It seems for the most part that when the Bengals ran nickel formation against the Colts, it presented of one of two likely scenarios: Moving Chris Crocker into a third cornerback role with Gibril Wilson replacing him at safety and/or Morgan Trent playing nickel. It's also possible that the team used Wilson as a nickel, but seems unlikely because Crocker, as a stronger cover option, would be the more logical choice to cover a cornerback or tight end during obvious passing situations. It'll be interesting to see how Adam Jones is incorporated upon his return against the Seattle Seahawks on October 30.
Also Carlos Dunlap may not have started, but he received a significant number of snaps, forcing the obvious conclusion that Dunlap and Michael Johnson are your primary defensive ends. However that conclusion might might be slightly saturated based on the game played out with the Colts passing the football on 56.7% of their offensive snaps, enabling the Bengals to use more Dunlap, Jonathan Fanene and Geno Atkins, who were three of the top four leaders on the defensive line Sunday.
It's also fair to say that the absence of Rey Maualuga isn't so much about replacing him with a single player like Dan Skuta -- rather it's about implementing a rotation that gave Brandon Johnson the team's most defensive snaps at linebacker whereas his defensive contributions have been limited (at best) earlier during the season.
(snap count account to Pro Football Focus)