Shashank Joshi is a senior research fellow of the Royal United Services Institute (RUSI) in London. He was previously a research associate at the Changing Character of War Programme at Oxford University, and a Kennedy Scholar at Harvard University. The opinions in this article belong to the author.

(CNN) President-elect Donald Trump has, according to his chief of staff, finally accepted the intelligence community's assessment of Russian interference in last year's election.

But this comes after four months in which the President-elect has repeatedly belittled the work of the intelligence agencies , turning away their briefings and disparaging "the same people that said Saddam Hussein had weapons of mass destruction".

Despite his grudging acknowledgment of Russian hacking , it is clear that the President-elect neither trusts, nor is trusted by, the very men and women whose jobs it will soon be to provide him with accurate and timely assessments of world politics and national security. How might this tension unfold in the Trump presidency?

Such a degree of mistrust is unprecedented, but it might be instructive to draw a comparison with another incoming President who faced a tense relationship with the national security establishment. Bill Clinton's history of avoiding the draft for Vietnam, his youthful admission to "loathing the military", and his plans to allow gays to serve openly contributed to serious civil-military friction. In 1993 alone, the year he took office, Clinton faced remarkable hostility from the armed forces.

Just as a skeptical military sought to resist and sabotage many of Clinton's policies, from the repeal of "don't-ask-don't tell" to the use of force in Bosnia, we can imagine that the intelligence agencies -- whose size and complexity means they cannot be purged or transformed overnight -- will push back against many of Trump's statements and initiatives.

That pushback, which the political scientist Peter Feaver has called "shirking", could take many forms. It might include foot-dragging in implementing policy, unauthorized leaks to the press, subversive speeches by senior officials, direct appeals to Congress and the withholding of information from the White House.

If, for instance, Trump orders the CIA to cooperate with its Russian counterpart, perhaps on Syria, the agency might raise a flurry of objections, send only junior staff, or share low-grade intelligence. Should Trump renew his attack on the agencies' assessment of Russian hacking, they might choose to leak further information to US newspapers and broadcasters, undercutting the President's claims.

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Perhaps the easiest way for any intelligence agency to wound a President is to leak that, in any particular crisis, their warnings went unheeded. With Trump's record of turning away briefings, this charge would easily stick.

A more open approach is for the heads of the agencies or the director of national intelligence (DNI) to give public speeches where they subtly -- or more brazenly -- divert from the White House's line on controversial subjects.

They might highlight the continued importance of NATO, contrary to the President's contempt for allies, or warn of the consequences of policies such as abandoning the longstanding One-China Policy, which Trump has called into question.

Intelligence officials can also reach around the White House, appealing directly to Congress. Clinton's military officials did just this during the war in Bosnia, much as President Dwight D. Eisenhower's generals had done in the 1950s to undermine his ambitious reforms. The intelligence community has well over a thousand meetings with members of Congress and their staffs each year, affording many opportunities for such lobbying.

Finally, the control of information is also a powerful bureaucratic instrument. Agencies might hold back information from the President to shape his views or, given the president's loquaciousness on Twitter, to prevent leaks. We find an example of this in the 2014 Senate Intelligence Committee report on torture , which noted that the "CIA repeatedly provided incomplete and inaccurate information to White House personnel", in order to protect their torture program.

Many of these steps reflect forms of minor rebellion that occur during any administration. President Obama was profoundly suspicious of military efforts to box him into higher troop numbers on Afghanistan in 2010, with his National Security Adviser Tom Donilon calling the military "insubordinate" and "in revolt." But this dynamic is likely to be particularly pronounced under Trump, given his lurid public style and erratic behavior.

While the President could ultimately prevail on any given policy, he may have to dismiss senior appointees, drawing attention to the dysfunction, and so making it harder for mainstream Republicans to support the President-elect.

We should also consider that different intelligence agencies are likely to respond differently. A number of reports have indicated widespread support for Trump in the FBI, for instance.

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Other intelligence officials may welcome his advocacy of stronger pressure on Iran and escalation against ISIS. While divisions between agencies are commonplace, on matters of turf, analysis, and policy, political rivalries may impede intelligence sharing and cooperation, with adverse effects for counter-terrorism and other areas.

Trump's transition team is also reportedly looking at ways to limit the power of the DNI. This may further disrupt inter-agency coordination, which has been considerably improved in the 15 years since the 9/11 attacks. Sustained criticism by the President is also likely to have demoralized many intelligence officers and analysts, which may impede staff recruitment, retention, and performance. Should the Trump administration carry out purges of staff perceived to be disloyal, this could have a far-reaching and damaging impact on US capabilities.

Just as Clinton's relationship with the military improved over time, so too might Trump settle down to an amicable relationship with his spies.

As he settles into office, he may come to view the question of Russian hacking as a decreasing political threat to his legitimacy, and may therefore have less cause to cast doubt on the official assessments. Like many leaders, he may also come to appreciate the value of secret information, and its value to sound policy. But it will be difficult to overcome the poisonous atmosphere of these past months.