Health benefits & enzymes different between Thermophilic and Mesophilic Probiotic cultures?
Thermophilic and mesophilic enzymes differ in the optimal working temperature, due to a structural adaptation: thermophilic enzymes have more stiff surface-exposed loops than their mesophilic orthologs. Human is mesophile, which means that mesophilic enzymes, no matter whether human or bacterial, will work in human more efficiently.



Bjelic, Brandsdal, and Aqvist (2008) Cold adaptation of enzyme reaction rates. Biochemistry 47: 10049-10057; emphasis mine:


  [P]sychrophilic, mesophilic, and hyperthermophilic citrate synthases
  ... have increasingly stronger electrostatic stabilization of the
  transition state, while the energetic penalty in terms of internal
  protein interactions follows the reverse order with the cold-adapted
  enzyme having the most favorable energy term. The lower activation
  enthalpy and more negative activation entropy observed for
  cold-adapted enzymes are found to be associated with a decreased
  protein stiffness. The origin of this effect is, however, not
  localized to the active site but to other regions of the protein
  structure.


https://www.ncbi.nlm.nih.gov/pubmed/18759500



Aqvist (2017) Cold adaptation of triosephosphate isomerase. Biochemistry 56: 4169-4176; emphasis mine:


  The results show that the enzyme from the psychrophilic bacterium
  Vibrio marinus indeed displays the characteristic shift in
  enthalpy-entropy balance, compared to that of the yeast ortholog. The
  origin of this effect is found to be located in a few surface-exposed
  protein loops that show differential mobilities in the two enzymes.
  Key mutations render these loops more mobile in the cold-adapted
  triosephosphate isomerase, which explains both the reduced activation
  enthalpy contribution from the protein surface and the lower
  thermostability.


https://www.ncbi.nlm.nih.gov/pubmed/28731682