This article shows that there is variability in the degree that bacteria bind to phosphate in the gut. Is it possible that intestinal bacterial overgrowth results in hypophosphatemia?
Chronic small intestinal bacterial overgrowth (SIBO) can be associated with decreased calcium and vitamin D absorption, which can result in increased parathormone secretion, which can result in increased excretion of phosphate through the kidneys and thus in hypophosphatemia. In short-term cases, there would be no hypocalcemia, because calcium would be leached from the bones and maintain normal blood levels.
SIBO can be diagnosed by a hydrogen breath test. If the test is negative, other malabsorption conditions can be considered, for example, fructose malabsorption, lactose intolerance, celiac disease, Crohn's disease, etc.