ArticlePLoS genetics2022
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics.
Article in PLoS genetics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.Microbiology spectrum · 2026Article
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- A syntenic pangenome of Gardnerella reveals novel plasmids and phage, taxonomic boundaries, and species-level stratification of metabolic and virulence potential.Nature communications · 2026Article
- Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.Nature communications · 2026Article
- Methane-fed microbial communities enriched from field-grown rice support diverse heterotrophic bacteria.FEMS microbiology ecology · 2026Article
- Denitrification is a community trait with partial pathways dominating across microbial genomes and biomes.Nature communications · 2025Article
- RB-TnSeq elucidates dicarboxylic-acid-specific catabolism in β-proteobacteria for improved plastic monomer upcycling.Applied and environmental microbiology · 2025Article
- Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis.NPJ biofilms and microbiomes · 2025Article
- Abundant and active community members respond to diel cycles in hot spring phototrophic mats.The ISME journal · 2025Article
- Assessing horizontal gene transfer in the rhizosphere ofApplied and environmental microbiology · 2024Article
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- Interactive tools for functional annotation of bacterial genomes.Database : the journal of biological databases and curation · 2024Article
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- Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance.Nature communications · 2024Article
- Emerging tools and best practices for studying gut microbial community metabolism.Nature metabolism · 2024Review
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- Nitrosative stress under microaerobic conditions triggers inositol metabolism in Pseudomonas extremaustralis.PloS one · 2024Article
- Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.Molecular systems biology · 2023Article
- Cultivation of marine bacteria of the SAR202 clade.Nature communications · 2023Article
- Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta.PLoS biology · 2023Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind's predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server (http://papers.genomics.lbl.gov/carbon) and takes just 30 seconds for the typical genome.
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