ArticleCell reports methods2023
Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.
Article in Cell reports methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed, 1 synthesis or guideline pooled it, 78 citations in OpenAlex.
- A Systematic Review on Microbial Profiling Techniques in Goat Milk: Implications for Probiotics and Shelf-Life.International journal of molecular sciences · 2025Pooled it
- From gene detection to resistome ecology: targeted hybrid capture in AMR surveillance.mSphere · 2026Article
- CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.mSystems · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.International journal of molecular sciences · 2026Review
- Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.Scientific reports · 2026Article
- Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.Nature microbiology · 2026Article
- The microbial metabolome: remodeling the therapeutic landscape in hematologic malignancies.NPJ biofilms and microbiomes · 2026Review
- Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agentMicrobiology spectrum · 2026Article
- Genotype-Environment-Driven Dysbiosis in the Skin Microbiome of Ichthyosis.The Journal of investigative dermatology · 2026Article
- Age-driven dysbiosis: gut microbiota in the pathogenesis and treatment of aging disorders.Biogerontology · 2026Review
- Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting.The ISME journal · 2026Article
- Decoding the microbial blueprint of pancreatic cancer.Frontiers in medicine · 2026Review
- Gut microbiome dysbiosis and functional alterations inGut microbes reports · 2026Article
- Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.Frontiers in veterinary science · 2026Review
- Metagenomic Tools as Predictive Approaches to Decipher Soil and Rhizosphere Microbial Communities and Their Functions for Sustainable Agriculture.International journal of genomics · 2026Review
- Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.BMC oral health · 2025Article
- High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons.Microbiome · 2025Article
- How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.Applied and environmental microbiology · 2025Article
- Freezing of Vaginal Swabs Prior to DNA Purification Does Not Statistically Significantly Affect Microbiome Composition.MicrobiologyOpen · 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
15 authors at 9 institutions in 1 country.
Funding
Abstract
In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.
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.