ArticleMicrobiome2021
Reduced metagenome sequencing for strain-resolution taxonomic profiles.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 24 citations in OpenAlex.
- Probiotic-Induced Gut Microbiota Modulation: A Comparative Analysis Using 16S rRNA V3-V4 and Targeted Sequencing.Microorganisms · 2026Article
- Characteristic genes and immune infiltration analysis of gastric cancer based on bioinformatics analysis and machine learning.Discover oncology · 2025Article
- Development and validation of a risk model for effective immune and stromal related signature predicting prognosis of patients with ovarian cancer.Scientific reports · 2025Article
- Readsynth: short-read simulation for consideration of composition-biases in reduced metagenome sequencing approaches.BMC bioinformatics · 2024Article
- A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child SharedApplied and environmental microbiology · 2023Article
- The microbiota as a modulator of mucosal inflammation and HIV/HPV pathogenesis: From association to causation.Frontiers in immunology · 2023Review
- Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle.PloS one · 2023Article
- Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives.Computational and structural biotechnology journal · 2022Review
- Plant-Microbe Interaction: Aboveground to Belowground, from the Good to the Bad.International journal of molecular sciences · 2021Review
- HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data.Microbiome · 2021Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.
resultsWe suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.
conclusionWe find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.
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