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Spore germination of Bacillus stearothermophilus was progressively inhibited as the concentrations of sodium bicarbonate(NaHCO3) in the germination media increased from 0% to 1·0%(w/v). The inhibitory effect of NaHCO3 was attributed to the release of HCO3- and its alkaline properties, each of which played a different role. At low concentrations (< 0·3%), the inhibitory effect of NaHCO3 was mainly due to bicarbonate. As NaHCO3 increased from 0·3% to higher concentrations, the effect of HCO3- reached a plateau while the alkalinating effect became the more dominant inhibitory factor. Fourier transform infrared (FTIR) analysis reveals that sodium bicarbonate reacted with the carboxyl group(1570 cm-1) of some acidic amino-acid residues of protein in the spore, leading to a less orientated structure. A shift of two units towards the longer frequency for carboxyl groups indicates that a stronger interaction was formed between the carboxyl group and the Na+ ion. The largest ratio of peak height between the absorbance of carboxylate (1570 cm-1) and of amide II (1546 cm-1) of spores after pretreatment with 0·3% sodium bicarbonate reflects the biggest structural alterations of keratin-like proteins in the spore. The role of NaHCO3 in enhancing the sporicidal effect of glutaraldehyde is discussed.