What is mmgenome?
The mmgenome toolbox enables reproducible extraction of individual genomes from metagenomes. It builds on the multi-metagenome concept, but wraps most of the process of extracting genomes in simple R functions. Thereby making the whole process of binning easy and at the same time reproducible through the Rmarkdown format.
The mmgenome R package also facilitates effortless integration with additional data sources and hence should not be seen as "yet another binning method", but rather a package to integrate different binning strategies.
All functions in the mmgenome R package has associated documentation, check it out in R by e.g. ?mmplot.
How to cite?
A short paper describing the mmgenome toolbox is available as a preprint at bioRxiv.
Karst SM, Kirkegaard RH and Albertsen M. (2016).
mmgenome: a toolbox for reproducible genome extraction from metagenomes.
bioRxiv, doi:10.1101/059121
How does it work?
Check out our examples of loading data and extracting genomes in the mmgenome R package. The associated Rmarkdown files can be found in the folder mmgenome/workflows.
Getting started
Install the latest version of R (>3.1), Rtools and RStudio. Then go ahead and install the mmgenome R package directly from github using the devtools package.
install.packages("devtools")
devtools::install_github("MadsAlbertsen/mmgenome/mmgenome")
You might need to install Biostrings through bioconductor depending on your version of R. However, it's quite easily done.
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
To generate your own data simply clone repository and setup the shell script mmgenome/workflows/data.generation.2.1.0.sh.
git clone https://github.com/MadsAlbertsen/mmgenome.git
Papers using mmgenome
Daims et al. Nature 2015
Complete nitrification by Nitrospira bacteria (2015). Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH and Wagner M. Nature. doi:10.1038/nature16461
The mmgenome package was used to extract genome bins from a number of metagenomes. All raw data can be downloaded from figshare. Each metagenome bin can be recreated using the Rmarkdown files here and the results for each bin can be seen below:
ENR4: The comammox enrichment reactor with 3 other species: Comammox, Actinobacteria, Betaproteobacteria and Alphaproteobacteria.
ENR6: The comammox enrichment reactor with a single contaminant: Commamox.
MBR: Activated sludge from a pilot scale membrane bio reactor treating municipal wastewater (Aalborg West, Denmark) that had both "normal" and comammox Nitrospira: Overview, Nitrospira 1 and Nitrospira 2.
VetMed: Activated sludge from a full-scale wastewater treatment plant at the University of Veterinary Medicine (Vienna, Austria) that contained comammox Nitrospira. In this dataset we also integrated binning using ESOM maps: Overview and Nitrospira.
GWW: Metagenomes from pasty and suspended iron sludge from a groundwater well (GWW) of a waterworks (Wolfenbüttel, Germany). These samples contained an extreme diversity of Nitrospira species: Overview, Nitrospira 1, Nitrospira 2, Nitrospira 3, Nitrospira 4, Nitrospira 5, Nitrospira 6, Nitrospira 7, Nitrospira 8, Nitrospira 9 and Nitrospira 10.
The individual genome bins after re-assembly using SPAdes can be found here.
van Kessel et al. Nature 2015
Complete nitrification by a single microorganism (2015). van Kessel MAHJ, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJM, Kartal B, Jetten MSM and Lücker S. Nature. doi:10.1038/nature16459
The mmgenome package was used to extract genome bins from an enrichment anammox reactor that also contained 2 Nitrospira comammox genomes: Nitrospira 1 and Nitrospira 2.
Albertsen et al. Frontiers in Microbiology 2016
“Candidatus Propionivibrio aalborgensis”: a novel glycogen accumulating organism abundant in full-scale enhanced biological phosphorus removal plants (2016). Albertsen M, McIlroy SJ, Stokholm-Bjerregarrd M, Karst SM and Nielsen PH. Frontiers in Microbiology. doi:10.3389/fmicb.2016.01033
The mmgenome package was used to extract genome bins from metagenomes. All raw data can be downloaded from figshare. Each metagenome bin can be recreated using the Rmarkdown files here and the results for each bin can be seen below:
Holmes: The enrichment reactor with Propionivibrio and Accumulibacter as the dominant species: Overview/Figure2, Accumulibacter and Propionivibrio.