ArticleNature communications2025
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- The reference shapes the signal: chrX genotype summaries and classifier sex disparity between GRCh38 and T2T-CHM13 callsets.Genomics & informatics · 2026Article
- Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.Research square · 2026Article
- Article
- [Multi-omics integration deciphers immune-metabolic heterogeneity in colorectal cancer: a prognostic model and therapeutic strategies targeting ANGPTL4/FABP4/RBP7].Nan fang yi ke da xue xue bao = Journal of Southern Medical University · 2026Article
- Antibiotic Exposure Through Human Milk Influences the Infant Gut Microbiome.bioRxiv : the preprint server for biology · 2026Article
- Household environmental characteristics influence the house dust metagenome.Environmental research · 2026Article
- Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.Cancer causes & control : CCC · 2026Article
- SCiMS: Sex Calling in Metagenomic Sequences.bioRxiv : the preprint server for biology · 2026Article
- Community assembly modeling of the microbiome within Barrett's esophagus and esophageal adenocarcinoma.BMC genomics · 2026Article
- Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.Bioinformatics (Oxford, England) · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- Calculating fast differential genome coverages among metagenomic sources using micov.Communications biology · 2025Article
- The multi-kingdom cancer microbiome.Nature microbiology · 2025Review
- Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.Research square · 2025Article
- Targeted decontamination of sequencing data with CLEAN.NAR genomics and bioinformatics · 2025Article
- Smart Microbiomes: How AI Is Revolutionizing Personalized Medicine.Bioengineering (Basel, Switzerland) · 2025Review
- Environmental and Maternal Imprints on Infant Gut Metabolic Programming.bioRxiv : the preprint server for biology · 2025Article
- The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.Frontiers in medicine · 2025Review
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Authors and funding
19 authors.
Funding
Abstract
As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.
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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.