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Diet and Gut Microbiome of African Viverrids Malou Fabricius Rægaard Storm Emilia Marie Rolander Langkjær

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Diet and Gut Microbiome of African Viverrids Malou Fabricius Rægaard Storm Emilia Marie Rolander Langkjær UNIVERSITY OF COPENHAGEN Diet and gut microbiome of African viverrids Malou Fabricius Rægaard Storm Emilia Marie Rolander Langkjær Supervisor: Michael Poulsen & Kristine Bohmann Submitted: 18. December 2018 Name of department: Biology Author(s): Malou Fabricius Rægaard Storm & Emilia Marie Rolander Langkjær Title and subtitle: Diet and gut microbiome of African viverrids Diet assessment and comparison of African viverrids; Civettictis civetta and Genetta spp. in southern Africa Gut microbiome of African viverrids reflect the omnivorous diet of the host Topic description: Lorem ipsum in eternum, per ardua ad astra in ipsum in eternum, per ardua ad astra in ipsum in eternum, per ardua ad astra in ipsum in eternum, per ardua ad astra. Supervisor: Michael Poulsen & Kristine Bohmann Submitted on: 18. December 2018 Grade: Number of characters: 151,613 Table of Contents General Introduction ........................................................................................................................... 4 Background ................................................................................................................................................... 4 Use of next generation sequencing to detect multiple taxa ........................................................................... 7 Study species ................................................................................................................................................ 8 Study Sites .................................................................................................................................................. 11 Introducing the manuscripts ........................................................................................................................ 12 Chapter 1: Manuscript 1 ................................................................................................................... 14 Diet assessment and comparison of African viverrids; Civettictis civetta and Genetta spp. in southern Africa ................................................................................................................................. 14 Abstract ....................................................................................................................................................... 15 Introduction ................................................................................................................................................ 16 Materials and Methods ................................................................................................................................ 18 Results ........................................................................................................................................................ 23 Discussion ................................................................................................................................................... 32 Data deposition ........................................................................................................................................... 36 References .................................................................................................................................................. 36 Supplementary material .............................................................................................................................. 40 Chapter 2: Manuscript 2 ................................................................................................................... 48 Gut microbiome of African viverrids reflect the omnivorous diet of the host .................................. 48 Abstract ....................................................................................................................................................... 49 Introduction ................................................................................................................................................ 50 Materials and methods ................................................................................................................................ 51 Results ........................................................................................................................................................ 54 Discussion ................................................................................................................................................... 59 References .................................................................................................................................................. 63 Supplementary material .............................................................................................................................. 66 Conclusions and perspectives ........................................................................................................... 75 References ........................................................................................................................................ 77 1 Preface This thesis was carried out at the University of Copenhagen from September 4th 2017 to December 18th 2018. The project was supervised by Michael Poulsen from the section of Ecology and Evolution, department of Biology, and Kristine Bohmann from the EvoGenomics group at the Natural History Museum. Furthermore, this project was co-supervised by Ara Monadjem from the University of Eswatini. The work was funded by the Carlsberg foundation with additional funding from the EvoGenomics MSc thesis grant, the Oticon foundation, the Danish microbiology societies travel grant and the Lemvigh-Müller foundation. The data presented in this thesis are faecal samples from Civettictis civetta and Genetta spp. collected in collaboration with Lajuma Research Centre, South Africa, Gorongosa National Park, Mozambique, and the Savanna Research Centre at Mbuluzi Game Reserve, Eswatini. Field work was carried out from the 11th of September to the 3rd of December 2017. DNA extractions and lab work for the gut microbiome analysis was conducted at the Section of Ecology and Evolution, Department of Biology, University of Copenhagen. Amplicon sequencing of the 16S rRNA gene was carried out at the Microbial System Molecular Biology lab, University of Michigan. Lab work for the diet analysis was conducted at the EvoGenomics group at the Natural History Museum, University of Copenhagen. Sequencing was carried out at the National High-throughput sequencing Centre. Both authors collaborated on all field and lab work. Overall, the aim of this master thesis was to investigate, if using metabarcoding could optimise the study of diet in omnivorous species. Furthermore, the aim was to investigate the link between diet composition and gut microbiome through DNA sequencing. The thesis contains a general introduction, presenting the background of the project and aims. Furthermore, it contains two manuscripts (manuscript 1 written by Malou Fabricius Rægarrd Storm and manuscript 2 by Emilia Marie Rolander Langkjær). In manuscript 1, we investigate the diet of C. civetta and Genetta spp. and in manuscript 2 we investigate their gut microbiome. Lastly, the thesis contains a perspectives and conclusions of the project as a whole. 2 Acknowledgements First, we would like to say thanks to our main supervisors Michael Poulsen and Kristine Bohmann for your guidance and support throughout this project. Thank you for your reliability throughout our work, and for your engagement in our wish to make this project a reality. A big thanks to our fellow researchers at Gorongosa National Park, the Savannah Research Center and Lajuma Research Centre for the help with the sampling; especially thanks to Jason Denlinger, Ana Gledis Miranda, Celina Alfredo Dias, Phumlile Simelane, Ryan van Huyssteen, Melissa Petford and Bibi and Jabu Linden for all of your help. Furthermore, we would like to say a big thanks to Rafael Rodrigues da Costa, Kasun Bodawatta, Christina Islas Lynggaard, Luisa Nielsen, Stine Raith Richter and Martin Nielsen for help in the lab, with the data analysis and the writing process. Also, we would like to say thanks to the eDNA group and the UCPH Social and Symbiotic Evolution Group for feedback throughout the project. Lastly, a special thanks to our co-supervisor Ara Monadjem for your interest in our project and for putting us in contact with the research center in Eswatini as well as our collaborators at Gorongosa, as well as supervision throughout the project. 3 General Introduction Background Species across the world play different roles in ecosystems, depending on different aspects of their respective ecology, such as habitat choice (Edelaar, Siepielski and Clobert, 2008) and feeding habits. Species belong to different dietary niches and studies are often focused on organisms feeding on a single category of food. These include predators; feeding on vertebrates and invertebrates (Carbone et al., 1999), herbivores; feeding on plant material (KowalcZyk et al., 2011), detritivores; feeding on detritus (Dobson et al., 2002) and frugivores; feeding on fruits (Jordano et al., 2007). Species dietary niches influence the ecosystem in various ways, depending on diet choice and composition (Duffy et al., 2007; Pompanon et al., 2012). For example, the diet of a given species in an ecosystem may influence species interactions. Therefore , knowing the diet composition of a species can help shed light on how it influences the habitat choice,
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