Evidence map›Paper›PMID 41317787›Full record

ArticleJournal of molecular biology2026

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota.

Yijun Zhu, Hannah E Augustijn, Victòria Pascal Andreu, Arjan Draisma, Gilles P van Wezel, Dylan Dodd, Michael A Fischbach, Marnix H Medema

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of molecular biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Genomic Insights and Inactivation Strategies forFoods (Basel, Switzerland) · 2026
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Yijun ZhuInstitute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands. Electronic address: zhuyj67@mail.sysu.edu.cn.
Hannah E AugustijnBioinformatics Group, Wageningen University, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands. Electronic address: hannah.augustijn@wur.nl.
Victòria Pascal AndreuInstitut Germans Trias i Pujol, Epigenetic Mechanisms of Cancer and Cell Differentiation Group, Barcelona, Spain. Electronic address: vpascal@igtp.cat.
Arjan DraismaBioinformatics Group, Wageningen University, Wageningen, The Netherlands. Electronic address: arjan.draisma@wur.nl.
Gilles P van WezelInstitute of Biology, Leiden University, Leiden, The Netherlands. Electronic address: g.wezel@biology.leidenuniv.nl.
Dylan DoddDepartment of Pathology, Stanford University, Stanford, USA; Department of Microbiology & Immunology, Stanford University, Stanford, USA. Electronic address: ddodd2@stanford.edu.
Michael A FischbachDepartment of Microbiology & Immunology, Stanford University, Stanford, USA; Department of Bioengineering, Stanford University, Stanford, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA. Electronic address: fischbach@fischbachgroup.org.
Marnix H MedemaBioinformatics Group, Wageningen University, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands. Electronic address: marnix.medema@wur.nl.

Funding

Microbiota-based probiotics to treat inborn errors in metabolismR01AT011396 · NCCIH · STANFORD UNIVERSITY · PI Dylan Dodd · 2022 to 2026
$2.9M
Physiology of bacterial metabolism in the human gut microbiomeR35GM142873 · NIGMS · STANFORD UNIVERSITY · PI DODD, DYLAN · 2021 to 2025
$2.0M
NCCIH NIH HHS R01 AT011396NIGMS NIH HHS R35 GM142873
6 · The paper itself

Abstract

Microbiota-derived metabolites serve as key messengers mediating host-microbe and microbe-microbe interactions, often through specialized primary metabolic pathways. gutSMASH was initially developed to systematically identify the metabolic gene clusters (MGCs) that encode these pathways in anaerobic gut microbial genomes. Here, we present gutSMASH 2.0, a major update that significantly expands its functionality. This version introduces 14 new detection rules covering 12 additional types of MGCs. The comparative genomics framework was enhanced with 26 experimentally validated MGCs and 15,024 gene clusters from the Cultivated Genome Reference 2 (CGR2) collection. Furthermore, gutSMASH 2.0 integrates transcription factor binding site prediction using LogoMotif's methodology, enabling investigation of MGC regulatory elements. Together, these improvements make gutSMASH a more powerful tool for automated discovery and analysis of niche-determining metabolic pathways in the gut microbiome. gutSMASH 2.0 is freely available at https://gutsmash.bioinformatics.nl/.

Indexed as

Computational BiologyGastrointestinal MicrobiomeMetabolic Networks and PathwaysMultigene FamilySoftwareGenomicsHumansgenome analysisgut microbiomemetabolic gene clusterweb server

Identifiers

PMID41317787
PMCPMC13494760

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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.