The Congress has now rejected the Trump proposal:
Lawmakers increased the budget for the National Institutes of Health (NIH) in its bipartisan deal to fund the government, effectively ignoring the Trump administration’s proposal.
Congress bolstered funding by $2 billion over the next five months, securing $34.1 billion for the NIH. It's the biggest boost the NIH has received in more than a decade, higher than at any point during the Obama administration.
The explanation for the Congressional resistance is multi-layered, and certainly the visibility of the NIH proposal was very high and the resistance was very public. In addition, Democratic strategizing in the budget process negotiations played a key role. The recent 21st Century Cures Act (see here) which focuses on breakthrough projects (but was not explicitly funded; see here) is now specifically funded in this new bill. More funding fights loom, however, as the 2017-2018 fiscal year is not far away, and the future proposed cuts to NIH are not resolved. But it's fair to say that the collective resistance to this year's NIH cuts (followed by its success) demonstrated significant political muscle, likely to be exercised in the next round of annual negotiations.