Cyanobacteria are notorious for their potential to produce hepatotoxic microcystins (MCs), but other bioactive compounds synthesized in the cells could be as toxic, and thus present interest for characterization. Ultra performance liquid chromatography and high-resolution accurate mass spectrometry (UPLC-QTOF-MS/MS) combined with untargeted analysis was used to compare the metabolomes of five different strains of the common bloom-forming cyanobacterium, Microcystis aeruginosa. Even in microcystin-producing strains, other classes of oligopeptides including cyanopeptolins, aeruginosins, and aerucyclamides, were often the more dominant compounds. The distinct and large variation between strains of the same widespread species highlights the need to characterize the metabolome of a larger number of cyanobacteria, especially as several metabolites other than microcystins can affect ecological and human health.Key Contribution: Metabolome variation between M. aeruginosa strains, highlighted by oligopeptide detection and identification, using a new, untargeted analytical workflow.Toxins 2019, 11, 723 2 of 18 and Planktothrix [17,18], MCs cause the inhibition of protein phosphatases 2A and 1 in vertebrates, which leads to an accumulation of phosphorylated proteins in cells. This accumulation can affect different metabolic pathways, including the inhibition of tumor suppressor proteins, cell proliferation and eventually, death [9,[19][20][21]. Despite many ecological impacts, the biological role of MCs within cyanobacteria remains unknown, which makes their control difficult. Remarkably, the cell concentrations of MCs in toxigenic taxa can reach those of chlorophyll a [22], the primary pigment involved in photosynthesis in cyanobacteria, algae and higher plants.Thus far over 269 variants have been identified with molecular weights varying between 880 and 1200 Da [10,23]. Amino acid variation in various positions of the cyclic molecule affects the degree of toxicity in vertebrates, as shown by LD 50 values between 50 µg/kg (MC-LA) and 800 µg/kg (MC-RR) in mice after intraperitoneal injection [16]. Microcystins are thus potentially more lethal to vertebrates than several highly potent poisons, such as sarin [24]. Increasing toxic effects are observed when hydrophobic amino acids (e.g., methylated amino acids) are present in the molecule, which can facilitate MC penetration into the tissues [25]. However, the ADDA moiety of the molecule (3-amino-9-methoxy-10-phenyl-2,6,8-trimethyldeca-4,6-dienoic acid), found in all MC variants, is known to have a major role in the toxicity [25].In addition to microcystins, cyanobacteria can produce a wide range of bioactive compounds. These include an extraordinary diversity of oligopeptides (e.g., cyanopeptolins, aeruginosins, microviridins) [26]. Several may also be bioactive or even toxic to vertebrates since many are produced through the same metabolic pathway as the MCs [27] and have similar structures [28]. Besides the public and environmental health needs for more research on these co...