ReviewComputational and structural biotechnology journal2020
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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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.
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Who cites it
46 citing papers in PubMed, 107 citations in OpenAlex.
- Whole metagenome sequencing: not deep enough for complete microbial function recovery.Microbiome · 2026Article
- Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories.Ecology letters · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Infant gut microbiota coverage by different culture media.BMC microbiology · 2026Article
- Contrasting the gut microbiome in Colombian patients with diarrhea: a comparative metagenomic study in hospitalization and emergency room services.Gut pathogens · 2026Article
- Metabolic modeling and functional genomics reveal taxa and host gene interactions in colorectal cancer.bioRxiv : the preprint server for biology · 2026Article
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- Metagenomic Applications to Herbivore Gut Microbiomes: A Comprehensive Review of Microbial Diversity and Host Interactions.Animals : an open access journal from MDPI · 2025Review
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- A blueprint for contemporary studies of microbiomes.Microbiome · 2025Article
- Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance.ISME communications · 2025Article
- Bacterial Diversity, Metabolic Profiling, and Application Potential of Antarctic Soil Metagenomes.Current issues in molecular biology · 2024Article
- Characterizing a stable five-species microbial community for use in experimental evolution and ecology.Microbiology (Reading, England) · 2024Article
- Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology.Heliyon · 2024Review
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- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- MCSS: microbial community simulator based on structure.Frontiers in microbiology · 2024Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Metagenomic sequencing of complete microbial communities has greatly enhanced our understanding of the taxonomic composition of microbiotas. This has led to breakthrough developments in bioinformatic disciplines such as assembly, gene clustering, metagenomic binning of species genomes and the discovery of an incredible, so far undiscovered, taxonomic diversity. However, functional annotations and estimating metabolic processes from single species - or communities - is still challenging. Earlier approaches relied mostly on inferring the presence of key enzymes for metabolic pathways in the whole metagenome, ignoring the genomic context of such enzymes, resulting in the 'bag-of-genes' approach to estimate functional capacities of microbiotas. Here, we review recent developments in metagenomic bioinformatics, with a special focus on emerging technologies to simulate and estimate metabolic information, that can be derived from metagenomic assembled genomes. Genome-scale metabolic models can be used to model the emergent properties of microbial consortia and whole communities, and the progress in this area is reviewed. While this subfield of metagenomics is still in its infancy, it is becoming evident that there is a dire need for further bioinformatic tools to address the complex combinatorial problems in modelling the metabolism of large communities as a 'bag-of-genomes'.
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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.