Microorganisms exhibit an amazing variety of metabolic processes. Understanding how macro evolutionary processes like innovation and diversification operate in the microbial world is necessary to comprehend the origin of this variety. The regulation of microbial resource usage by metabolic networks can occur via a variety of processes, such as horizontal gene transfers or the de novo evolution of enzymes and pathways. Environmental variables, selective pressures, and limitations imposed by the genetic design of metabolic networks all work together to control this process. A significant part of microbial innovation and diversification may also be attributed to the process of niche construction, in which organisms actively alter their own and one another's habitats and selective pressures. However, the fundamental mechanisms by which niche formation affects the patterns of microbial macroevolution are still completely unknown. Here, we describe a number of novel theories and lines of research and offer metabolic modelling techniques that may enable us to investigate extensive empirical Genotype-Phenotype-environment (G-P) spaces and analyse the macro-evolutionary consequences of niche formation. This brief essay should encourage greater systematic and quantitative characterisation of macro evolutionary patterns and processes in microbial metabolism, in our opinion.