The prevalence and phylogenetic description of fungal organisms and their role as part of the intestinal ecosystem have not yet been studied extensively in dogs. This study evaluated the fungal microbiome of 19 dogs (12 healthy dogs and 7 dogs with acute diarrhea) using fungal tag-encoded FLX-Titanium amplicon pyrosequencing. Five distinct fungal phyla were identified, with Ascomycota (medians: 97.9% of obtained sequences in healthy dogs and 98.2% in diseased dogs) and Basidiomycota (median 1.0% in healthy dogs and median 0.5% in diseased dogs) being the most abundant fungal phyla. A total of 219 fungal genera were identified across all 19 dogs with a median (range) of 28 (4–69) genera per sample. Candida was the most abundant genus found in both the diseased dogs (median: 1.9%, range: 0.2%–38.5% of sequences) and healthy dogs (median: 5.2%, range: 0.0%–63.1% of sequences). Candida natalensis was the most frequently identified species. No significant differences were observed in the relative proportions of fungal communities between healthy and diseased dogs. In conclusion, fecal samples of healthy dogs and dogs with acute diarrhea harbor various fungal genera, and their role in gastrointestinal health and disease warrants further studies. 1. Introduction Recent molecular-phylogenetic studies have revealed diverse microbial communities in the canine gastrointestinal (GI) tract and have emphasized the importance of the intestinal microbiota for gastrointestinal health [1]. The intestinal microbiota plays a vital role in the health of the GI tract, participates in the development of the host immune system, and also provides protection from invading pathogens [2]. Several studies have characterized the bacterial communities in the canine GI tract in health and disease [3–5]. However, limited information is available about the prevalence and classification of other members of the intestinal microbiome, such as fungal organisms. Previous studies that have described fungal organisms in the canine GI tract have either used culture based methods [6, 7], have utilized molecular-phylogenetic methods on pooled intestinal samples [8, 9], or have analyzed only a limited number of fungal sequences [10]. Studies in humans have suggested that the fungal microbiome may play a role in chronic GI disorders [11, 12]. Therefore, a more detailed description of the fungal microbiome (mycobiome) is needed to better understand the role of fungi in the GI tract of healthy dogs and dogs with GI disease. The aim of this study was to describe the fungal communities present in fecal
References
[1]
J. S. Suchodolski, “Companion animals symposium: microbes and gastrointestinal health of dogs and cats,” Journal of Animal Science, vol. 89, no. 5, pp. 1520–1530, 2011.
[2]
A. S. Neish, “Microbes in gastrointestinal health and disease,” Gastroenterology, vol. 136, no. 1, pp. 65–80, 2009.
[3]
J. S. Suchodolski, J. F. Garcia-Mazcorro, S. Unterer et al., “The fecal microbiome in dogs with acute diarrhea and idiopathic inflammatory bowel disease,” PLoS ONE, vol. 7, no. 12, Article ID e51907, 2012.
[4]
J. F. Garcia-Mazcorro, J. S. Suchodolski, K. R. Jones et al., “Effect of the proton pump inhibitor omeprazole on the gastrointestinal bacterial microbiota of healthy dogs,” FEMS Microbiology Ecology, vol. 80, no. 3, pp. 624–636, 2012.
[5]
J. A. Bell, J. J. Kopper, J. A. Turnbull, N. I. Barbu, A. J. Murphy, and L. S. Mansfield, “Ecological characterization of the colonic microbiota of normal and diarrheic dogs,” Interdisciplinary Perspectives on Infectious Diseases, vol. 2008, Article ID 149694, 17 pages, 2008.
[6]
Y. Benno, H. Nakao, K. Uchida, and T. Mitsuoka, “Impact of the advances in age on the gastrointestinal microflora of beagle dogs,” The Journal of Veterinary Medical Science, vol. 54, no. 4, pp. 703–706, 1992.
[7]
S. Mentula, J. Harmoinen, M. Heikkil？ et al., “Comparison between cultured small-intestinal and fecal microbiotas in beagle dogs,” Applied and Environmental Microbiology, vol. 71, no. 8, pp. 4169–4175, 2005.
[8]
S. Handl, S. E. Dowd, J. F. Garcia-Mazcorro, J. M. Steiner, and J. S. Suchodolski, “Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats,” FEMS Microbiology Ecology, vol. 76, no. 2, pp. 301–310, 2011.
[9]
K. S. Swanson, S. E. Dowd, J. S. Suchodolski et al., “Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice,” The ISME Journal, vol. 5, no. 4, pp. 639–649, 2011.
[10]
J. S. Suchodolski, E. K. Morris, K. Allenspach et al., “Prevalence and identification of fungal DNA in the small intestine of healthy dogs and dogs with chronic enteropathies,” Veterinary Microbiology, vol. 132, no. 3-4, pp. 379–388, 2008.
[11]
S. J. Ott, T. Kühbacher, M. Musfeldt et al., “Fungi and inflammatory bowel diseases: alterations of composition and diversity,” Scandinavian Journal of Gastroenterology, vol. 43, no. 7, pp. 831–841, 2008.
[12]
T. Kühbacher, S. J. Ott, U. Helwig et al., “Bacterial and fungal microbiota in relation to probiotic therapy (VSL#3) in pouchitis,” Gut, vol. 55, no. 6, pp. 833–841, 2006.
[13]
J. S. Suchodolski, C. G. Ruaux, J. M. Steiner, K. Fetz, and D. A. Williams, “Application of molecular fingerprinting for qualitative assessment of small-intestinal bacterial diversity in dogs,” Journal of Clinical Microbiology, vol. 42, no. 10, pp. 4702–4708, 2004.
[14]
M. E. Lucero, A. Unc, P. Cooke, S. Dowd, and S. Sun, “Endophyte microbiome diversity in micropropagated Atriplex canescens and Atriplex torreyi var griffithsii,” PLoS ONE, vol. 6, no. 3, Article ID e17693, 2011.
[15]
V. Gontcharova, E. Youn, R. D. Wolcott, E. B. Hollister, T. J. Gentry, and S. Dowd, “Black box chimera check (B2C2): a windows-based software for batch depletion of chimeras from bacterial 16S rRNA gene datasets,” The Open Microbiology Journal, vol. 4, pp. 47–52, 2010.
[16]
J. S. Suchodolski, S. E. Dowd, V. Wilke, J. M. Steiner, and A. E. Jergens, “16S rRNA gene pyrosequencing reveals bacterial dysbiosis in the duodenum of dogs with idiopathic inflammatory bowel disease,” PLoS ONE, vol. 7, no. 6, Article ID e39333, 2012.
[17]
J. S. Suchodolski, J. Camacho, and J. M. Steiner, “Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis,” FEMS Microbiology Ecology, vol. 66, no. 3, pp. 567–578, 2008.
[18]
A. J. Scupham, L. L. Presley, B. Wei et al., “Abundant and diverse fungal microbiota in the murine intestine,” Applied and Environmental Microbiology, vol. 72, no. 1, pp. 793–801, 2006.
