EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data

By Christopher S. Miller, B. Baker, Brian C. Thomas, Steven W. Singer, Jillian F. Banfield. Genome Biology, 2011

355 citations recorded by the source corpus.

Recovery of ribosomal small subunit genes by assembly of short read community DNA sequence data generally fails, making taxonomic characterization difficult. Here, we solve this problem with a novel iterative method, based on the expectation maximization algorithm, that reconstructs full-length small subunit gene sequences and provides estimates of relative taxon abundances. We apply the method to natural and simulated microbial communities, and correctly recover community structure from known and previously unreported rRNA gene sequences. An implementation of the method is freely available at https://github.com/csmiller/EMIRGE.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eebe00d691a9c717274fb300364d9d3730595009

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Citations in the corpus

Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples (2018, methodology): “With this approach, full-length small subunit rRNA genes (16S and 18S/18S-ITS) can be simultaneously recovered from both the eukaryotic and prokaryotic fractions of metagenomes using a reference guided algorithm (Miller et al. 2011), if researchers have access to large memory computational resources”
New CRISPR-Cas systems from uncultivated microbes (2016, methodology): “…sites were analyzed: (1) Acid mine drainage (AMD) samples collected between 2006 and 2010 from the Richmond Mine, Iron Mountain, California 36,37 (2) Groundwater and sediment samples collected between 2007 and 2013 from the Rifle Integrated Field Research (IFRC) site, adjacent to the…”
PhyloSift: phylogenetic analysis of genomes and metagenomes (2014, background): “A variety of computational approaches are now available to investigate 115 the community composition of metagenome datasets, including: AMPHORA (bacterial protein markers 116 and tree insertion via parsimony) [66] and AMPHORA2 (bacterial/archael protein and DNA markers 117 and tree insertion via lik”
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics (2014, methodology): “Finally, to gain further insight into individual populations, fulllength 16S sequences were reconstructed separately from each of the AUG1–SEPT metagenomes [51] and were compared to the 16S rDNA amplicon OTUs in terms of sequence similarity and abundance patterns over the timepoints.”