ArticleBMC genomics2012
Evaluation method for the potential functionome harbored in the genome and metagenome.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Functional Metagenomics Reveals Gut Microbial Biosynthetic Potential for Essential Nutrients in Juvenile Chum Salmon.Environmental microbiology · 2026Article
- Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.Animal microbiome · 2026Article
- Beyond genomes: functional signatures reveal evolutionary patterns across the tree of life.Molecular biology and evolution · 2026Article
- Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean.The ISME journal · 2023Article
- Metagenomic approach to infer rumen microbiome derived traits of cattle.World journal of microbiology & biotechnology · 2023Article
- Dynamics and ecological reassembly of the human gut microbiome and the host metabolome in response to prolonged fasting.Frontiers in microbiology · 2023Article
- Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor.MicrobiologyOpen · 2021Article
- Community structure and metabolic potentials of the traditional rice beer starter 'emao'.Scientific reports · 2021Article
- The physiological potential of anammox bacteria as revealed by their core genome structure.DNA research : an international journal for rapid publication of reports on genes and genomes · 2021Article
- Genomics, Exometabolomics, and Metabolic Probing Reveal Conserved Proteolytic Metabolism ofFrontiers in microbiology · 2021Article
- Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.Environmental microbiology · 2019Article
- Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.Frontiers in microbiology · 2019Article
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- Complete Genome Sequence of Sphingobium sp. Strain YG1, a Lignin Model Dimer-Metabolizing Bacterium Isolated from Sediment in Kagoshima Bay, Japan.Genome announcements · 2018Article
- Complete Genome Sequence of Altererythrobacter sp. Strain B11, an Aromatic Monomer-Degrading Bacterium, Isolated from Deep-Sea Sediment under the Seabed off Kashima, Japan.Genome announcements · 2018Article
- An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.The ISME journal · 2017Article
- Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling.Frontiers in microbiology · 2017Article
- An automated system for evaluation of the potential functionome: MAPLE version 2.1.0.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the main goals of genomic analysis is to elucidate the comprehensive functions (functionome) in individual organisms or a whole community in various environments. However, a standard evaluation method for discerning the functional potentials harbored within the genome or metagenome has not yet been established. We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules.
resultsDistribution of the completion ratio of the KEGG functional modules in 768 prokaryotic species varied greatly with the kind of module, and all modules primarily fell into 4 patterns (universal, restricted, diversified and non-prokaryotic modules), indicating the universal and unique nature of each module, and also the versatility of the KEGG Orthology (KO) identifiers mapped to each one. The module completion ratio in 8 phenotypically different bacilli revealed that some modules were shared only in phenotypically similar species. Metagenomes of human gut microbiomes from 13 healthy individuals previously determined by the Sanger method were analyzed based on the module completion ratio. Results led to new discoveries in the nutritional preferences of gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host.
conclusionsThe method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various uncultivable microbes within unidentified phyla.
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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.