Comparative analyses of the digestive tract microbiota of New Guinean passerine birds
Digestive tract microbiota (DTM) play many important functions in animals and the evolution of this symbiosis has enabled many animal groups to exploit novel niches. The DTM of mammals and insects has been well studied, but our understanding of avian DTM is limited to commercial animals and a few charismatic species such as penguins and hoatzin. My MSc project focused on increasing our understanding of passerine (Order Passeriformes) DTMs through investigating the DTM in multiple digestive tract compartments of nine passerine bird species in Papua New Guinea, using MiSeq amplicon sequencing of the V4 region of 16s rRNA gene. A high diversity of bacteria was found within the passerine digestive tract and in most species few bacterial OTUs dominated the digestive tract compartments. There was a significant different between DTM of different species but DTM did not clustered according to the digestive tract compartments. However, the DTM of different compartments from same individuals clustered close to each other. Species with similar feeding guilds (insectivores vs. omnivores) had similar microbial communities and some omnivorous DTMs clustered within insectivorous DTMs indicating the flexibility in the diet of omnivores. Except for Ifrita kowaldi, Insectivorous DTMs were dominated by Firmicutes and were low in diversity compared to the Proteobacteria-dominated omnivorous DTMs. When looking at the 20 most abundant bacterial genera in insectivores, low-diverse stomach regions were dominated by few genera while the number of genera increased at the end regions of the digestive tract. Even though the diversity of DTM did not change notably along the digestive tract of omnivores, the dominant genera in different compartments changed along the digestive tract. Furthermore, the inter-species variability of DTMs in omnivores was higher than the variation among insectivores. Overall I found that the diet plays a major role in shaping the species-specific passerine DTMs. I also found evidence for change in dominant bacterial groups between different digestive tract compartments in well-sampled species, indicating the importance of investigating the DTM of the entire digestive tract in order to capture the total diversity in DTM.