Is There A Metagenomics Resource That Lists The Abundance Of Species In A Particular Environment?

Question

[fm271]

In the context of microbiome, Is there any online database from where I can get the frequency of different species in a particular environment? For example, I am interested to find what is the frequency of different species in the gut of human with obesities.

Update: I found a resource on http://www.hmpdacc.org/HMSCP/ where I can get "abundandace table" for a particular sample. First few entries in this table is as follows. Is there a way to get at lease relative abundance using the following information?

Reference Name    Group    Depth    Breadth    Total reference bases
Streptococcus parasanguinis ATCC 15912    Bacteria    546.925954703539    95.4601684855376    2159948
Streptococcus salivarius SK126      Bacteria    520.58396101736    96.269332040302    2128332
Veillonella dispar ATCC 17748      Bacteria    196.692650948446    94.3962085773803    2116567
Rothia mucilaginosa ATCC 25296      Bacteria    155.224897164633    90.6639357419746    2255158
Rothia mucilaginosa DY-18     Bacteria    132.65    90.1404352109398    2264603
Streptococcus thermophilus LMD-9     Bacteria    61.3305084707576    82.3263121869264    1864178
Prevotella melaninogenica ATCC 25845      Bacteria    58.6451860472016    86.5324172532622    3168282
Granulicatella adiacens ATCC 49175     Bacteria    55.7879021396837    75.2977502849584    1923088
Prevotella melaninogenica D18     Bacteria    31.5585166299603    69.1128895822152    3292341
Actinomyces odontolyticus ATCC 17982     Bacteria    30.0428265346789    80.4829895085468    2393758
Actinomyces odontolyticus F0309    Bacteria    28.9803390960919    80.5965061605801    2431995

[Neilfws]

I think that information is more likely to be found in the literature than a database.

[Daniel]

I agree that literature will be the best bet, and if you're lucky they might have supplied an open table to peruse. But there is a large human microbes dataset available at http://www.microbio.me/emp/ which might be of use for comparison/interest

Answer 1

[Istvan Albert]

What you will find that there is no such thing as the expected abundance of different species in the human gut.

The strongest statement you could make perhaps is that there are species that are never seen, but among those that have been seen there are few if any rules.

This might be a good starting point: Structure, function and diversity of the healthy human microbiome, Nature, 2012

What you will see from this paper that there was not a single species that would have been found in all of the samples! let alone in similar abundances - quite shocking I might say.

[fm271]

@Istvan, thanks for reply. I modified my post and see an abundance table there. I am now more interested to find relative abundance in a sample using the information I provided above. Is there a way to do so? Or at least to rank these organism.