ArticleGenome research2015
Using populations of human and microbial genomes for organism detection in metagenomes.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT03229863 (The Infant MiND Study), which is not on this map. Cited by 24 papers.
What it found
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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.
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.
The Infant MiND Study: An Examination of Infants' Microbiome, Nutrition, and Development Study.
Who cites it
24 citing papers in PubMed.
- High-qualityMicrobiology spectrum · 2026Article
- Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification.mSystems · 2025Article
- Comparison of Three DNA Isolation Methods and Two Sequencing Techniques for the Study of the Human Microbiota.Life (Basel, Switzerland) · 2025Article
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.Nature microbiology · 2023Article
- Article
- Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds.Scientific reports · 2022Article
- Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.Microbiome · 2022Article
- Standardization of microbiome studies for urolithiasis: an international consensus agreement.Nature reviews. Urology · 2021Article
- Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.Frontiers in microbiology · 2021Article
- Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere.Scientific reports · 2020Article
- Article
- Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.PLoS computational biology · 2019Article
- Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.Molecular ecology · 2019Article
- Article
- Article
- Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis.Journal of clinical microbiology · 2017Article
- Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases.Clinical & translational immunology · 2017Review
- Review
- A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.Scientific reports · 2016Article
- A vision for ubiquitous sequencing.Genome research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Identifying causative disease agents in human patients from shotgun metagenomic sequencing (SMS) presents a powerful tool to apply when other targeted diagnostics fail. Numerous technical challenges remain, however, before SMS can move beyond the role of research tool. Accurately separating the known and unknown organism content remains difficult, particularly when SMS is applied as a last resort. The true amount of human DNA that remains in a sample after screening against the human reference genome and filtering nonbiological components left from library preparation has previously been underreported. In this study, we create the most comprehensive collection of microbial and reference-free human genetic variation available in a database optimized for efficient metagenomic search by extracting sequences from GenBank and the 1000 Genomes Project. The results reveal new human sequences found in individual Human Microbiome Project (HMP) samples. Individual samples contain up to 95% human sequence, and 4% of the individual HMP samples contain 10% or more human reads. Left unidentified, human reads can complicate and slow down further analysis and lead to inaccurately labeled microbial taxa and ultimately lead to privacy concerns as more human genome data is collected.
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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.