foreach ($messages as $message) {
    $message->get_likes();
    $message->get_comments();
    ...
}

$arr = array();
        foreach ($messages as $message) {
            $arr[$message->id] = $message->as_array();
            $arr[$message->id]['comment'] = array();
            foreach ($comments as $comment) {
                if ($comment->message_id == $message->id) {
                    $arr[$message->id]['comment'][$comment->id] = $comment->as_array();
                }
            }