Evolutionary genomics of host-microbe interactions

Research output: ThesisDoctoral Thesis (compilation)


The microbes living inside hosts have highly important consequences for host health and fitness. From the host’s perspective, some microbes exhibit mutualistic tendencies, others parasitic, and some commensal, but this is context-dependent and opportunistic lifestyles are widespread in nature. Our knowledge of how hosts interact molecularly with different microbes is, however, poor, and little research has been done on non-model organisms from a genomic and community-wide perspective. In this PhD thesis, I investigate host-microbe interactions from multiple angles, and utilize high-throughput sequencing techniques to paint a broad, overarching picture of the relationship between hosts and microbes. My PhD comprised two related projects, 1) host-microbiome interactions and 2) host-parasite interactions. In the former, I have evaluated how to best sample and measure the gut microbiomes of avian hosts (Paper I and II). Different sections of the ostrich gastrointestinal tract were characterized and shown to harbour divergent microbial communities (Paper I, II, and IV). I have further demonstrated that the gut microbiome of juvenile ostriches is colonized in a successional manner and gradually develops over time (Paper III), and is strongly linked to growth and mortality (Paper III and IV). In the second project I described the avian transcriptome response to malaria infection over time and to parasites with different virulence (Paper V and VI). Birds with malaria infection experience a range of transcriptional changes that involves for example the immune system, stress response, cell death regulation, and regulatory genes. To evaluate the molecular response of the malaria parasite, I assembled the blood transcriptome of Plasmodium ashfordi and showed that parasite gene expression is host-specific (Paper VII). This transcriptome was subsequently used, together with a genome assembly of Haemoproteus tartakovskyi, to construct a phylogeny of haemosporidian parasites which showed strong support for a monophyletic clade of mammalian malaria parasites (Paper VIII). Finally, the assembled transcriptome and genome were utilized to identify thiamine biosynthesis enzymes in avian Plasmodium (Paper IX), and to demonstrate that the avian Plasmodium parasites exhibit the most AT-rich genes of eukaryotes (Paper X). In summary, this work offers new insights into host-microbiome and host-parasite interactions, and enables a greater understanding of the multifaceted relationship between hosts and their microbes.


  • Elin Videvall
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Biological Sciences


  • host, microbiota, avian malaria, ostrich, parasite, dual RNA-seq
Original languageEnglish
Supervisors/Assistant supervisor
Award date2018 Apr 6
Place of PublicationLund
  • Lund University, Faculty of Science, Department of Biology
Print ISBNs978-91-7753-577-5
Electronic ISBNs978-91-7753-578-2
Publication statusPublished - 2018
Publication categoryResearch

Bibliographic note

Defence details Date: 2018-04-06 Time: 13:00 Place: Lecture hall “Blå hallen”, Ecology building, Sölvegatan 37, Lund External reviewer(s) Name: Perkins, Susan Title: Dr. Affiliation: Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA ---

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Related research output

Videvall, E., Maria Strandh, Engelbrecht, A., Cloete, S. & Charlie K. Cornwallis, 2018 May, In : Molecular Ecology Resources. 18, 3, p. 424-434

Research output: Contribution to journalArticle

Videvall, E., 2018 Jan 23, In : Microbial Genomics.

Research output: Contribution to journalArticle

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