Mongoose 4.0.2 doesn't create indexes automatically for some reason despite of its docs.
So I've found if you add {autoIndex: true} as it's shown bellow, it solves the issue.

var path = require('path');

module.exports = function (mongoose) {
    var Schema = new mongoose.Schema({
        name: {type: String, trim: true, required: true},
        uuid: {type: String, required: true, unique: true, index: true},
        device: {type: mongoose.Schema.Types.Mixed},
        updated_at: {type: Date, default: Date.now}
    }, {autoIndex: true});
    return mongoose.model(path.basename(module.filename, '.js'), Schema);
};