In this paper, we discuss data and methodological challenges for building bacterial communication networks using two examples: E. coli as a flagellate bacterium and G. sulfurreducens as a biofilm forming bacterium. We first highlight the link between the bacterial network communication design with respect to metabolic information processing design. The potentialities of designing routing network schemes described previously in the literature and based on bacteria motility and genetic message exchanges will depend on the genes coding for the intracellular and intercellular signalling pathways. In bacteria, the "mobilome" is related to horizontal gene transfer. Bacteria trade-off the acquisition of new genes which could improve their survival (and often their communication bandwidth), keeping their genome small enough to ensure quick DNA replication and fast increase of the biomass to speed up cell division. First, by using a multi-objective optimisation procedure, we search for the optimal trade-off between energy production, which is a requirement for the motility, and biomass growth, which is related to the overall survival and fitness of the bacterium. We use flux balance analysis of the genome-scale biochemical network of E. coli k-13 MG1655. Then, as a second case study, we analyse the electric properties and biomass trade-off of the bacterium G. sulfurreducens, which constructs an electric biofilm where electrons move across the nanowires. Here we discuss the potentialities of optimisation methodologies to design and select bacterial strains with desiderata properties. The optimisation methodologies establish also a relation between metabolism, network communication and computing. Moreover, we point to genetic design and synthetic biology as key areas to develop bacterial nano communication networks.