Filtration is an important industrial production processes to treat particle dispersion systems. In this paper we show the filtration characteristics of suspensions of agglomerated streptobacteria (chain bacteria), Bacillus amyloliquefaciens, by asymmetric depth filter membranes of poly(L-lactic acid) (PLLA). The permeation flux was higher in the filtration with the depth filter membrane than in that with a screen filter membrane at a transmembrane pressure of 50-150 kPa. The bacterial cell layer had a high compressibility index of the specific resistance (0.60) in the filtration with the screen filter membrane. However, the cell layer formed in the internal structure of the depth filter membrane of PLLA showed a low apparent compressibility index (0.11). Scanning electron micrographs revealed that the agglomerated cells were captured on the depth filter membrane at 10 kPa while those cells were captured within the membrane at 150 kPa. Thus the filtration performance with the depth filter membrane increased at higher transmembrane pressures. The biodegradable PLLA membrane showed high performance in the filtration of bacterial cell suspensions and has an advantage in disposal after use because it can be compostable with bacterial cells clogged in the membrane.