You would have to add a parameter in_reply_to_status_id to your request (which is the status id of user's tweet you are replying to. Ref: POST statuses/update
Here's an example.
function startStreaming() {
bot.stream('statuses/filter', { track: 'certain word' }, function(stream) {
console.log('Listening for Tweets...');
stream.on('data', function(tweet) {
if (tweet.text.match('certain word')) {
bot.updateStatus('@' + tweet.user.screen_name + ' True that' ,
{in_reply_to_status_id: tweet.id_str}, callback);
}
});
});
}
startStreaming();