ArticleNature biotechnology2023
gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers.
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Who cites it
81 citing papers in PubMed, 114 citations in OpenAlex.
- Article
- Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia.Molecular biology and evolution · 2026Article
- gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota.Journal of molecular biology · 2026Article
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- Article
- MAAMOUL: metabolic network-based discovery of microbiome-metabolome shifts in disease.Bioinformatics (Oxford, England) · 2026Article
- Draft genome sequence ofMicrobiology resource announcements · 2026Article
- Characterization of bacteriocin, probiotic attributes and genomic information of Bacillus subtilis S1.World journal of microbiology & biotechnology · 2026Article
- Microbiota-derived metabolites as modulators of cancer immunotherapy response.Nature communications · 2026Review
- Gut microbiota and metabolic function in leeches with distinct feeding niches.BMC microbiology · 2026Article
- Article
- MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.bioRxiv : the preprint server for biology · 2026Article
- Fecal microbiota transplantation combined with anti-PD-1 therapy in refractory microsatellite-stable gastric cancer: a phase I feasibility and safety study.Journal for immunotherapy of cancer · 2026Article
- Infant gut microbiomes contribute to metabolic states that impact brain function.bioRxiv : the preprint server for biology · 2026Article
- The impact of weight cycling on gut microbiome richness and diversity in female rats.Physiological reports · 2026Article
- Unlocking therapeutic impacts of the gut microbiota with computational tools.Current opinion in biotechnology · 2026Review
- BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters.Nature communications · 2026Article
- Gut microbiota drives cancer evolution and therapy resistance.Molecular cancer · 2026Review
- Beneficial impacts of postbiotic components -- Crosstalk between gut and organs.Current research in food science · 2026Review
- Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.Frontiers in microbiology · 2026Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 4 institutions in 3 countries.
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Abstract
The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.
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