Yes, and no. Many "traditional" staining methods dont really offer up much information, like a gram-stain (common when learning microbiology, not so common in research) can only divide bacteria into two groups: gram-positive and gram-negative. More to the point, if these bacteria have no known methods of culturing (which was correctly noted at 90%+), you can not get them in a pure culture and can only stain them in mixed groups, which isnt that useful.

That being said, there are some staining-like methods you can use to identify what taxonomic group a given bacteria is from. You can use a fluorescent DNA probe that binds to a specific target region of DNA that is highly conserved in groups of bacteria (the 16S rRNA). It is not 100% accurate, and it requires reference data from known organisms, but it can be a good tool for initial surveys of mixed samples. You can also get some cool looking pictures from it.

>I'm guessing their sequencing process prevents the concurrent use of these methods, so we can't match up DNA to known bacteria.

Nope! The above method is actually used in some single-cell sequencing techniques. The cell is florescently tagged, then you can use a microfluidic device (or other methods) to isolate the cell, extract its DNA, and sequence. It is however difficult to assemble a complete genome from a single cell's DNA.