A native isolate, 9C, identified as Rhodococcus ruber (Genbank Accession number - KY029073) was studied for dibenzothiophene degradation and subsequent bio-desulphurization of three different sulphur bearing materials (NE coal containing organic sulphur; lignite containing pyritic sulphur and a calcined petroleum-coke) of Indian origin. The isolate could degrade 0.25 mM DBT through the 4S pathway within 7 days. Preliminary studies for sulphur removal using the 9C isolate indicated NE coal to be more amenable (29% sulphur removal) followed by Lignite (15.87%) and CPC (14.83%) respectively. Characterization through XRD and FTIR along with the proximate and ultimate analysis of all the samples provided more insights into the changes in calorific values as well as the chemical constitution of the samples following microbial treatment. Owing to the amenability of NE coal, the effect of time, size fraction and pulp density were optimized. The best bio-desulphurization conditions for NE coal indicated 36% total sulphur removal (organic-53%, pyritic-18% and sulphate sulphur-14% respectively). Analytical characterization studies confirmed that the energy value of the NE coal was not affected due to bio-desulphurization, rather it contributed towards an increase in gross calorific value from 6698 cal/g to 6812 cal/g following microbial treatment. (C) 2017 Elsevier Ltd. All rights reserved.