ArticleNature communications2022
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
47 citing papers in PubMed, 75 citations in OpenAlex.
- Microbiota-Mediator-Host Signaling Networks in Metabolic Syndrome: From Mechanistic Insights to Therapeutic Targeting.Microorganisms · 2026Review
- Innovative technologies and future perspectives in tumor microbiomics.Science China. Life sciences · 2026Review
- Microbiota-host interaction in colorectal cancer: emerging computational technology, multi-omics integration, and mechanisms.Cancer biology & medicine · 2026Review
- High-throughput single-cell isolation ofMicrobiology spectrum · 2026Article
- Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data.Genome biology · 2026Article
- Functional divergence of the gut microbiome associated with lifestyle and helminth infection in Indigenous Peninsular Malaysian.Research square · 2026Article
- Review
- gutMSNP: a comprehensive database for human gut microbial single-nucleotide polymorphisms.Nucleic acids research · 2026Article
- dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.Nucleic acids research · 2026Article
- Gems From the Caves: Genomic Insights Into the Biosynthetic Potential of Antimicrobial-Producing Bacteria Associated With Tropical Cave-Dwelling Sponges.Environmental microbiology · 2026Article
- Comparative analysis of adhesin-like proteins fromFrontiers in microbiology · 2026Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.Scientific reports · 2025Article
- Phages with a broad host range are common across ecosystems.Nature microbiology · 2025Article
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.Cell host & microbe · 2025Article
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- Assessing Zoonotic Risks ofPathogens (Basel, Switzerland) · 2025Article
- Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.Nature microbiology · 2025Article
- Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
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.