ArticleNature microbiology2020
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota.
Article in Nature microbiology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07169123 (Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD), which is not on this map. Cited by 54 papers.
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.
Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD
Who cites it
54 citing papers in PubMed, 94 citations in OpenAlex.
- Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise.Nature communications · 2025Trial
- Optimizing a culture-enriched hybrid metagenomics pipeline to assess the AMR footprint of livestock manure in anaerobic digestate.Microbiology spectrum · 2026Article
- DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.Clinical microbiology reviews · 2026Review
- How the social lives of bacteria affect their pangenome.Essays in biochemistry · 2026Review
- Microbial Signals in Cancer: Dissecting Host-Microbiota-Tumor Interactions and Potential Therapeutic Strategy.MedComm · 2026Review
- An ode to the 16S rRNA gene: its history, importance, caveats and future in microbiome research.Microbial genomics · 2026Review
- Differential Metabolite Production Underlies Disruption of the Cystic Fibrosis Airway Microbiota by Pathogens.bioRxiv : the preprint server for biology · 2026Article
- Small intestinal microbial fiber metabolism dysfunction in celiac disease.Nature communications · 2026Article
- Unlocking the unexplored AMPSphere in marine rare species.Microbiome · 2026Article
- From natural assemblages to synthetic communities in theFrontiers in plant science · 2026Article
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Co-infection withISME communications · 2026Article
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Article
- Article
- Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study.The European respiratory journal · 2025Article
- Genomic diversity inMicrobial genomics · 2025Article
- Gut microbiome evolution from infancy to 8 years of age.Nature medicine · 2025Article
- Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.Communications biology · 2024Article
- Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Amplicon sequencing (for example, of the 16S rRNA gene) identifies the presence and relative abundance of microbial community members. However, metagenomic sequencing is needed to identify the genetic content and functional potential of a community. Metagenomics is challenging in samples dominated by host DNA, such as those from the skin, tissue and respiratory tract. Here, we combine advances in amplicon and metagenomic sequencing with culture-enriched molecular profiling to study the human microbiota. Using the cystic fibrosis lung as an example, we cultured an average of 82.13% of the operational taxonomic units representing 99.3% of the relative abundance identified in direct sequencing of sputum samples; importantly, culture enrichment identified 63.3% more operational taxonomic units than direct sequencing. We developed the PLate Coverage Algorithm (PLCA) to determine a representative subset of culture plates on which to conduct culture-enriched metagenomics, resulting in the recovery of greater taxonomic diversity-including of low-abundance taxa-with better metagenome-assembled genomes, longer contigs and better functional annotations when compared to culture-independent methods. The PLCA is also applied as a proof of principle to a previously published gut microbiota dataset. Culture-enriched molecular profiling can be used to better understand the role of the human microbiota in health and disease.
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.