The complex and dynamic nature of soil makes the assessment of soil biodiversity difficult. Findings presented here form part of a wider scheme to develop ‘bio-sampling’ methods based on earthworm cast analysis. Our overall aim is to achieve high throughput, metabolic procedures to monitor soil biological activity and, in particular, to investigate the potential for gene transfer from plants to soil micro-organisms and its consequences. Here experiments were carried out to assess several potential foods (oat grain, fresh and aged tobacco) for Lumbricus terrestris and Lumbricus rubellus, species being considered for later experimentation. These experiments provided temporal microbial composition and activity data in ageing casts, an environment where gene transfer might occur. For both earthworm species, there was a predictable microbial succession (from bacteria to fungi) as casts aged. Species also differed in their cast microbiology in response to food type, but less so with more processed food. Analysis of ageing casts by FT-IR spectroscopy coupled with cluster analysis indicated greater chemical changes in casts of L. terrestris than for L. rubellus, regardless of food type.