A newly-isolated Lysinibacillus sp. strain WH could precipitate CaCO3 using calcium acetate (Ca(C2H3O2)2), calcium chloride (CaCl2) and calcium nitrate (Ca(NO3)2) via non-ureolytic processes. We developed an algorithm to determine CaCO3 crystal structures by fitting the simulated XRD spectra to the experimental data using the artificial neural networks (ANNs). The biogenic CaCO3 crystals when using CaCl2 and Ca(NO3)2 are trigonal calcites with space group R3c, while those when using Ca(C2H3O2)2 are hexagonal vaterites with space group P6522. Their elastic properties are derived from the Voigt–Reuss–Hill (VRH) approximation. The bulk, Young's, and shear moduli of biogenic calcite are 77.812, 88.197, and 33.645 GPa, respectively, while those of vaterite are 67.082, 68.644, 25.818 GPa, respectively. Their Poisson’s ratios are ~ 0.3–0.33, suggesting the ductility behavior of our crystals. These elastic values are comparable to those found in limestone cement, but are significantly larger than those of Portland cement. Based on the biocement experiment, the maximum increase in the compressive strength of Portland cement (27.4%) was found when Ca(NO3)2 was used. An increased strength of 26.1% was also found when Ca(C2H3O2)2 was used, implying the transformation of less-durable vaterite to higher-durable calcite. CaCO3 produced by strain WH has a potential to strengthen Portland cement-based materials.