Rapid metagenomics classifiers on long read data
You should also keep in mind that single read accuracy of ONT still is a bit lacking, a 2D or 1D^2 accuracy of 95% still means that on average there's one error every 20 bp, and due to the nature of the data some stretches may be more junky than others. Maybe centrifuge doesn't like that.

Getting a feel of what the data can tell you (and what not) is pretty important.

You may want to try other classification tools to get an idea how well centrifuge works, Kraken comes to mind. But also: what about BLASTing some of these reads at NCBI and simply look at the results to get a first impression?