Organosilanes contain hydrocarbon backbones, allowing them to react with silicone-based agents in the presence of a catalyst and enabling them to polymerize into membranes with tunable transport and mechanical properties. For instance, Poly(dimethylsiloxane) (PDMS) membranes, and more particularly, Sylgard 184, have been used to control the delivery of hydrophobic substances, vary gas permeability, remove trace organic compounds from aqueous solutions, and fabricate microfluidic devices. Here, we are designing new siloxane-based membranes to study microbial dynamics. We developed a culture system referred to as nanoculture to encapsulate microbes in semipermeable membranes, which enable the growth of challenging species in environmental conditions. We explore the mechanical strength and the permeability of the new siloxane-based membranes to signaling biomolecules, sugars, and antibiotics to understand how microbial growth dynamics in the nanocultures could be controlled with these molecules. We screen a wide variety of polymethylhydrosiloxane membranes to achieve levels of permeability different from that of commercially available Sylgard 184 commonly used in the laboratory. The mechanical properties of the membranes are reinforced through the incorporation of silica nanoparticles, which enable the nanocultures to withstand high shear stress similar to environmental conditions while maintaining transport properties essential to microbial communication and growth.