ArticleComputational and structural biotechnology journal2022
Bacterial low-abundant taxa are key determinants of a healthy airway metagenome in the early years of human life.
Article in Computational and structural biotechnology journal, 2022. 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, 28 citations in OpenAlex.
- Trial
- The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.Molecular and cellular pediatrics · 2026Review
- Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.mSystems · 2026Review
- Lung microbiota analysis in early-stage lung adenocarcinoma.Microbiology spectrum · 2026Article
- Human Sputum Microbiome Composition and Sputum Inflammatory Cell Profiles Are Altered with Controlled Wood Smoke Exposure as a Model for Wildfire Smoke.American journal of respiratory and critical care medicine · 2025Article
- GIMIC: smoothed graph-image representation of microbiome samples induce an optimal distance.Genome biology · 2025Article
- The Effect of 6-Week Advanced Oral Care on Oral Microbiome and Mycobiome Composition in People With Dementia Living in Residential Aged Care.Clinical and experimental dental research · 2025Article
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
- Rapid species-level metagenome profiling and containment estimation with sylph.Nature biotechnology · 2025Article
- Unique Changes in the Lung Microbiome following the Development of Chronic Lung Allograft Dysfunction.Microorganisms · 2024Article
- Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies.Cell reports. Medicine · 2024Review
- Microbial underdogs: exploring the significance of low-abundance commensals in host-microbe interactions.Experimental & molecular medicine · 2023Review
- Prenatal exposures to endocrine disrupting chemicals: The role of multi-omics in understanding toxicity.Molecular and cellular endocrinology · 2023Review
- Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.BMC biology · 2023Article
- Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life.ISME communications · 2023Article
- Effect of in vitro cultivation on human gut microbiota composition using 16S rDNA amplicon sequencing and metabolomics approach.Scientific reports · 2023Article
- Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome.Microbiology spectrum · 2022Article
- CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies.Scientific data · 2022Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The default removal of low-abundance (rare) taxa from microbial community analyses may lead to an incomplete picture of the taxonomic and functional microbial potential within the human habitat. Publicly available shotgun metagenomics data of healthy children and children with cystic fibrosis (CF) were reanalysed to study the development of the rare species biosphere, which was here defined by either the 15th, 25th or 35th species abundance percentile. We found that healthy children contained an age-independent network of abundant (core) and rare species with both entities being essential in maintaining the network structure. The protein sequence usage for more than 100 bacterial metabolic pathways differed between the core and rare species biosphere. In CF children, the background structure was underdeveloped and random forest bootstrapping based on all constituents of the early airway metagenome and host-associated factors indicated that rare taxa were the most important variables in deciding whether a child was healthy or suffered from the life-limiting CF disease. Attempts failed to make the age-independent CF network as robust as the healthy structure when an increasing number of bacterial taxa from the healthy network was incorporated into the CF structure by computer-based model simulations. However, the transfer of a key combination of taxa from the healthy to the CF network structure with high species diversity and low species dominance, correlated with a more robust CF network and a topological approximation of CF and healthy graph structures. Rothia mucilaginosa, Streptococci and rare species were essential in improving the underdeveloped CF network.
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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.