Penguins are a distinctive group of flightless seabirds found exclusively in the southern hemisphere, occupying an extensive geographical range extending from the Galapagos Islands to the Antarctic continent (Stonehouse 1975). Penguins, like all seabirds, spend most of their lives at sea, only coming to land to breed and molt (Stonehouse 1975; Reilly 1994; Roeder et al. 2002). Penguins have a unique digestive physiology that enables them to store large amounts of undigested food, build up large reserves of adipose tissue (fat), and store large amounts of protein and lipids for long periods of fasting during breeding and molting (Stonehouse 1975; Reilly 1994; Roeder et al. 2002). The gastrointestinal (GI) tract contains a diverse and complex microbial ecosystem made up of hundreds of different species of microorganisms, which has coevolved with its host (Collins et al. 1994; Koutsos and Arias 2006; Lumpkins et al. 2008; Torok et al. 2008). The GI microbiota has a profound influence on the nutritional, physiological, immunological, and metabolic processes of the host (Mackie et al. 1999; Zoetendal et al. 2004a,b; Musso et al. 2011) playing a significant role in energy harvest, fat metabolism, secretion and synthesis of nutrients, vitamins, amino acids, and the production of short-chain fatty acids from the diet consumed by the host (Collins et al. 1994; Suau et al. 1999; Flint et al. 2007; Torok et al. 2008). Rawls et al. (2004, 2006) identified that in the absence of microbial colonization, the GI tract results in an immature and arrested differentiation. Furthermore, research has shown that the absence of a GI microbiota reduces an animal's ability to secrete and absorb essential vitamins and nutrients from their diet (Penders et al. 2006; Blaut and Clavel 2007).
To date, the mammals and poultry GI microbiota have been extensively studied and shown to be dominated by two main phyla: Firmicutes (usually 60–80% of total composition) and Bacteroidetes (usually 20–40% of total composition) in multiple vertebrate species including mammals (such as humans, rodents, and pinnipeds), poultry, and livestock (i.e., cattle and pigs). (Ley et al. 2005; Gabriel et al. 2006; Ley et al. 2006a,b, 2008a,b; Glad et al. 2010a,b). The avian microbiota, however, comprise approximately 640 species from 140 genera, with only 10% of the avian microbiota being cultured in the laboratory (Torok et al. 2008). However, much of what we know about the avian microbiota is based from research on poultry (DeGolier et al. 1999; Zhu et al. 2002; Apajalahti and Kettunen 2005).
Despite the enormous amount of data available on the importance of microbes in mammals, it is surprising that so little research has been carried out on avian species, with the exception of poultry (chicken, turkey) (Zhu et al. 2002; Apajalahti and Kettunen 2005). To date, the composition and role of this ecosystem remain incomplete for many seabird species, including penguins, with earlier studies being based on the use of culture dependant techniques to provide description on the composition and abundance of members of the microbial community (Potti et al. 2002; Thouzeau et al. 2003; Zoetendal et al. 2004a,b; Bonnedahl et al. 2005) or to look for specific microbial pathogens, such as Salmonella (Olsen et al. 1996; Palmgren et al. 2000), Campylobacter (Quessy and Messier 1992; Broman et al. 2000; Hubalek 2004; Bonnedahl et al. 2005; Leotta et al. 2006a,b; Griekspoor et al. 2009), and Pasteurella multocida (DeLisle et al. 1990; Leotta et al. 2003; Weimerskirch 2004; Leotta et al. 2006a,b). However, these techniques do not accurately reflect the actual microbial composition but only those that can be cultured using selective media and as a result, providing an inaccurate account on the composition and abundance of microbes from complex biological systems such as the GI tract. Therefore, earlier studies on microbial composition of penguins may be considered incomplete. For this reason, many microbiologists have turned to molecular methods, such as quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene pyrosequencing, to characterize and explore the microbial composition of complex ecosystems, such as the GI tract, ocean, and soil. These methods are extensively used in studies of humans and other vertebrate species (predominantly livestock and poultry). For penguins, the use of molecular-based methods to examine the microbial composition is limited to two studies: Zdanowski et al. (2004) and Banks et al. (2009). Zdanowski et al. examined the microbial composition of freshly deposited Adélie penguin guano, whereas Banks et al. examined the influence of geographical separation and host phylogeny on the microbial composition of Adélie penguins. Both studies documented that Adélie penguins are highly dominated by Firmicutes (41%), Actinobacteria (35%), and Proteobacteria (12.5%), while Banks et al. (2009) also noted the presence of Bacteroidetes (5%). In addition, Banks et al. (2009) documented that a negative correlation exists between host relatedness and microbial community similarity and no significant correlation between geographical location and microbial composition, indicating that host phylogeny influences the microbial composition of an individual.
Characterization of the vastly diverse ecosystem of the GI tract is the first step in exploring its role in digestive physiology, health, and disease (Eckburg et al. 2005). Therefore, this study aims to use quantitative real-time PCR and 16S rRNA, sequencing to characterize the microbial composition and diversity of the fecal microbiota of four species of penguins.