Tag Archives: Integrated Microbial Genomes with Microbiome Samples

Video Tip of the Week: Microbiome Resources From JGI


Just over a month ago an issue of Nature had two articles from the Human Microbiome Project Consortium – you may have seen them, or noticed the Friday SNPets items we had on them. I promised myself that I’d read the articles (which I did), and that I’d visit my old friends the IMG (Integrated Microbial Genomes) & IMG/M (IMG with Microbiome Samples) to see what is new at these powerful microbial genome resources. In today’s tip I decided to take you along on my visit with me, because I found that IMG now has a resource dedicated to the analysis of genomes related to the Human Microbiome Project called the Integrated Microbial Genomes-Human Microbiome Project, or IMG/HMP. We visit both IMG/M (briefly) and the IMG/HMP in today’s tip.

When I referred to IMG as an old friend, I really do feel that way – our tutorial on IMG* was one of my first projects for OpenHelix. I was new, and IMG was new, having been released in March of 2005, only a few months before I created our tutorial (on their June 2005 release, if I am remembering correctly). They have grown into such an extensive, powerful resource. To give you an idea of how fast they have grown & developed, our current IMG tutorial is version 12 and I’ll be working on version 13 as soon as I finish updating our SGD tutorial. When we first created our IMG/M tutorial*, metagenomes were a relatively new concept and the resource included a total of 24 microbiome samples – now it has over 1000!

But enough with the nostalgia, let’s get to the resources! :) IMG/M integrates metagenome data with isolate microbial genome sequences from the integrated microbial genome (IMG) system to enable the analysis of phylogenetic composition and functional or metabolic potential of the aggregate genomes (metagenomes) in microbial communities (microbiomes). Genomes generated as part of the Human Microbiome Project (HMP) are included into IMG/M from RefSeq via IMG. IMG/M resources allow users analyze metagenomes, genomes, genes and functions by making lists of items and then manipulating them in “analysis carts”. Metagenomes can also be analyzed using the tools provided from their ‘Metagenome Details’ page. These options are explained in much more detail than I can cover here in the IMG/M reference that I site below. I also link to the most recent IMG publication, since an understanding of it is essential to understand any IMG/M-based resource.

* OpenHelix tutorial for this resource available for individual purchase or through a subscription.

Quick Links:
Integrated Microbial Genomes (IMG): http://img.jgi.doe.gov/cgi-bin/pub/main.cgi

Integrated Microbial Genomes with Microbiomes (IMG/M): http://img.jgi.doe.gov/cgi-bin/m/main.cgi

Integrated Microbial Genomes-Human Microbiome Project (IMG/HMP): http://www.hmpdacc-resources.org/imgm_hmp/

OpenHelix Introductory Tutorial on IMG: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=54

OpenHelix Introductory Tutorial on IMG/M: http://www.openhelix.com/cgi/tutorialInfo.cgi?id=24

References:
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012).
IMG/M: the integrated metagenome data management and comparative analysis system Nucl. Acids Res. , 40 DOI: 10.1093/nar/gkr975

Victor M. Markowitz1, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavromatis, Natalia N. Ivanova, & Nikos C. Kyrpides (2012). IMG: the integrated microbial genomes database and comparative analysis system Nucl. Acids Res., 40 DOI: 10.1093/nar/gkr1044

Tip of the Week: Functional Abundance Profile Searching in Genomes

Wow, how can you resist blogging about an article who’s title begins “Dissecting biological ‘‘dark matter’’…”? I found the article while working on a new ‘sponsored’ (read ‘free’) tutorial on the Integrated Microbial Genomes with Microbiome Samples (or IMG/M) resource. (I’m hoping the tutorial will be released in the near future & I’ll post when it is available.) IMG/M is a microbial resource that specializes in the analysis of metagenomes. Metagenomes are becoming hot – we’ve blogged about them in the past, as have lots of others. According to the article I found, “biological dark matter” refers to our paltry knowledge & understanding of the Earth’s microbial diversity. The article reports a method for isolating individual bacterial cells from the microbiome of the human mouth, but for my contribution to understanding microbial diversity, I want to give you a tip on using the IMG/M resource to select protein families in genomes based on their relative abundance. Click the image above to view the tip, or follow the links in this post to learn more on your own.
ResearchBlogging.orgMarcy, Y., Ouverney, C., Bik, E.M., Losekann, T., Ivanova, N., Martin, H.G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D.A., Quake, S.R. (2007). Inaugural Article: Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proceedings of the National Academy of Sciences, 104(29), 11889-11894. DOI: 10.1073/pnas.0704662104

http://img.jgi.doe.gov/cgi-bin/m/main.cgi