Granules are large, self-supporting biofilms that form naturally in high-rate anaerobic treatment systems and are extremely important to reactor functionality. The biofilm structure has functional and phylogenetic layering, important both scientifically and to function. Fermenters, found on the surface of anaerobic granules, are associated with granule strength and uptake of the primary substrate. Compared to acetogens and methanogens, very limited work has been done on fermenters, particularly in granules. Due to their high diversity and difficulty in selective isolation, fermenters are best studied through culture-independent techniques. Until now, the microbial distribution could only be analysed through sectioning and microscopic analysis with fluorescent in situ hybridization. The whole granule could be analysed by DNA extraction and microbial community profiling methods but this did not provide spatial information. This thesis develops a method to remove microbes selectively from successive spatial layers through hydraulic shearing and demonstrates its application on anaerobic granules of three different types (collected from brewery, cannery and dairy wastewater treatment plants). Outer layers, in particular, could be selectively sheared as confirmed by FISH and TRFLP. Further analysis with 454 pyrosequencing showed that a shift in dominant population from presumptive fermenters (such as Bacteroidales and Anaerolinea) in outer layers to syntrophs (such as Syntrophomonas and Geobacter) in inner layers, with progressive changes through the depth. The method was further leveraged through covariance based deep metagenomic sequencing, with metagenomic analysis used so far to align phylogenetic information. This leveraged the shear based method to provide covariance information for the metagenomic analysis. Shear based phylogenetic and metagenomic aligned well internally and with cryosection-FISH analysis. Information provided could be used with more specific probes (particularly Bacteroidales and Anaerolinea) to confirm that these organisms were key fermenters and highly abundant in outer layers. This study indicated that fermenters were a relatively diverse but discrete population within the granule. Further analysis of the metagenomic information is required to identify roles of specific microbes. The phylogenetic approach was also used in a reactor study with different feeds (gelatine, glucose, VFA) to identify how the microbial population shifted during growth of fermenters. While physical strength was not influenced, the dominant fermentative groups were strongly impacted by the feed matrix, and inner layer community less changed, but still substantially affected.