How to get metagenomic healthy reference?

Question

[agata88]

Hi all!

I would like to ask you about the Human Microbiome Project database. I need fastq SRA samples for 16S metagenomic analysis that will include healthy stool results in 3 groups of age:

• infants

• adults

• old people

Do you know if such data is publicly available? And if it is could somebody tell me were I should look for it?

I would really appreciate for help,

PS. Maybe you know other database including such information?

Agata

[natasha.sernova]

Dear Agata, look at the upper site.

http://ihmpdcc.org/HMQCP/healthy/index.php

and a paper below:

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374619/

This database contains 198 samples you are looking for, almost at the bottom of the page:

http://www.hmpdacc.org/HMASM/

[agata88]

Thank you natasha,

Do you know where I can find information about the age of SRR samples? I need to group 20 fastq SRR samples to group of 0-2 age, 3-18 etc.

[natasha.sernova]

I understand it, but I think it may be the hardest part.

If you simply ask in google "the age of SRR samples"

you get this:

http://www.epidemiolog.net/evolving/Standardization.pdf the age is inside

But there are many other parameters, I have some doubts if these data are available.
The main problem - you need healthy people.

In case of any disease these age groups are usually available.

http://jvi.asm.org/content/89/4/2425.full

[agata88]

I know that the data about age is not publicly available in HMP database, unfortunately. To get this information I need an extra access authorized by a group of people. I am not sure I am going to get this since I am no longer a student ... too bad ...