I plan to get my microbiome tested at some point, so this page is just the notes I've been jotting down on the companies available to do the testing. From the looks of them so far, I'll probably go with uBiome (seems like the most popular, and isn't complicated by offering "gut customized" products) or American Gut (as an open, academic project).
ExplorerPlus (combination of metagenomic and marker-based sequencing): $399 for four tests
May be able to get "free" testing through their SmartGut pilot program that bills your insurance, with any remaining balance paid by uBiome. It sounds like it's less comprehensive than the standard $89 Explorer test though, see the comment below.
Reportedly: "it takes roughly 8 weeks to get results, even longer with smart gut."
"The smart gut report shows if a genus is high, low, or normal. These limits are defined as 0.5% and 99.5%-tiles respectively (the middle 99% are normal)." (source)
Also has vaginal and 5-site (gut, mouth, nose, genitals and skin) microbiome testing
$399 per year (one test kit which also includes "metabolic" testing). Additional (gut-only) tests are $199.
Reportedly "a few weeks" turnaround time
"Metatranscriptome" testing that they believe is superior to others' 16S testing because of its ability to identify all bacteria, and to identify viruses, archaea, yeast, fungi, parasites, and bacteriophages.