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A much-changed Barca line-up went down 2-1 at Camp Nou, with Messi, Luis Suarez and club captain Andres Iniesta unable to salvage matters having appeared as second-half substitutes.
The five-time Ballon d’Or winner returned from international duty with Argentina having aggravated a groin complaint and Luis Enrique will guard against further fitness problems in Tuesday’s Champions League opener against Celtic.
“Messi, I would like him to play every single minute. He would like that as well,” the Barca coach told a pre-match news conference.
“But it is about what the player is feeling here, what he feels in his leg.
“Tomorrow we will see if he can play many minutes. It is how well his legs are that will dictate how much he can play.”
Left-back Jordi Alba, an unused substitute on Saturday, is under no illusions over Messi’s importance among Barcelona’s galaxy of stars.
“I would be stupid if I didn’t say Messi is the best for us, we have a lot of quality players but Leo makes us a different team.
“He has been the best in the world for a long time and that’s incredible.”
New recruits Jasper Cillessen and Paco Alcacer endured debuts to forget last time out but Luis Enrique is confident they and his close-season signings will adapt without too many similar setbacks.
“We need to keep working on certain aspects but there is nothing I’m surprised about because I’ve been a coach for a few years already. We need to reinforce certain habits.
“As for the new players, we know what we want out of them. I think we play completely differently to most teams.
“We have to give them a lot of information to help them so that journey is as less traumatic as possible.”