Microbial genomic sequence data is available by conducting searches using accession numbers associated with  the sequence of interest.

Examples of of searches are:
Entrez search, easily search by single accession number; returns sequence and publication information.  Link: http://www.ncbi.nlm.nih.gov/sites/gquery
Batch Entrez, Batch search a series of accession numbers after creating a Fasta-formatted text file;  returns links to GenBank, Fasta, Graphics, Population Set and Related Sequences for each accession number.
Link: http://ncbi.nlm.nih.gov/sites/batchentrez

Batch Entrez Fasta-formatted text file should be a  single column list of accession numbers with a ".1" added like a file extension. File should have no header line. Go to http://ncbi.nlm.nih.gov/sites/batchentrez, follow the web site directions for  using Batch Entrez

Fasta-formatted text file example:
AY836800.1
AY836801.1
AY836802.1
AY836803.1
etc..

To access  MG-RAST annotation and raw sequences, the user will need to navigate to this page:
http://www.mg-rast.org/mgmain.html?mgpage=search
and enter the project id listed in the PIE-Microbe-Genomics tab (e.g. mgp84173) into the text box at the upper left of the page adjacent to the "search" button. 
The search will return a list of the samples associated with the project and a link to download the annotation, fasta files, and associated metadata.

Data can also be accessed through the API according to the instructions here
http://api-ui.mg-rast.org/api.html

Also available, courtesy of Joe Vineis, is a small git repository that includes some simple instructions for handling the API for beginners:
https://github.com/jvineis/mg_rast_processing