ArticleNature microbiology2023
Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.
Article in Nature microbiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 45 citations in OpenAlex.
- Large-scale estimation of bacterial and archaeal DNA prevalence in metagenomes reveals biome-specific patterns.mSystems · 2026Article
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- SCiMS: Sex Calling in Metagenomic Sequences.bioRxiv : the preprint server for biology · 2026Article
- Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.Genome biology · 2026Article
- Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.Bioinformatics (Oxford, England) · 2026Article
- Pharmacomicrobiomics.Clinical pharmacology and therapeutics · 2025Review
- Benchmarking of human read removal strategies for viral and microbial metagenomics.Cell reports methods · 2025Article
- nf-core/detaxizer: a benchmarking study for decontamination from human sequences.NAR genomics and bioinformatics · 2025Article
- The new microbiome on the block: challenges and opportunities of using human tumor sequencing data to study microbes.Nature methods · 2025Review
- Microbial genomics: a potential toolkit for forensic investigations.Forensic science, medicine, and pathology · 2025Review
- Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.Nature communications · 2025Article
- Genomic privacy and security in the era of artificial intelligence and quantum computing.Discover computing · 2025Review
- Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.Research square · 2024Article
- Article
- SWGTS-a platform for stream-based host DNA depletion.Bioinformatics (Oxford, England) · 2024Article
- Body mass index stratification optimizes polygenic prediction of type 2 diabetes in cross-biobank analyses.Nature genetics · 2024Article
- Deep learning methods in metagenomics: a review.Microbial genomics · 2024Review
- A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome.Communications biology · 2024Article
- Mouse Adaptation of Human Inflammatory Bowel Diseases Microbiota Enhances Colonization Efficiency and Alters Microbiome Aggressiveness Depending on Recipient Colonic Inflammatory Environment.bioRxiv : the preprint server for biology · 2024Article
- A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.Frontiers in microbiology · 2024Review
Corrections and comments
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Authors and funding
27 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
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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.