ArticleAdvanced genetics (Hoboken, N.J.)2022
Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.
Article in Advanced genetics (Hoboken, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 12 citations in OpenAlex.
- Robust, Open-Source and Automation-Friendly DNA Extraction Protocol for Hologenomic Research.Molecular ecology resources · 2025Article
- Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.Genetics, selection, evolution : GSE · 2025Article
- Allochrony in Atlantic Lumpfish: Genomic and Otolith Shape Divergence Between Spring and Autumn Spawners.Ecology and evolution · 2025Article
- Short communication: imputation accuracy of host genomic data from metagenomic sequence information.Journal of animal science · 2025Article
- Sampling fish gut microbiota - A genome-resolved metagenomic approach.Ecology and evolution · 2024Article
- A practical introduction to holo-omics.Cell reports methods · 2024Review
- Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.Nature microbiology · 2023Article
- AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap.Scientific data · 2023Article
- Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.Advanced genetics (Hoboken, N.J.) · 2022Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
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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.