ArticlemSystems2021
BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.Cell host & microbe · 2025Pooled it
- Diverse biosynthetic pathways in Arctic hydrothermal biofilms.Nature communications · 2026Article
- Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.Nature communications · 2026Article
- Infant gut microbiomes contribute to metabolic states that impact brain function.bioRxiv : the preprint server for biology · 2026Article
- Amplicon-based prediction of secondary metabolic potential of microbiomes facilitates natural product discovery.Synthetic and systems biotechnology · 2026Article
- BiG-SCAPE 2.0 and BiG-SLiCE 2.0: scalable, accurate and interactive sequence clustering of metabolic gene clusters.Nature communications · 2026Article
- Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.mSystems · 2025Article
- Predicting rhizosphere-competence-related catabolic gene clusters in plant-associated bacteria with rhizoSMASH.Nature communications · 2025Article
- Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Exploring the Biosynthetic Potential of Microorganisms from the South China Sea Cold Seep Using Culture-Dependent and Culture-Independent Approaches.Marine drugs · 2025Article
- Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.Microbiome · 2025Article
- Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.mSystems · 2025Review
- Identifying rhizosphere bacteria and potential mechanisms linked to compost suppressiveness towards Fusarium oxysporum.Environmental microbiome · 2025Article
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- The encoded and expressed biosynthetic potential of Greenland Ice Sheet microbes.Frontiers in microbiology · 2025Article
- Plasmid Library Construction From Genomic DNA.Current protocols · 2025Article
- Metatranscriptomics-guided discovery and characterization of a polyphenol-metabolizing gut microbial enzyme.Cell host & microbe · 2024Article
- Overlooked Vital Role of Persistent Algae-Bacteria Interaction in Ocean Recalcitrant Carbon Sequestration and Its Response to Ocean Warming.Global change biology · 2024Article
- Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.Nature communications · 2024Article
- Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients.Microbiology spectrum · 2024Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Microbial gene clusters encoding the biosynthesis of primary and secondary metabolites play key roles in shaping microbial ecosystems and driving microbiome-associated phenotypes. Although effective approaches exist to evaluate the metabolic potential of such bacteria through identification of these metabolic gene clusters in their genomes, no automated pipelines exist to profile the abundance and expression levels of such gene clusters in microbiome samples to generate hypotheses about their functional roles, and to find associations with phenotypes of interest. Here, we describe BiG-MAP, a bioinformatic tool to profile abundance and expression levels of gene clusters across metagenomic and metatranscriptomic data and evaluate their differential abundance and expression under different conditions. To illustrate its usefulness, we analyzed 96 metagenomic samples from healthy and caries-associated human oral microbiome samples and identified 252 gene clusters, including unreported ones, that were significantly more abundant in either phenotype. Among them, we found the
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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.