Oxford has been ranked the best university in the world, the first time an institution from the UK has taken the accolade.



It topped the Times Higher Education (THE) world university rankings for the first time, knocking the California Institute of Technology, the five-times best, into second place.



Cambridge and Imperial College London join Oxford in the top 10 for 2016/17, named fourth and eighth respectively, vying for positions in the rankings with the likes of Stanford, Harvard and Princeton universities and Massachusetts Institute of Technology, all in the US.



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But there were warnings that the vote to leave the European Union could pose a threat to higher education in the UK, destabilising it and hindering academics from working with colleagues on the continent.



And there are fears the looming departure from the EU could discourage overseas students from applying to British universities, with some research suggesting more than 40% are looking elsewhere.



Phil Baty, editor of the THE world university rankings, said: “The UK must ensure that it limits the damage to academics, students, universities and science during its Brexit negotiations to ensure that the UK remains one of the world leaders in higher education.”



The global rankings saw 91 UK universities placed in the top 980 , which represents 5% of the world’s higher education institutions, judged on areas such as teaching, research and industry income.



With 88 universities in the top 800, up from 78 last year, the UK is second only to the US for the number institutions in the world’s best 800.



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Despite this success, UK universities lagged behind on the industry income indicator, which assesses the ability to help industry with innovations, inventions and consultancy, the extent to which businesses are willing to pay for research and a university’s ability to attract funding – with the nation’s best-placed appearing at just 127 in the rankings.



The UK is the world’s second most popular destination for overseas students, according to the British Council, with 493,570 enrolled in universities in 2013/14, up around 80,000 on the 415,585 five years before.



But Baty said that Asia was continuing to grow as a higher education “superpower”, with China’s leading universities, Peking and Tsinghua, in the top 40 and the National University of Singapore at 24.



He said: “It is fantastic news that the University of Oxford has topped the world university rankings for the first time. It is a great result for the UK higher education sector and cements its position as one of the greatest university nations in the world.”



Baty added that the Brexit vote was a big threat to the higher education sector. He said: “As well as some top academics reporting they have been frozen out of collaborative research projects with EU colleagues, many are admitting that they might look to relocate to a university outside the country.



“A Times Higher Education survey conducted before the referendum found that 40% of university staff said they would be more likely to leave the country in the event of a Brexit.



“It is also having an impact on the UK’s potential to attract international talent in the future – more than two-fifths of prospective overseas students said they were less likely to go to a UK university due to the referendum result, according to a survey by Hobsons.”



The education secretary, Justine Greening, said: “Britain has long been home to some of the best universities in the world, and it’s fantastic to see a UK university top these world rankings for the first time.



“We want to see this success continue and provide real opportunities for students up and down the country. That is why we are reforming higher education to make sure it delivers the quality teaching and skills that students and employers expect.

“We are also looking at proposals to require universities to open or sponsor schools to help create more great school places and ensure every child can fulfil their potential.”