Pyrosequencing was used to investigate biofouling-causing microbial consortia at the community level in bulk sludge and cake layers within a full-scale membrane bioreactor (MBR). The analysis revealed Chao's estimates of total operational taxonomic units (OTUs) of 1726, 1806, and 1362 for bulk sludge, cake outer layer, and cake inner layer, respectively. The bulk sludge and cake outer layer OTUs clustered together, whereas the cake inner layer OTUs formed a separate group, indicating that environmental conditions affected the microbial community composition within the MBR. Bacteroidetes, Proteobacteria, and Chloroflexi were the dominant phyla in both the bulk sludge and the cake layers. Comparison at the genus level showed twelve distinct genera in the cake layers that were absent in bulk sludge. Twenty distinct genera were recorded in the inner cake layer. Those genera are likely the microbial colonization pioneers in full-scale membrane bioreactors. (C) 2016 Elsevier Ltd. All rights reserved.