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Humboldt-Universitaet zu Berlin - Ecology and Evolution of molecular Parasite-Host Interactions

Ecology and Evolution of molecular Parasite-Host Interactions

Prof. Dr. Emanuel Heitlinger

 

Main projects of my group

 

Eimeria and other Pathogens in a house mouse hybrid zone

My group's work combines evolutionary questions with mechanistic aspects of the interaction between parasites and their hosts. For this purpose we aim to establish a model system for coevolution and local adaptation approachable both in its original ecological settings and in laboratory experiments.

The hybrid zone of the two subspecies of the house mouse Mus musculus musculus und Mus musculus domesticus often determines population structure of parasites and can thus be regarded as a natural laboratory for adaptations and coevolution. It is possible to identify parasite genotypes adapted to a subspecies on the background of the well investigated mouse genomes. We use the house mouse as an approachable model host in both the field and the laboratory and establish its parasites as novel parts of a model system for coevoltionary processes.

We have made first progress establishing such a system using whole genome sequencing of the mouse parasite Eimeria falciformis. Eimeria, with over one thousand species, is the largest genus in the phylum Apicomlexa. These species are highly host-specific and tightly adapted, each to its own of a huge variety of vertebrates. Up zu 16 Eimeria species have been described in house mice and are found at high prevalence throughout their hosts range, including the hybrid zone.

My group tests in how far the population structure of these Eimeria species coincides with the host hybrid zone. We analyze whether specific genetic elements in Eimeria strains and species correlate with host genotypes and whether this is driven by an „adaptive introgression“ via hybridization.

To this end we analyze neutral marker genes as well as candidate genes for parasite-host interaction and additionally develop high throughput approaches („genome wide capture“) for unbiased genome scans with an ultra dense set of makers.

Many pathogenicity factors, well investigated in the close relative Toxoplasma gondii, are found in the genomes of Eimeria spp. We test the hypothesis, that especially variation in these factors determines the specificity of parasite strains. We analyze in a comparative genomics approach whether identified candidate regions and genes for a reciprocal adaptation are hot spots of differentiation acting as speciation genes.

In future experiments we will compare naturally occurring compatible and incompatible combinations of host and parasite strains in cross-infections. We will analyze how the identified combinations of host and parasite genotypes influence parasitological, histological and immunity related phenotypes. We will especially compare gene expression data from field studies with these infection experiments and infections with immunized and immune deficient (knock-out) mice. This work has the potential to link phenotypes of a productive infection with genotypes of both host and parasite and to provide an understanding of the underlying molecular mechanisms.

 

Collaborating scientists:

Joelle Gouy de Bellocq, Stuart J.E. Baird and Jaroslav Pialek (Institute of Vertebrate Biology of the Academy of Sciences of the Czech Republic).

Richard Lucius, Nishith Gupta and Simone Spork (Humboldt University Berlin)

 

 

Metabarcoding analyses of parasite community ecology

It is often necessary to go beyond a „one host one parasite“ system to infer reciprocal adaptation and to include the whole parasite community of a host species and its ecology in the analysis. As a first goal we want to test whether the occurrence of a specific parasite correlates with ecological and immunological parameters of the host and therefore need a fine resolution in diagnosing parasite species or strains. Secondly we want to study interactions between components of the parasite community and the interactions of this community composition with the mentioned ecological and immunological parameters of host individuals. To achieve this we need both comprehensive diagnosis of infections and high sample sizes.

To this end we develop DNA-sequencing based high throughput methods to investigate non-invasive samples (i.e. fecal samples) for the presence of eukaryote parasites and other pathogens based on marker genes. These methods use highly conserved regions to enrich crude DNA extractions for marker genes of parasites. The enriched DNA contains variable in addition to the conserved regions, which are sequenced on high throughput platforms (currently predominantly Illumina MiSeq).

We develop universal and specific primers and probes, which are sensitive for a broad variety of pathogens, while avoiding binding to host genes. We work on solutions for bioinformatic data analysis to complement the wet-lab approaches and to make full use of the generated information.

We amplify for example large proportions of the rDNA gene clusters for all bigger taxonomic groups of parasites using parallelized microfluidics PCRs (the Fuidigm Access Array), resulting in sufficient genetic resolution to allow differentiation of parasite species. Doing so we provide a universal high throughput assay for the diagnosis of eukaryote parasites and other pathogens from fecal samples to groups of the IZW. The obtained data has the quality to not only group parasites into described species but to also define taxonomic units for unsubscribed species.

We want to expand the approach in future to allow quantitative assessment of parasite infections using correlations between DNA-content and classical infection parameters (i.e. egg counts). We will try to complement these classical microscopy methods for parasite eggs with particle differentiation and counting or flow cytometry to scale such approaches to the throughput of our sequencing based assay.

 

We apply these metabarcoding methods to target host species relevant for ecology and conservation collaborating with groups within the IZW:

1. We analyze the relation between reproduction, disease, immune and stress status of hyenae with the occurrence of different parasites and parasite strains. In this host the social status of the animals within the pack is considered and another focus is on the complex influence of dry and wet seasons, the resulting migrations and changes in prey spectrum on the parasite fauna.

2. We genotype the parasites of the wolf using intestinal contents of wolves found dead and wolf feces. We analyze whether wolves are infected by parasites of farm and companion animals and reciprocally whether new parasites are introduced by wolves, where they threaten humans and their animals.

3. We also asses the complete parasite community of the house mouse sampled in the project described above. This will allow us to include the effect of additional pathogens in our analysis of a correlation of host and parasite genotypes with immunological parameters and to control for them. Furthermore this provides an unbiased approach to screen for all parasites corresponding in their population structure to that of the house mouse hybrid zone.

 

Collaborating scientists: Oliver Krone and Ines Lesniak (IZW, wolf project)

Collaborating scientists: Marion East und Heribert Hofer (IZW, hyena project)