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This paper investigates a method for training bottleneck (BN) features in a more targeted manner for their intended use in GMM-HMM based ASR. Our approach adds a GMM acoustic model activation layer to a standard BN feature extraction (FE) neural network and performs lattice-based MMI training on the resulting network. After training, the network is reverted back into a working BN FE network by removing the GMM activation layer, and we then train a GMM system on top of the bottleneck features in the normal way. Our results show that this approach can significantly improve recognition accuracy when compared to a baseline system that uses standard BN features. Further, we show that our approach can be used to perform unsupervised speaker adaptation, yielding significantly improved results compared to global cMLLR adaptation.