The winds of war in the Middle East, specifically pitting Iran against Saudi Arabia, are turning into a full-blown sandstorm. And the latest evidence of this comes from a surprising source: An interview in a Saudi newspaper.

No, a relatively short interview in an Arabic-language paper in Riyadh isn't usually a big deal. But it is when that interview is with the Chief of Staff of the Israel Defense Forces, Lt. General Gadi Eisenkot.

The interview alone is big news, as it's the first of its kind with an Israeli military official in the Saudi press. But it's what Eisenkot said in the interview that really made history and made it clearer than ever that Saudi Arabia and Iran are marching ever closer to a direct confrontation.

Here are the three Eisenkot quotes from Saudi Arabia's Elaph newspaper that deserve the most attention:

"With President Donald Trump, there is an opportunity for a new international alliance in the region and a major strategic plan to stop the Iranian threat." "We are ready to share intelligence, (with Saudi Arabia), if necessary. There are many common interests between us." "Iran seeks to take control of the Middle East, creating a Shi'ite crescent from Lebanon to Iran, and then from the Gulf to the Red Sea. We must prevent this from happening."

The creation of once non-existent ties between Saudi Arabia and Israel has been widely reported, but never publicly confirmed by either government, ever since the Iran nuclear deal was signed by the U.S. and other key Western nations. There have been coy hints to be sure, like when Israeli Prime Minister Benjamin Netanyahu gave a halfhearted "no comment" to 60 Minutes reporter Leslie Stahl when she asked him last year if Israel had improved its relationship with Saudi Arabia as part of a coalition against Iran. And neither Israel nor Saudi Arabia has yet confirmed widespread reports in the Middle Eastern media that new Saudi Crown Prince Mohammad bin Salman secretly visited Israel in September.

In that context, General Eisenkot's very public interview in a government sanctioned newspaper, (as all official newspapers are in Saudi Arabia), is a relatively massive public admission of allegiance between former sworn enemies. And the point of that admission is not to strike up the band for a rendition of Kumbaya, but to get that new coalition's ducks in a row for the ever more inevitable direct war between Saudi Arabia and Iran.

To be clear, it's not a political hot potato for the Israeli government or Netanyahu if such an alliance becomes public. While some segments of the Israeli public rebuff political leaders who make peace process concessions to the Palestinians, peace deals or cooperation with Arab nations for mutual security reasons are welcome news in Tel Aviv and Jerusalem.

It's in the Arab nations where this is very dicey. That's especially true in Saudi Arabia, the birthplace of extremist Islamic Wahabbism, where any acknowledgement of Israel's legitimacy -let alone working with the country - can be met with massive and violent protest. The world saw that in stark terms when Muslim Brotherhood assassins murdered Egyptian President Anwar el-Sadat in 1981 in retaliation for the peace deal he signed with Israel two years earlier.

But Crown Prince bin Salman apparently isn't giving any quarter the extremist old guard. In addition to plowing ahead in his hawkish stance against Iran, he's also cracking down on extremist clerics in the kingdom in a way no Saudi leader has ever even tried. At the same time, the prince has been promoting clerics who speak of tolerance for Judaism and Christianity. He's taken away the religious police's power to make arrests for "crimes" like immodesty. And, as has been reported most widely of all, he and the king have finally started to lift the nation's ban on women driving.

There is a method and a correlation to all of this. Bin Salman clearly understands that to fight Iran effectively and earn the crucial support he needs from the U.S. and Israel, he must present the world with a clear difference in culture and intentions than Iran. If the Saudis continue to abandon the long-running race to lead the world in Islamic extremist and violent piety and show a willingness to recognize and respect Israel, that will be a stark enough difference for anyone to notice. And there's a time element here as both Saudi Arabia and Israel are clearly seeing the current Trump administration in Washington as at least a silent partner in all this. But they also know this can change, so the time to move is now.

The priorities the Saudis are making make sense in the context of the more bitter and much longer-running Sunni-Shia war that's been going in fits and starts since the year 632. Hatred for the U.S. and Israel may seem supreme in radical Islamist cultures, but the Sunni-Shia divide is worse and a lot older. And with the wars in Syria and Yemen showing no signs of slowing down, hostilities between the Sunni standard bearers in Riyadh and the Shia rulers in Tehran have never been more likely.

In the past, Israel has always been a potential deal breaker for any coalition of Muslim countries engaged in an alliance with the U.S. Saddam Hussein, for example, tried to destroy the coalition against him in the first Gulf War by launching Scud missiles at Tel Aviv in 1991. That effort failed, but it was one of the most serious challenges to the war. The George H.W. Bush administration fought hard to keep Israel out of the war to preserve the loose Arab coalition against Iraq.

Now, Saudi Arabia has gone many steps further than just hoping to keep Israel on the back burner. This newspaper interview is tantamount to openly flaunting a growing partnership against Iran.

The Saudis, long the biggest bank in the Middle East and the controlling force behind OPEC, are making it clearer than ever that it's okay to partner with Israel. On its face, that's a peaceful and modernizing move. Hopefully, it will endure and yield dividends long beyond the current political climate.

But as anyone who knows the history of the region will tell you, right now the growing ties between the Saudis and Israelis could be an ominous sign that war is coming.

Commentary by Jake Novak, CNBC.com senior columnist. Follow him on Twitter @jakejakeny.

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