It depends on type of biofilter applied and pollutant elimination targets. Some biofilters are used for gaseous pollutants elimination by especial strains of microorganisms like pseudomonases species. In wastewater treatment all thermophilic pathogens can be found depends on substrate, nutrients pH, and source of wastewater discharge. But they are removed in next steps of treatment. In order to detect an especial strain of microorganism among groups is used PCR techniques. For further information you can refer to this useful book.