The novel oligopeptide utilizing species M3/9, its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses.

Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative strain, M3/9 was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9 possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9 was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9 and closely related type strains, genome sequence comparisons were performed. M3/9 harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9 in other environments, large-scale fragment recruitments with the M3/9 genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.