ArticleGenome biology2021
Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers, 13 of them syntheses that pooled it.
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Who cites it
165 citing papers in PubMed, 13 syntheses or guidelines pooled it.
- Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.Nature communications · 2025Pooled it
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.Microbiome · 2025Pooled it
- Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease.Nature communications · 2025Pooled it
- Bibliometric analysis of the application of artificial intelligence techniques in bacteriology: a PRISMA-guided research agenda.Frontiers in microbiology · 2025Pooled it
- Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.BMC microbiology · 2024Pooled it
- Meta-analysis of gut microbiota alterations in patients with irritable bowel syndrome.Frontiers in microbiology · 2024Pooled it
- Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment.Journal of advanced research · 2023Pooled it
- MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.Cell reports · 2023Pooled it
- Multi-cohort analysis of depression-associated gut bacteria sheds insight on bacterial biomarkers across populations.Cellular and molecular life sciences : CMLS · 2022Pooled it
- Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.Genome biology · 2022Pooled it
- Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.PLoS computational biology · 2022Pooled it
- Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal.Genome biology · 2022Pooled it
- Pooled it
- Modified Crohn's Disease Exclusion Diet and exclusive enteral nutrition (EEN) resolve oral dysbiosis in pediatric Crohn's disease: a prospective cohort study.Inflammatory bowel diseases · 2026Trial
- Trial
- The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants.Vaccine · 2021Trial
- Advanced Dental Cleaning is Associated with Reduced Risk of COPD Exacerbations - A Randomized Controlled Trial.International journal of chronic obstructive pulmonary diseaseTrial
- Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.Gut microbes · 2026Review
- Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.Gut microbes · 2026Review
- Oral Butyrate Reduces Progression of Kidney Damage in an L-NAME-Induced Diabetic Kidney Disease Mouse Model.Diabetes, obesity & metabolism · 2026Article
105 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues. To address these, we developed SIAMCAT, a versatile R toolbox for ML-based comparative metagenomics. We demonstrate its capabilities in a meta-analysis of fecal metagenomic studies (10,803 samples). When naively transferred across studies, ML models lost accuracy and disease specificity, which could however be resolved by a novel training set augmentation strategy. This reveals some biomarkers to be disease-specific, with others shared across multiple conditions. SIAMCAT is freely available from siamcat.embl.de .
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