HOUSTON (AP) - Mets starter Jonathon Niese had pitched well through his first four starts this season and in his career against the Houston Astros.

He wasn't able to build on that success Tuesday night.

Chris Snyder hit a three-run home run and Jed Lowrie had a two-run shot to give the Astros a 6-3 win over the New York Mets.

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The two early mistakes cost Niese, and he was pulled after three innings against the Astros. Niese (2-1) allowed a season-high five runs and six hits in three innings. It was his shortest start since lasting just 2 2-3 innings on Sept. 29, 2010.

Lowrie's homer, which hit the inside of the foul pole in left field in the first inning, got things going for the Astros who have won the first two games of this three-game series. The Astros had lost six consecutive series entering Monday.

Snyder pushed the lead to 5-0 in the next inning with his first home run of the season.

``I thought, looking back, that Lowry pitch I regretted throwing it,' Niese said. ``I threw him a fastball, and I wanted to throw him a curveball. I threw one up and in on him, and he got it. The Snyder one he ambushed me. First pitch he got that one, too. Other than that, I felt great. It's just one of those games where it gets to you early.'

Niese entered the game 2-0 with a 2.81 ERA this season and was 1-1 with a 1.80 ERA in three career starts against Houston.

``Jon has too good of stuff, too many weapons,' Mets manager Terry Collins said. ``Again, it's tough for him. Those two home runs, if they were singles, we would still be in the game. When you're down that fast in a hurry, you have to somehow get yourself back in it, and we had a big inning going. I think Jon made a couple mistakes, and it came back to hurt him.'

Justin Turner doubled to start the fourth inning and Scott Hairston walked with one out. A two-out single by Andres Torres scored Turner to make it 5-1. Josh Thole followed with a RBI single to center field to get New York within 5-2.

Happ struck out pinch-hitter Lucas Duda to limit the damage.

Niese was disappointed he was pulled so early.

``Obviously, the competitiveness in me wanted to stay in the game,' he said. ``I had put up a zero, and I felt my stuff was good enough to keep the team in the game.'

Houston starter J.A. Happ (2-1) allowed six hits and three runs with seven strikeouts in 6 1-3 innings, which was his longest outing of the year.

Brett Myers threw a perfect ninth for his sixth save.

Reliever Miguel Bautista walked Justin Maxwell in the sixth inning, but Snyder grounded into a double play. Happ singled before Bautista walked Jose Altuve. He was replaced by Ramon Ramirez, who walked Lowrie.

His bases-loaded walk of J.D. Martinez gave Houston an insurance run and made it 6-3. The Mets finally got out of that inning on a fly out by Carlos Lee.

New York finished with eight walks, including three to Lowrie.

``You just can't put people on and expect to win major league baseball games, especially when you are walking in runs,' Collins said. ``It's going to come back to burn you.'

Turner walked with two outs in the fifth inning and scored after consecutive singles by David Wright and Hairston to cut Houston's lead to 5-3. Happ got out of that inning by striking out Ike Davis after a short coaching visit to the mound.

NOTES: Mets starter Mike Pelfrey had season-ending Tommy John surgery on his right elbow on Tuesday. The team said the surgery, done by Dr. James Andrews, went well. ... Mets catcher Mike Nickeas stayed at the team hotel on Tuesday with the flu. The Mets haven't decided whether they will call up another player to fill in while he's out. ... Duda was out of the starting lineup for the second game because of flulike symptoms, but pinch-hit in the fourth inning. ... The series wraps up on Wednesday when Houston left-hander Wandy Rodriguez faces Chris Schwinden.