By stating that the gut is the "right place" for these particular bacteria, you are begging the question. It is unquestionably the case that there are bacteria in our gut flora that we definitely do not want anywhere but the gut. It does not follow that this applies to all bacteria.
Compare pathology of the bacterium under discussion (http://microbewiki.kenyon.edu/index.php/Nitrosomonas_eutroph...) with one that more clearly doesn't belong anywhere but the gut (http://microbewiki.kenyon.edu/index.php/Escherichia_coli).