The microbial community structure of the cotton rat nose Diego Chaves-Moreno, 1 Iris Plumeier, 1 Silke Kahl, 1 Bernhard Krismer, 2,3 Andreas Peschel, 2,3 Andrew P. A. Oxley, 1† Ruy Jauregui 1‡ and Dietmar H. Pieper 1 * 1 Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany. 2 Interfaculty Institute of Microbiology and Infection Medicine, Cellular and Molecular Microbiology, Eberhard-Karls-University, Geschwister-Scholl-Platz, 72074, Tübingen, Germany. 3 German Center for Infection Research, Partner Site Tübingen, Tübingen, Germany. Summary The cotton rat nose is commonly used as a model for Staphylococcus aureus colonization, as it is both physiologically and anatomically comparable to the human nares and can be easily colonized by this organism. However, while the colonization of the human anterior nares has been extensively studied, the microbial community structure of cotton rat noses has not been reported so far. We describe here the microbial community structure of the cotton rat (Sigmodon hispidus) nose through next-generation sequencing of 16S rRNA gene amplicons covering the V1-V2 region and the analysis of nearly full length 16S rRNA genes of the major phylotypes. Roughly half of the microbial community was composed of two undescribed species of the genus Campylobacter, with phylotypes belonging to the genera Catonella, Acholeplasma, Streptobacillus and Capnocytophaga constituting the predominant community members. Thus, the nasal community of the cotton rat is uniquely composed of several novel bacterial species and may not reflect the complex interactions that occur in human anterior nares. Mammalian airway microbiota may, however, be a rich source of hitherto unknown microbes. Introduction It has been well established that the human anterior nares are the principal habitat for Staphylococcus aureus (Von Eiff et al., 2001) with roughly 20–30% of the human popu- lation persistently colonized by this organism which, thus, belongs to the normal and asymptomic microbial commu- nity (Van Belkum et al., 2009). As S. aureus is a major human pathogen and an important cause of death and morbidity worldwide, there are increasing efforts to better understand factors responsible for S. aureus carriage and the complex interplay between S. aureus and the host (Johannessen et al., 2012) with the goal to eliminate S. aureus nasal carriage (Perl et al., 2002; Van Rijen et al., 2008). As the study and manipulation of the in situ human microbiome is constrained by sampling difficulties (Marteau et al., 2001) as well as ethical issues and the immense interindividual differences in the microbiome composition (Pang et al., 2007), an alternative has been to use surrogate animal models such as mice (Hirayama and Itoh, 2005; Barc et al., 2008; Turnbaugh et al., 2009) and rats (Licht et al., 2007; Alpert et al., 2008; Wos-Oxley et al., 2012). The exploration of the intestinal microbiota has profited from complementary rodent models that allow defined manipulations and therapeutic interven- tions. The nose of cotton rats (Sigmodon hispidus) exhibit similar histological and colonization properties as the human nose (Burian et al., 2010) and is increasingly used for nasal colonization studies (Weidenmaier et al., 2004; Kokai-Kun, 2008). However, the cotton rat nasal microbiome and similarities or differences to human nasal microbiomes have yet to be described. A comparison of the fecal microbiota of 59 mammalian species to humans showed that host diet and phylogeny significantly influences bacterial community structure (Ley et al., 2008) and rodent gut communities differ signifi- cantly from those of humans (Wos-Oxley et al., 2012). The first murine skin microbiome analysed was the cuta- neous microbiota of the ear of C57BL/6 mice, which was indicated to mirror the microbiota found on human antecubital fossa (Grice et al., 2008). The authors reported that Proteobacteria formed the most abundant phylum with a predominance of Pseudomonas and Janthinobacterium. In contrast, a more recent analysis of the dorsal trunk skin of C57BL/6 mice indicated Received 15 May, 2015; revised 12 August, 2015; accepted 18 August, 2015. *For correspondence. E-mail dpi@helmholtz-hzi.de; Tel. +49 531 6181 4200; Fax +4953161815709. Present addresses: † South Australian Research and Development Institute – 2 Hamra Avenue, West Beach, SA 5024, Australia; ‡ AgResearch Grasslands, Tennent Drive, Palmerston North, New Zealand. Environmental Microbiology Reports (2015) 7(6), 929–935 doi:10.1111/1758-2229.12334 © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd