The impact of microbes on lithosphere starts with the change of minerals comprising rocks, whereas the impact of microbes on minerals starts with the change of the composition of minerals. Based on previous researches on the interaction between microbes and minerals, this paper studied the interaction between silicate bacteria Bacillus mucilaginosus and bentonite, which is mainly composed of layer silicate montmorillonite and a small amount of other silicate minerals such as quartz and feldspar, and analyzed the impact of microbes on betonite in such aspects as composition and microstructure. The concentrations of elements Si, Al and Mg in solution were tested by Inductively Coupled Plasma-Atomic Emission Spectrometer (ICP-AES), after being treated by hydrogen peroxide. The minerals after bacteria dissolution were analyzed by X-ray Diffraction (XRD) and Micro-Fourier Transform Infrared Spectroscopy (Micro-FTIR).The pH values of the reaction solution rapidly decreased from 7.5 to 4.3 in the first 2 days. Then the pH values became gradually stabilizing. The dissolution quantities of Si, Al and Mg from the mineral crystal lattice were unbalanced. The X-ray diffraction patterns (XRD) showed that the phase of calcite (Ca) disappeared in bacteria dissolution products (BM), which was probably caused by acid metabolic products of bacteria, and there was a new faint diffraction peak that appeared between 9° to 10° in the samples treated by bacteria. According to the Micro-FTIR spectra, the absorption peaks at 3620 and 3400 cm-1 shifted to higher wavenumber and the intensity decreased, and the intensity of weak absorption peak at 1635 cm-1 decreased too, suggesting that the content of ions in montmorillonite was changed. The disappearance of CO2-3 band absorption peak at 1434 and 880 cm-1 was consistent with the XRD result of the disappearance of calcite phase.Through analyzing pH changes in solution, variations of major elements in solution and minerals, and structural, infrared spectroscopic and specific surface area changes, the authors inferred that the bacteria dissolution process is like this: first, acidic metabolites produced during the growth of bacteria and contact interaction between minerals and bacteria dissolve the vulnerable parts of mineral surface, and some cations in mineral structure are dissolved. With the dissolution, the uneven exsolution of cations may cause the change of mineral grains surface and even the collapse of the silicate layer, and the mineral structure is changed at last.