ArticleNature communications2019
Microbial abundance, activity and population genomic profiling with mOTUs2.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 244 papers, 2 of them syntheses that pooled it.
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.
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Who cites it
244 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.Scientific reports · 2022Pooled it
- Identification of microbial markers across populations in early detection of colorectal cancer.Nature communications · 2021Pooled it
- Dynamics of Gut Microbiota After Fecal Microbiota Transplantation in Ulcerative Colitis: Success Linked to Control of Prevotellaceae.Journal of Crohn's & colitis · 2025Trial
- Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers.Microbiome · 2024Trial
- Phage-microbe dynamics after sterile faecal filtrate transplantation in individuals with metabolic syndrome: a double-blind, randomised, placebo-controlled clinical trial assessing efficacy and safety.Nature communications · 2023Trial
- Effects of Resistant Starch on Symptoms, Fecal Markers, and Gut Microbiota in Parkinson's Disease - The RESISTA-PD Trial.Genomics, proteomics & bioinformatics · 2022Trial
- Recovering anaerobic bacterial genomes in saliva, tumour and blood whole genome sequencing data from patients with prostate cancer.NPJ biofilms and microbiomes · 2026Article
- Single-cell quantification reveals divergent mixotrophic strategies underlying niche partitioning in marineScience advances · 2026Article
- Alcohol-related liver disease disrupts bile acid homeostasis and gut microbial bile acid metabolism.JHEP reports : innovation in hepatology · 2026Article
- Improving metagenome binning by integrating intrinsic features and taxonomy.Nature biotechnology · 2026Article
- 16S rRNA sequence captures microbial functional potential.bioRxiv : the preprint server for biology · 2026Article
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- Strain-level metagenomic profiling using pangenome graphs with PanTax.Genome research · 2026Article
- A signature-protein-based approach for accurate and efficient profiling of the human gut virome.Cell reports methods · 2026Article
- Deconvolving Phylogenetic Distance Mixtures.bioRxiv : the preprint server for biology · 2026Article
- Candidatus Dermatophostum as a novel genus of polyphosphate-accumulating organisms for high-strength wastewater treatment.The ISME journal · 2026Article
- Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.The ISME journal · 2026Article
- LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data.Frontiers in bioinformatics · 2026Article
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
184 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).
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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.