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11/18/11 5:16 PM EST

Mets shuffle roster before Rule 5 Draft deadline

NEW YORK -- With an abnormally large number of their top prospects vulnerable in next month's Rule 5 Draft, the Mets on Friday performed some extensive roster shuffling to keep their farm system intact.

The Mets added pitchers Robert Carson and Jeurys Familia, outfielders Juan Lagares, Kirk Nieuwenhuis and Cesar Puello, and infielders Wilmer Flores and Reese Havens to their 40-man roster, ensuring that no team can select those players in the Rule 5 Draft proceedings at the Winter Meetings in Dallas.

They opted not to protect pitcher Brad Holt and infielder Jefry Marte, among others, leaving those players exposed to other teams.

Familia, 22, has rocketed up the team's prospect depth chart in recent years, posting a 3.49 ERA at Double-A Binghamton this season after a sensational start with Class A St. Lucie. Familia ranked third on MLB.com's postseason Top 10 Mets prospect list and could crack the big league roster as soon as next season. Protecting him was a no-brainer.

Flores, 20, has long been one of the organization's top prospects, ranking fourth on MLB.com's Top 10 list and 39th in all of baseball. Despite questions surrounding his defensive position and ability -- not to mention a down season offensively that saw him hit .269 with a .309 on-base percentage -- Flores remains one of the team's most valuable chips.

Havens, 25, has done little but excel when healthy over the last four seasons, but rarely has he been healthy. Injuries undermined the second baseman for a third straight season in 2011, limiting him to 61 games. But when Havens played, he thrived, hitting .288 with six home runs and 17 doubles and prompting the Mets -- who have no obvious future second baseman within the organization -- to protect him.

Carson, 22, made his debut as a full-time reliever last month in the Arizona Fall League, walking 12 batters and striking out 11 over 17 1/3 innings. Despite those struggles, Mets general manager Sandy Alderson mentioned Carson by name this week as a left-handed candidate for the Opening Day bullpen, and subsequently protected him.

Nieuwenhuis, 24, was a prime candidate to crack the Major League roster this summer -- and perhaps enter next spring as a competitor for the starting center field job -- before he suffered a season-ending shoulder injury in June. A left-handed hitter, Nieuwenhuis was batting .298 with a .403 on-base percentage for Triple-A Buffalo prior to his injury.

Lagares, 21, hit well at all three of his stops this year, batting .303 in the AFL after posting a .370 average at Binghamton and a .338 mark for St. Lucie. Most impressive was the outfielder's .391 on-base percentage and .512 slugging mark following his midsummer promotion to Double-A.

Puello, 20, hit .259 with 10 home runs for Class A St. Lucie this season, though a lack of patience limited his strides at the plate. MLB.com ranked him seventh on its postseason Top 10 Mets prospects list, and the Mets protected him despite his raw skill set.

The only player on MLB.com's Top 10 list whom the Mets left exposed was Marte, 20, who has long ranked among the organization's most promising young infielders. A strong showing in the Arizona Fall League was not enough for the Mets to protect Marte, who struggled to the tune of a .313 on-base percentage in 131 games at St. Lucie.

The Mets also opted not to protect pitchers Mark Cohoon, Collin McHugh and Holt, the latter a former organizational favorite. A supplemental-round pick in the 2008 First-Year Player Draft, Holt posted an 8.34 ERA over two levels last season, then followed it up with a 4.71 mark at Double-A this year. He walked 57 batters in 93 2/3 innings.

Major League regulations stipulate that any player who signed his first professional contract before age 19 and has been in the organization for five years, or who signed after age 19 and has been in the organization for four years, is eligible to be selected in next month's Rule 5 Draft if not protected. Thus, players such as Familia and Flores must be added to the 40-man roster, while fellow top prospects Matt Harvey and Zack Wheeler are safe.

If selected, a player must remain on his new team's active roster or disabled list all season, or be offered back to his original club at a discounted price. The Mets made two selections in last year's Rule 5 Draft, second baseman Brad Emaus and reliever Pedro Beato, ultimately keeping Beato and returning Emaus to the Blue Jays. They also own the rights to one of the most famous Rule 5 Draft selections of all time, left-hander Johan Santana.

Anthony DiComo is a reporter for MLB.com. Follow him on Twitter @AnthonyDicomo. This story was not subject to the approval of Major League Baseball or its clubs.