Influence of external and internal environmental factors on intestinal microbiota of wild and domestic animals

Abstract

The intestinal microbiota has a profound effect on health and well-being of an individual. Microbiota composition has been shown to be associated with many aspects of a host’s intestinal health, however, at the same time lifestyle and genetic background strongly influence gut microbiota composition. The aim of this thesis was to contribute to understanding of forces that shape microbiota composition and its properties in wild and domestic animals. In the scope of this work we investigated composition and influence of various factors on intestinal microbiota of seven wild animal species and three breeds of domestic pigs. Chapter 1 provided state-of-the-art background information about microbial communities, their influence on health and a long history of prokaryote - eukaryote co-existence. This chapter also gave an overview of methods that are used for investigation of complex microbial communities. In Chapter 2 we investigated influence of occupancy and consequent differences in diet on gut microbiota of congeneric lemur species dwelling in ecologically distinct areas of Madagascar. Using amplicon sequencing of bacterial 16S rRNA genes we profiled faecal microbiota composition of free living red-fronted lemurs (E. rufifrons), common brown lemurs (E. fulvus) and red-bellied lemurs (E. rubriventer). We showed that environmental conditions of the habitation area were strongest modulators of microbiota, overshadowing the effects of genetic background, gender and social group identity. Lemurs of the same species but delving in different areas, and those exposed to different environmental conditions, showed to have distinct microbiota profiles, reflecting the importance of the habitation area in microbial consortium modulation. In Chapter 3 we build on knowledge obtained in the course of research described in Chapter 2 and greatly extended the sampling effort covering a larger number of lemur species and locations across Madagascar. In this chapter we more specifically addressed the influence of seasonality and logging on gut ecology of lemurs. Besides profiling of faecal microbiota we quantified the amount of eggs of nematodes from genera Callistoura and Lemuricola. We found that seasonality had a profound effect on microbiota composition and could be explained by variations in environmental conditions between wet and dry seasons. We furthermore observed a significantly higher bacterial diversity and prevalence of Lemuricola spp. in previously logged forest areas. In addition, we discovered a small but significant influence of nematodes’ egg load on overall microbiota composition. Research described in Chapter 4 of this thesis investigated relationships between genetic background and gut microbiota composition in pedigree pigs. To our knowledge this is the first large study that investigates variations in cecum microbiota of Italian Landrace (ILA), Italian Duroc (IDU) and Italian Large White (ILW) pigs that were kept in a controlled environment and have a defined genetic background. We demonstrated that microbiota correlated significantly with the pigs’ breed identity. We showed that a number of microbial genus-level taxa traditionally associated with health homeostasis, such as Ruminococcaceae UCG-005, Lachnospiraceae XPB1014, Oscillospira and Faecalibacterium were differentially abundant between breed groups. Resistance to antibiotics is a widespread phenomenon in the microbial world, and its development and spread across different environments is receiving increasing attention. In Chapter 5 we explored the correlation between the composition of faecal microbiota and its resistome in wild Great White-Toothed Shrews and Wood Mice delving around pig farms. Using a combination of 16S rRNA gene amplicon and shotgun metagenomic sequencing we profiled microbiota phylogenetic and resistome composition. We found that abundance and diversity of antibiotic resistance genes strongly correlated with the phylogenetic composition of microbiota and differed between investigated species. Finally, Chapter 6 summarised and discussed findings presented in this thesis and provided an outlook towards future research perspectives and needs. In addition, the chapter provided data that was not included in the previous chapters but was used to further illustrate discussed points.