Abstract
Birds represent a diverse and evolutionarily successful lineage, occupying a wide range of niches throughout the world. Like all vertebrates, avians harbor diverse communities of microorganisms within their guts, which collectively fulfill important roles in providing the host with nutrition and protection from pathogens. Although many studies have investigated the role of particular microbes in the guts of avian species, there has been no attempt to unify the results of previous, sequence-based studies to examine the factors that shape the avian gut microbiota as a whole. In this study, we present the first meta-analysis of the avian gut microbiota, using 16S rRNA gene sequences obtained from a range of publicly available clone-library and amplicon pyrosequencing data. We investigate community membership and structure, as well as probe the roles of some of the key biological factors that influence the gut microbiota of other vertebrates, such as host phylogeny, location within the gut, diet, and association with humans. Our results indicate that, across avian studies, the microbiota demonstrates a similar phylum-level composition to that of mammals. Host bird species is the most important factor in determining community composition, although sampling site, diet, and captivity status also contribute. These analyses provide a first integrated look at the composition of the avian microbiota, and serve as a foundation for future studies in this area.
Highlights
The role of the gut microbiota in shaping the health and physiology of vertebrate hosts is a well-established, highly exciting area in microbiology
The diversity and function of microbes in the gastrointestinal (GI) tract is an area of ongoing research, with recognized roles for the vertebrate microbiota in nutrition (Jin et al, 1998; Preest et al, 2003; Turnbaugh et al, 2006; Angelakis and Raoult, 2010; Stanley et al, 2012), gut development (Stappenbeck et al, 2002; Rahimi et al, 2009; Zhang et al, 2011; Cao et al, 2012) and regulation of host physiology (Bäckhed et al, 2004; Björkholm et al, 2009; Meinl et al, 2009). 16S rRNA gene sequencing has been employed in a range of studies to assess the diversity and phylogenetic relationships of gut microbes and this has proven to be a powerful tool for understanding the factors that shape microbial communities, due to both its informative and predictive potential
FUNCTIONAL PREDICTION OF GUT MICROBIOTA Following quality control of short-read data, sequences were mapped to operational taxonomic units (OTUs) using closed-reference OTU picking in QIIME 1.80 (Caporaso et al, 2010). 16S rRNA gene abundance levels were normalized against the known gene copy number for that OTU and function predictions made based on OTU membership using PICRUSt (Langille et al, 2013)
Summary
The role of the gut microbiota in shaping the health and physiology of vertebrate hosts is a well-established, highly exciting area in microbiology. 16S rRNA gene sequencing has been employed in a range of studies to assess the diversity and phylogenetic relationships of gut microbes and this has proven to be a powerful tool for understanding the factors that shape microbial communities, due to both its informative and predictive potential.
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