Question: Where Can I Find Wgs Data For Time-Course Metagenomics?
gravatar for Pawel Szczesny
5.4 years ago by
Pawel Szczesny3.2k
Pawel Szczesny3.2k wrote:

I know a few studies (like Western English Channel) where analysis of biodiversity was conducted over time. However, all of the studies I found were based on the sequencing of 16S rRNA amplicons. Do you know any research where full shotgun sequencing was done in time-course on the same sample/spot?

data metagenomics • 2.0k views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 5.4 years ago by Pawel Szczesny3.2k

Some of the HMP subjects were sampled at the same body site up to 3 different times. Ignore this if that is too few points and/or you don't want host-associated microbiomes.

ADD REPLYlink written 5.4 years ago by Cliff Beall450

Interesting pointer. Thanks!

ADD REPLYlink written 5.4 years ago by Pawel Szczesny3.2k
gravatar for Josh Herr
5.4 years ago by
Josh Herr5.5k
University of Nebraska
Josh Herr5.5k wrote:

There's a few places with time-course data for WGS metagenomes, but for me the unequivocal choice would be MG-RAST. I was not impressed with early versions - so I ignored the site for a while - but in the last year it has really ramped up and now there are 64,000 metagenomics datasets available, and plenty open WGS data sets to choose from.

ADD COMMENTlink written 5.4 years ago by Josh Herr5.5k

MG-RAST was a one of the first places I started to look at (see the link in my question), but it does not have any project meeting my criteria, as far as I can tell.

ADD REPLYlink written 5.4 years ago by Pawel Szczesny3.2k

Sorry, I should have clicked on the link you provided first. How specific a project are you looking for? A specific habitat or environment? I just checked and there are 2618 WGS metagenome samples that I have access to publicly. Some of these appear to be from the same location over multiple time courses. The new metadata requirement provides more information on when and where samples were made. Other than MG-RAST, I can't think of a place that has as much publicly available data.

If you can't find anything that suits what you are looking for, I would be willing to send you some of my time-course sampling data from soil. Just let me know and agree not to scoop me on the paper from it!

ADD REPLYlink modified 5.4 years ago • written 5.4 years ago by Josh Herr5.5k

I've went through MGRAST database and no luck so far. JGI has also some metagenomics data, but again not exactly what I'm looking for. Basically, I need WGS of the same community in the same (roughly) conditions but in a different time frame (I'm working on estimators of "volatility"). Thanks for the offer - I will ping you by email with details.

ADD REPLYlink written 5.4 years ago by Pawel Szczesny3.2k

Sounds like you and I are interested in similar questions. I'm interested in "patchiness" in soil, where differences on a level of centimeters and millimeters can yield different microbes. We also have seasonal data for the same location in soil but at different times of the year. Soil and sea can be quite different inherently, but nutrient availability (and other drivers) can influence species composition. I'd be eager to se what you figure out about volatility.

ADD REPLYlink written 5.4 years ago by Josh Herr5.5k
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