Abstract
Gut microbial communities play a fundamental role in health and disease, but little is known about the gut microbiota of pet bird species. This is important to better understand the impact of microbes on birds’ health but may also be relevant in a context of zoonoses. Total genomic DNA samples from pooled fecal samples from 30 flocks (4–7 pet birds per flock) representing over 150 birds of six different species (two Passeriformes: Northern Mockingbird (Mimus polyglottos) and Zebra Finch (Taeniopygia guttata), and four Psittaciformes: Lovebird (Agapornis, different species), Cockatiel (Nymphicus hollandicus), Red-rumped Parrot (Psephotus haematonotus), and Rose-ringed Parakeet (Psittacula krameri) were used for 16S rRNA gene analysis. Several taxa were found to be different among the bird species (e.g., lowest median of Lactobacillus: 2.2% in Cockatiels; highest median of Lactobacillus: 79.4% in Lovebirds). Despite marked differences among individual pooled samples, each bird species harbored a unique fecal bacterial composition, based on the analysis of UniFrac distances. A predictive approach of metagenomic function and organism-level microbiome phenotypes revealed several differences among the bird species (e.g., a higher proportion of proteobacteria with the potential to form biofilms in samples from Northern Mockingbirds). The results provide a useful catalog of fecal microbes from pet birds and encourage more research on this unexplored topic.
Highlights
Our results indicate that, with the exception of NH samples, the number and diversity of OTUs were similar among the pet birds studied, including domesticated wild representatives such as Northern Mockingbirds, but that each bird species harbored a unique combination of bacterial taxa in feces
Our results provide a useful catalog of fecal bacteria in pet birds living in their regular environment
The data suggest that each bird species carry a specific set of microbes in feces, and based on the available literature, it is likely that these microbes are representatives of the distal gut
Summary
The avian gastrointestinal tract (GI tract) is inhabited by millions of microorganisms (the gut microbiota) that are important to study because of their involvement in health, immunity, adaptation, and overall survival in the environment [2,3]. Microorganisms can be studied using traditional culture techniques, but cultivable communities have little utility in contemporary microbial ecology partly due to our inability to grow them in vitro [8]. Molecular methods (e.g., DNA sequencing of universal marker genes) do not depend on cultivable communities and offer a suitable alternative to study microbial life in a wide range of environments. Molecular methods have been used to study the chicken GI microbiota mostly for commercial reasons [9,10]
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