Hello everyone,
For bacterial taxonomy based on the 16S rRNA gene, it is currently accepted the similarity cutoff of
I don't think there is a standard MLSA approach, but several variations (see link). It is more powerful than 16S to differentiate organisms, particularly at species level, but the cutoff would depend on a number of factors, mainly the genes you use and the genus considered
http://www.sciencedirect.com/science/article/pii/S0723202015000508
As can be observed in the works below the technique mlsa is able to distinguish bacteria at the species level. It is important to note that at least 5 to 7 housekiping genes are required to perform the mlsa properly.
To identify bacteria at the genere level you can continue only with the sequencing partial 16S rRNA gene and would not need to use the MLSA technique.
http://onlinelibrary.wiley.com/doi/10.1111/lam.12626/full
http://www.sciencedirect.com/science/article/pii/S0044848616303738
http://www.microbiologyresearch.org/docserver/fulltext/ijsem/58/1/200.pdf?expires=1486671603&id=id&accname=guest&checksum=580FEC409267BEB2BF1286D47D4927EC
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