We present results on the isoscalar form factors including the disconnected contributions, as well as on the strange and charm quark form factors. Using previous results on the isovector form factors, we determine the flavor decomposition of the nucleon axial form factors. These are computed using an ensemble of $N_f=2+1+1$ twisted mass fermions simulated with physical values of quark masses. We investigate the SU(3) flavor symmetry and show that there is up to 10% breaking for the axial and up to 50% for the induced pseudoscalar form factors. By fitting the $Q^2$-dependence, we determined the corresponding root mean square radii. The pseudoscalar coupling of the $eta$ meson and the nucleon is found to be $g_{eta NN}=3.7(1.0)(0.7)$, and the Goldberger-Treiman discrepancy for the octet combination about 50%.