Bolt was again slow out of the blocks, came back strong and coasted to the line. But that was only good enough for second in his world championship semifinal heat behind Christian Coleman today.
The American won the heat in 9.97 seconds, .01 seconds ahead of the Jamaican great.
Bolt, who has been struggling with form for much of the season, hasn't had a strong start yet at the Olympic Stadium, and it could cost him in the final.
Still, Bolt and Coleman were the only two sprinters to break the 10-second mark, with 2011 champion Yohan Blake winning his semifinal heat in 10.04 for third fastest.
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Two years ago, Bolt just held off Gatlin in the world championship final. The 2004 Olympic champion also finished second in his heat today, behind Akani Simbine. The South African had a time of 10.05 seconds, an edge of .04 seconds over Gatlin.
Other finals today are the men's discus and long jump, and the women's 10,000. Earlier, there was another runner who put on a show that was almost vintage Bolt.
Like Bolt, a rival setting off faster no longer phases him. Van Niekerk just made sure he produced some extra power on the final straight to rein in Brenes.
Van Niekerk is seeking to win gold in both the 400 and 200 meters over the next week. He is tipped by many to become the sport's next star now that Bolt is retiring after the world championships.
"Wayde van Niekerk is my brother," Makwala said. "We want to conquer the world together and make the final for Africa. He is so friendly and a lovely guy."
The two-day heptathlon also started and after two events Olympic champion Nafi Thiam took the lead. She scaled 1.95 meters in the high jump to reach a total of 2,215 points.
One of Thiam's toughest rivals, Katarina Johnson- Thompson, only cleared 1.80 in the high jump, well short of her best of 1.98, to dent her gold-medal hopes. She was in fifth position with 2,053 points.
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