Browsing by Subject "gut microbiome"

The gut microbiome of mammals plays many important roles in the host, including preventing colonization of pathogens, maintaining intestinal homeostasis, helping digest nutrients and even affecting host behavior. The composition of mammalian gut microbiota varies greatly between individuals, species and in time. When a mammal is born, it acquires its first, mostly anaerobic, gut microbiota through maternal transmission in the birth canal. After the initial transmission of bacteria, host genotype, especially genes related to immunity, become an important factor that helps determine which species get to stay in the gut and prosper. In adulthood age, sex, diet, disease and contact with others all become important shapers of microbiome composition. Since microbial communities are comparable to any macroecological communities, they can be explained through ecological theories. For example, community assembly theory can help distinguish the effects of input (e.g. transmission) from selective processes (e.g. filtering host genotype) on gut microbiome composition. Community assembly can lead to multiple stable equilibria determined by which species colonized the area first (“priority effect”), emphasizing the importance of early transmission, such as that maternal transmission birth. Metacommunity theory on the other hand, views a large ecosystem as a mosaic of patches and can be helpful in describing the composition of the microbiome in adult individuals. In this thesis, I use community assembly theory and metacommunity theory as a framework to explore determinants of individual gut microbiome composition in wild European wood mice (Apodemus sylvaticus). Specifically, I set out to investigate how much of the gut microbial community variation was accountable for host relatedness and how much of this effect is due maternal transmission (input) versus host genotype (filtering). To find out more about what affects the composition of the gut microbiome in wild animals, I collected both tissue and microbiome samples from wood mice in the Wytham woods research area near Oxford, Great Britain. In addition to the data collected in Wytham, I was given another similarly collected dataset from Silwood Park. My study questions were: What proportion of gut microbiome composition in wood mice is determined by host genotype? Do mothers affect their offspring’s microbiome more than fathers through maternal transmission of bacteria? DNA extractions and mouse genotyping were done by me in the MES laboratory at the University of Helsinki. Sequencing of microbial DNA was done by my co-supervisor at Royal Veterinary College in London. Microbiome similarity was compared to host genetic relatedness using Mantel test and likelihood ratio tests on linear models with dyadic data (comparing relatedness and microbiome similarity of each pair). According to the results, related individuals had a significantly more similar microbiome in Wytham, but not in Silwood. In both populations, microbiome similarity was also affected significantly by age and home range area. The general trend was, that mother-pup and fullsib pairs had more similar microbiome than unrelated pairs (though this effect was significant only in Wytham) and father-pup pairs had a more different microbiome than unrelated pairs (though this effect was significant only in Silwood). All data combined, mice had significantly more similar microbiome with their mother than father. The higher similarity between mother-pup pairs and full siblings can be explained by maternal transmission and postnatal physical contact. Since the father’s effect is purely genetic, their microbiome differing from their offspring even more than from unrelated individuals could be explained by lack of physical contact and different age. Alternatively, females could even be choosing to mate with males with different immunogenotypes, and thus more different microbiome from themselves than expected by chance. Based on my results, transmission of bacteria during and shortly after birth is a key factor shaping microbiome composition and it might even account for the “genetic” effect seen in previous studies.