DDx involves genetic disorders with impaired carboxylation.
Biotinidase Deficiency (see above)
Holocarboxylase Synthetase Deficiency (see above)
Carnitine Deficiency
Methylmalonic Acidemia
Propionic Acidemia
Pyruvate Carboxylase Deficiency
Starvation
Medication Use - Antibiotics or anticonvulsants
Other vitamin deficiencies:
Biotinidase Deficiency (see above)
Holocarboxylase Synthetase Deficiency (see above)
Carnitine Deficiency
Methylmalonic Acidemia
Propionic Acidemia
Pyruvate Carboxylase Deficiency
Vitamin A deficiency
Vitamin B deficiencies<unk>  (Thiamine)
Beriberi
Wernicke-Korsakoff syndrome<unk>  (Pellagra)<unk>  (Biotin)<unk>  (Folate)
Vitamin B12 deficiency
Vitamin C deficiency (Scurvy)
Vitamin D deficiency (Rickets)
Vitamin E deficiency
Vitamin K deficiency<unk>  (Thiamine)
Beriberi
Wernicke-Korsakoff syndrome<unk>  (Pellagra)<unk>  (Biotin)<unk>  (Folate)
Vitamin B12 deficiency
Beriberi
Wernicke-Korsakoff syndrome
Vitamin B7 deficiency
DDx involves genetic disorders with impaired carboxylation.
Vitamin B9 deficiency
Biotinidase Deficiency 
Vitamin B12 deficiency
Holocarboxylase Synthetase Deficiency 
Vitamin A deficiency
Carnitine Deficiency