chemoreceptors with C-terminal pentapeptides for CheR and CheB binding are abundant in bacteria that maintain host interactions.Computational and structural biotechnology journal · 2020Article
- Fingerprinting cities: differentiating subway microbiome functionality.Biology direct · 2019Article
- HFSP: high speed homology-driven function annotation of proteins.Bioinformatics (Oxford, England) · 2018Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality.
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