ArticleNPJ biofilms and microbiomes2025
Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.
Article in NPJ biofilms and microbiomes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.Frontiers in microbiology · 2026Pooled it
- The role of the respiratory microbiome in acute and chronic respiratory diseases.Nature reviews. Microbiology · 2026Review
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- Beyond Pathogens: Modulating the Commensal Microbiota to Reshape Immunity for Respiratory Disease Intervention.Pathogens (Basel, Switzerland) · 2026Review
- Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology.Nature communications · 2026Article
- Empowering One Health with metagenomics.One health outlook · 2026Review
- Genome-guided generative adversarial learning enables nanopore adaptive sequencing.Nature communications · 2026Article
- IntratumoralScience advances · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- The lung microbiome and asthma: from inflammatory phenotype differentiation to microbe-based immunomodulatory strategies.Frontiers in immunology · 2026Review
- Effect of sialidase inhibitors on a plaque community biofilm model.Access microbiology · 2026Article
- Immune-oncology-microbiome axis in lung cancer: from carcinogenesis to therapy-a narrative review.Translational lung cancer research · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors.
Funding
Abstract
Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.
Indexed as
Identifiers
What OpenQuestion holds
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.