Gut microbiota in health and disease

Water fleas of the genus Daphnia are hosts for many vertically and/or horizontally transmitted parasites, which are mostly harmful for their hosts reducing reproduction and survival, and influencing the evolution and dynamic of host populations, and interaction with other species. A significant host- parasite interaction (genotype specificity, adaptation, defence mechanisms) exist, however, the role of the gut microbiota for host defence and parasite virulence is unclear. Gut microbiota (microbial community) are associated with most multicellular organisms and plays an important role in nutrition, development, health and disease. Nowadays, only a small minority of gut microbes can be cultured in the laboratory, but culture-independent high-throughput sequencing techniques greatly expand our knowledge about the diversity and function of microbiota. The main goals of this project are to understand the interaction, community structure and dynamics of gut microbiota in health and disease using water fleas of the genus Daphnia, a model system that is excellent suited to comparative and experimental work. To tackle my project, I will apply various techniques such as fluorescence in situ hybridization, denaturing gradient gel electrophoresis, multiplex amplicon pyrosequencing, symbiont-specific PCR assays, quantitative PCR, as well as phylogenetic analyses and bioinformatics. Furthermore, this system allows manipulation of microbiota of individual hosts, allowing experimental tests of hypotheses. I will investigate a common, but phylogenetically uncharacterized parasite causing the White Fat Cell Disease in Daphnia magna in respect to mode of infection, phylogeny, inter-population dynamics and host microbiota. In addition, using a comparative microbiota approach, I will study the community composition of indigenous (healthy) microbiota in comparison to the community composition of infected hosts. Furthermore, I will test the effect of manipulated gut microbiota on sensitivity of parasite infection. Finally, I will test the influence of the gut community composition in parasite resistance. Illuminating this tripartite symbiosis (host parasite microbiota) will have impact far beyond the chosen model system, ranging for ecology, limnology, microbiology, evolutionary biology to applied science (ecotoxicology) and medicine.

Zooplankton is a hotspot of aquatic as well as pathogenic bacteria. For instance, water fleas of the genus Daphnia are hosts for many transmitted parasites that are harmful for their hosts. Furthermore, Daphnia harbours a large number of intestinal microbes. The role of the gut microbiota (microbial communities) for host defense and parasite virulence is largely unknown. The microbiota of Daphnia consists predominantly of bacteria belonging to the Proteobacteria, which play a role in host nutrition. In my project, I showed that the Daphnia microbiota contains beneficial bacteria, as well as bacteria, which have no or a negative effect on host fitness. In unhealthy animals infected by a microsporidium, the microbiota composition did not influence the host and pathogen growth, or the host offspring number. Interestingly, this microsporidium compensated the beneficial effect of different microbiota compositions; therefore, we hypothesize that this pathogen may alter the microbiota composition of its host. In contrast, the microbiota composition of animals infected by a Daphnia virus significantly influenced the offspring number by reducing or increasing the host fecundity. In nature, the microbiota-virus- interaction may influence the host population size, which may affect the whole ecosystem. The increase of offspring number during infection may show an adaption between the virus and its host. We showed that the microbiota composition influences the host offspring production during infection depending on the respective pathogen. Furthermore, we investigated the first genome sequence of a Daphnia virus belonging to the virus family Iridoviridae, a widely spread group of dsDNA viruses containing economically and ecologically emerging pathogens of fish and frogs, respectively. The virus genome is rather large (~289 kbp) and contains 367 predicted coding sequences. Interestingly, the Daphnia virus encodes proteins probably playing a role in mRNA capping for mRNA stability and efficient translation, representing the first invertebrate iridovirus that conducts mRNA capping. In addition, the virus contains unique genes probably involved in host-pathogen interaction and pathogenicity likely representing genes important for the infection of the water flea D. magna. Furthermore, some proteins of the Daphnia virus are potential candidates for horizontal gene transfer events between the virus and its host, which may play a role in the evolution and adaption to novel environmental conditions likely helping the ancestor of this Daphnia virus to infect and replicate in a novel host. This study should further be relevant to researchers working in the fields of virology, limnology, zoology, ecology, evolutionary biology, conservation and symbiosis research, and might help to develop novel strategies to fight iridoviruses containing emerging pathogens and disease vectors, which are mostly arthropods such as Daphnia.