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Far infrared spectra of Bacillus subtilis and Bacillus thuringiensis were recorded using Terahertz time-domain spectroscopy (THz-TDS). Multiple dilutions of each species were prepared to enable the analysis of spectral data up to 2,5 THz. The optical constants of pure spores were then extracted using the well know Maxwell-Garnett effective medium model. We show that the refractive index can be used to discriminate the two sporulated species, contrarily to absorption coefficient.