The San Francisco 49ers returned to practice Wednesday to prepare for their Week 16 matchup against the Miami Dolphins. Running back Isaac Guerendo (hamstring) will not practice. Kyle Shanahan said it was an injury Guerendo sustained during last week’s game against the Los Angeles Rams.

Left tackle Trent Williams will also miss Wednesday’s session as he continues to battle an ankle injury. Those are the only two players who will sit out. Shanahan was asked if Williams would play the rest of the season:

“I mean, if he could get back to [being] healthy, we’d play him. But it’s not looking like that right now, so it’s getting closer to being that way.”

That does not sound like the 49ers believe it’s worth risking any further injury to the 36-year-old All-Pro in a season that’s all but lost.

Shanahan was asked about the cost/benefit of playing players when they’re not quite 100 percent, referencing Williams battling through an ankle injury and Nick Bosa’s oblique injury, and whether he goes back and thinks about the move or regrets it in hindsight:

“You always do. Trent, just with what we had and what we’re still trying to deal with, we felt safe putting him out there that it couldn’t get worse. That it would just stay the same. And, um, Nick, we felt good with his oblique, but he ended up hurting his other one. It was a completely different injury. But yeah, we do that with everything. We always worry about that stuff. There’s a very fine line in that stuff.”

The following players are limited:

DE Nick Bosa (hip/oblique)

LT Jaylon Moore (hip)

S Malik Mustapha (chest)

LB Dre Greenlaw (knee/Achilles)

OL Nick Zakelj (illness)

Shanahan said that Greenlaw had a good recovery over the weekend and that the team “took care of him” during Monday’s bonus practice. Greenlaw told Shanahan that he felt good to go to practice Wednesday.

According to Shanahan, the plan against the Rams was for Greenlaw to play at least half the game. They felt so good about putting him out there series after series because of the multiple three-and-outs the defense forced.

Shanahan said the Niners wanted Greenlaw available for the fourth quarter and intended to rest him in the third. But Dre felt tightness when he attempted to go onto the field, and that’s why he was shut down.