Step #1: Find Your Barcode(s)
Each sample has a nine digit barcode. If you see a smaller number, add leading zeros.
For example, my barcodes were 2683 (fecal) and 2684 (oral), so I need to use 000002683 and 000002684 as my sample IDs.
Step #2: Search For Your Sample
Go to the European Nucleotide Archive (ENA) website: http://www.ebi.ac.uk/ena/
Copy and paste your 9-digit barcode into the text search
I get a single result for each of my samples when I do this. If you get multiple results, choose the metagenome sample (see image below).
If you want to double-check you have the right sample, click on the "Sample accession" link (which will start with "ERS"). If you then click the "Attributes" tab, you should be able to see your metadata. For example, I know I live in Los Angeles, so my state better not be GA.
Step #3: Download Your FASTQ Files
If you are certain you have the right sample, click the the link for "Fastq files (ftp)" to start the download. Note that the sample will be labeled based upon the "Run accesssion" (starting with "ERR"). For example, here are the different IDs for my samples:
Fecal: 000002683 --> ERS345317 --> ERR336561
Oral: 000002684 --> ERS344890 --> ERR336138
The .fastq files will be compressed, so you should unzip them. I would recommend using 7zip for this. I would also recommend renaming your files (like fecal.fastq and oral.fastq) to make it easier for you to keep track of them.