Metagenomic species profiling using universal phylogenetic marker genes

@article{Sunagawa2013MetagenomicSP,
  title={Metagenomic species profiling using universal phylogenetic marker genes},
  author={Shinichi Sunagawa and Daniel R. Mende and Georg Zeller and Fernando Izquierdo-Carrasco and Simon A. Berger and Jens Roat Kultima and Lu{\'i}s Pedro Coelho and Manimozhiyan Arumugam and J. Tap and Henrik Bj{\o}rn Nielsen and Simon Rasmussen and S{\o}ren Brunak and Oluf Pedersen and Francisco Guarner and Willem M. de Vos and Jun Wang and Junhua Li and Jo{\"e}l Dor{\'e} and Stanislav Dusko Ehrlich and Alexandros Stamatakis and Peer Bork},
  journal={Nature Methods},
  year={2013},
  volume={10},
  pages={1196-1199}
}
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome–based methods. An implementation of the method is available at http://www.bork.embl.de… 

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References

SHOWING 1-10 OF 36 REFERENCES
Metagenomic microbial community profiling using unique clade-specific marker genes
TLDR
This work presents an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches, and validated the metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads.
Accurate and universal delineation of prokaryotic species
The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments
TLDR
Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others, and enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences
TLDR
A novel taxonomic classifier MetaPhyler is presented, which uses phylogenetic marker genes as a taxonomic reference and is much more accurate in estimating the phylogenetic composition of whole-metagenome shotgun sequences.
Re-evaluating prokaryotic species
TLDR
The current and future impact of multilocus nucleotide-sequence-based approaches to prokaryotic systematics are discussed and the potential, and difficulties, of assigning species status to biologically or ecologically meaningful sequence clusters are considered.
Experimental factors affecting PCR-based estimates of microbial species richness and evenness
TLDR
The results show that both amplicon length and primer pair markedly influence estimates of richness and evenness, however, estimates of species evenness are consistent among different primer pairs targeting the same region, highlighting the importance of experimental methodology when comparing diversity estimates across communities.
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
TLDR
The latest developments of 454 and Illumina technologies offered higher resolution compared to their previous versions, and showed relative consistency with each other, but the majority of the Illumina reads could not be classified down to genus level due to their shorter length and higher error rates.
A human gut microbial gene catalogue established by metagenomic sequencing
TLDR
The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data
TLDR
This research developed metagenomic read simulators with platform-specific (Sanger, pyrosequencing, Illumina) base-error models, and simulated metagenomes of differing community complexities, and examined the effect of rigorous quality control on Illumina data.
Enterotypes of the human gut microbiome
TLDR
Three robust clusters (referred to as enterotypes hereafter) are identified that are not nation or continent specific and confirmed in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous.
...
1
2
3
4
...