A 26-day trial with 18 Pietrain×(Landrace×Duroc) pigs was conducted to investigate the effect of two dose levels of a specifically selected Bacillus spp. direct-fed microbial (DFM) product, on the emission of environmentally harmful gasses (methane, ammonia and hydrogen sulphide) from manure. Pigs were assigned to one of three treatments in a randomized complete block design according to their sex and initial BW. Each treatment contained three replications with two pigs per pen. The test treatments included a Bacillus spp. DFM containing 3×108 colony-forming unit/g, added at a low (250 mg/kg) and high (500 mg/kg) dose to an antibiotic free high fibre-based diet, and a non-supplemented control diet. Manure from pigs fed with the supplemented diets emitted lower amounts of atmospheric contaminants. The most significant reduction was observed with low DFM supplementation, in which methane and ammonia volatilization decreased (P<0.05) by >40% and 50%, respectively, on fresh weight basis in relation to the control. Microbiome analysis of manure by high through put sequencing techniques on eubacterial and archaeal 16S rRNA genes highlighted the complex interactions between indigenous gut microflora and inoculated Bacillus spp. The tested Bacillus DFM could be considered as a best available technique in reducing the environmental impacts of growing pigs fed with high fibre-based diets.