A reader asked, what probiotics can I take while taking minocycline. Minocycline and tetracyclines are members of the same family — so the same general rules apply. The good news is that not all probiotics will be killed, the bad new is we do not know which strains will be killed or survive.. Some brands may be 100% kill, other brands perhaps 25-35% will survive.
As many species as possible since most will be killed, but 14% is expected to survive.
- “Bifidobacterium breve, which appeared to be generally more resistant. Potentially acquired resistance was only observed against tetracycline and minocycline, in 14% of the strains.” http://jac.oxfordjournals.org/content/55/1/38.long
- “Susceptibility to trimethoprim, trimethoprim/sulfamethoxazole, ciprofloxacin, clindamycin, tetracycline and minocycline was variable. Thetet gene was responsible for tetracycline resistance in 15 strains including 7 probiotic isolates belonging to the taxa Bifidobacterium animalis subsp. lactis and Bifidobacterium bifidum. ” http://jac.oxfordjournals.org/content/58/1/85.long
Note: Some commercial L.Reuteri are very sensitive to minocycline according to FDA filings…. being sensitive is a PLUS for the FDA.
- “Acquired resistance percentages to these antibiotics( tetracycline and minocycline) were extremely high for L. crispatus, L. reuteri, L. gallinarum, and L. salivarius subsp. salivarius (75%-100%). L. amylovorus on the contrary, displayed lower resistance percentages (25%) toward minocycline and tetracycline. In several strains, resistance against the tetracycline antibiotics was associated with the presence of the resistance genes tet(K), tet(L), tet(M), tet(W), and tet(Z).” 
- “93 Lactobacillus strains isolated from domestic geese raised on Polish farms… strains were resistant to… 23.6% to tetracycline (MIC ≥ 32 μg/ml), …. 18.3% to doxycycline (MIC ≥ 32 μg/ml),
- “Antimicrobial activity and antibiotic susceptibility were tested for 23 Lactobacillus and three Bifidobacterium strains isolated from different ecological niches… All strains were susceptible to ampicillin, gentamicin, erythromycin and tetracycline.” 
I could not find anything specific for Mutaflor or Symbioflor-2
- “We conducted a study of Escherichia coliisolates obtained from human and food samples to assess the prevalence of antimicrobial resistance and to determine the genotype and clonal relationship of 84 E. coli isolates (48 from humans and 36 from foods). An antimicrobial susceptibility test was performed using the disk diffusion method.All isolates were susceptible to ceftriaxone. Overall, 26%, 20.2%, 15.4% and 6% of the isolates were resistant to tetracycline, ampicillin, sulfamethoxazole/trimethoprim and cephalotin, respectively. 
Prescript Assist and GeneralBiotics Equilibrium
Both of these are very heavy species (150 in combination) so resistance of many species would be expected.