Investigators were working to untangle the motive of Omar Mateen, as witnesses said the 29-year-old American of Afghan descent -- who was married with a child -- frequented the popular nightspot and used gay dating apps.
The Islamic State group claimed responsibility for the shooting early Sunday. The FBI said Mateen pledged allegiance to the IS leader in 911 calls made during the killing spree -- the worst mass shooting in US history.
New York Muslims gather in hundreds to pray for Orlando shooting victims
Forty-nine people were killed and 53 wounded after Mateen opened fire at the Pulse nightclub in Orlando, a resort city in central Florida best known as the home of Walt Disney World.
After a meeting of his National Security Council, Obama said the country's thoughts were with survivors and relatives of the dead, as well as the lesbian, gay, bisexual and transgender (LGBT) community "who were targeted."
"You are not alone. The American people and our allies and friends all over the world stand with you," Obama said.
He reiterated the official belief that Mateen -- a practicing Muslim -- had absorbed extremist propaganda online, noting: "He appears to have been an angry, disturbed, unstable young man who became radicalized."
Obama will travel to Orlando on Thursday.
The president spoke by phone Tuesday with French President Francois Hollande, who expressed his condolences. Both leaders reaffirmed their commitment to destroying IS, the White House said.
Obama calls Orlando shooting homegrown extremism
MSNBC and ABC News, citing unnamed law enforcement officials, reported that Mateen's wife may have had prior knowledge of her husband's plan and could face criminal charges.
Noor Mateen, 30, was cooperating with the Federal Bureau of Investigation, and claims she tried to convince her husband not to go through with the shooting, the networks said.
An FBI spokeswoman declined to confirm the reports to AFP.
Security has been stepped up at Disney theme parks amid reports -- based on his wife's statements to investigators -- that Mateen may have scouted Disney World as a possible target.
The probe took a new turn after witnesses said Mateen -- who was killed in a shootout with police when they stormed the venue -- had been a regular at Pulse.
"Sometimes he would go over in the corner and sit and drink by himself, and other times he would get so drunk he was loud and belligerent," Ty Smith told the Orlando Sentinel.
Another Pulse regular, Kevin West, told the Los Angeles Times that Mateen messaged him on and off for a year using a gay chat app.
Clubgoers told local media and MSNBC that Mateen had been using multiple gay apps, including the "hook up" app Grindr.
And a man who attended law enforcement training classes with Mateen in 2006 told the Palm Beach Post that the gunman had once asked him out on a date.
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Mateen's ex-wife, Sitora Yusufiy, who has said he beat her, told CNN he "confessed to me... that he very much enjoyed going to clubs and the nightlife."
"I feel like it's a side of him or a part of him that he lived but probably didn't want everybody to know about."
Authorities have identified all 49 victims, who ranged in age from 18 to 50. Of the 53 wounded, 27 remained hospitalized Tuesday, with six in critical condition, doctors at Orlando Regional Medical Center said.
Angel Colon suffered three bullet wounds to his leg -- which was shattered as people trampled him to escape Pulse -- and offered a harrowing account of the carnage.
"I can hear the (gunshots) closer, and I look over and he shoots the girl next to me. And I'm just there laying down. I'm thinking, 'I'm next. I'm dead,'" Colon told reporters.
"Everybody could hear him talking to 911, saying that the reason why he is doing this is because he wants America to stop bombing his country," recounted another survivor, Patience Carter.
She told of a chilling moment when the gunman asked if there were any African Americans present -- before telling them: "You know I don't have a problem with black people, this is about my country."
The shooting hit Orlando's Latino community hard -- the club was hosting a Latin-themed party that night. Thousands joined a vigil late Monday.
Still, the response was not all supportive. A Baptist preacher in California sparked uproar after praising the massacre as "great," saying he wasn't sad that "50 sodomites died."
Deadly rampage: Orlando hit by worst shooting in US history
"It's like the equivalent of asking me... ' Hey, are you sad that 50 pedophiles were killed today?'" pastor Roger Jimenez of the Verity Baptist Church said in his sermon just hours after the carnage.
"Um, no, I think that's great... I think Orlando, Florida is a little safer tonight."
His comments, posted on YouTube before being taken down, were denounced by LGBT activists and local officials.
Jimenez said his remarks were taken out of context.
The slaughter has raised questions about US counterterror strategy -- the FBI said it had investigated Mateen but cleared him of extremist ties.
But a fiery Obama lashed out at Republicans, especially presidential hopeful Donald Trump, for anti-Muslim rhetoric that he said was counterproductive to the fight on extremism.
"Where does this stop?" he said.
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"Are we going to start treating all Muslim Americans differently? Are we going to start subjecting them to special surveillance? Are we going to start discriminating against them because of their faith?"
The rampage has also raised questions about gun laws. Mateen legally bought the assault rifle and handgun used in the attack.
Obama has demanded that the Republican-controlled Congress pass legislation to curb the sale of assault-type weapons -- a measure that conservatives say violates their constitutional right to bear arms.
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