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The breakfast meeting came amid US media reports that Mattis risks being isolated by Trump's more bellicose coterie of advisors, including Bolton, an Iraq War-era hawk who has advocated for military action in both Iran and North Korea.
Bolton "was here this morning," Pentagon spokeswoman Dana White said.
The two men decided to have "regular" meetings, she added, noting that CIA Director Mike Pompeo, Trump's pick to run the State Department, could join them.