Diversity of anaerobic gut fungal populations analysed using ribosomal ITS1 sequences in faeces of wild and domesticated herbivores |
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| Authors: | Matthew J. Nicholson Christopher S. McSweeney Roderick I. Mackie Jayne L. Brookman Michael K. Theodorou |
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| Affiliation: | 1. Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystywth, Ceredigion SY23 3EB, UK;2. School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK;3. CSIRO Livestock Industries, Queensland Bioscience Precinct, Carmody Road, St. Lucia, Brisbane, Australia;4. Department of Animal Sciences, 1207 West Gregory Drive, University of Illinois, Champaign-Urbana, IL 61801, USA;1. Department of Evolutionary Microbiology, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;2. Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Sciences, Instytucka 3, PL 05-110 Jablonna, Near Warsaw, Poland;3. I.N.R.A., Station de Recherches sur la Nutrition des Herbivores, Centre de Recherches de Clermont-Theix, F 63122 St Genès Champanelle, Theix, France;4. Institute of Animal Physiology, Slovak Academy of Sciences, Soltesovej 4, SK 040 01 Kosice, Slovakia;5. Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK;6. Institute of Biological Environmental and Rural Science, Aberystwyth University, Ceredigion SY23 3DA, Wales, UK;7. Department of Microbial Ecology, Faculty of Life Sciences, University of Vienna, Althanstr. 14, A-1090 Wien, Austria;8. Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands;1. Agriculture and Agri-Food Canada, Lethbridge Research Centre, 5403 1st Ave S. Lethbridge, Alberta T1J 4B1, Canada;2. School of Environmental Sciences, University of Guelph Ridgetown Campus, Ridgetown, Ontario N0P 2C0, Canada;1. Institute of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020 Innsbruck, Austria;2. ACIB Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria;2. Institute of Biological Sciences, University of Wales, Aberystwyth, UK;3. Chair of Animal Hygiene, WZW, TUM, Weihenstephaner Berg 3, 85354 Freising, Germany |
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| Abstract: | Gut fungal-specific PCR primers have been used to selectively amplify the ITS1 region of gut fungal rDNA recovered from faeces of domestic and wild animals to investigate population diversity. Two different gel-based methods are described for separating populations of gut fungal rDNA amplicons, namely (1) denaturing gradient gel electrophoresis (DGGE) and (2) separation according to small size differences using Spreadex, a proprietary matrix for electrophoresis. Gut fungal populations were characterised by analysis of rDNA in faeces of seventeen domesticated and ten wild herbivores. Sequences derived from these gel-based characterisations were analysed and classified using a hidden Markov model-based fingerprint matching algorithm. Faecal samples contained a broad spectrum of fungi and sequences from five of the six recognised genera were identified, including Cyllamyces, the most recently described gut fungal genus, which was found to be widely distributed in the samples. Furthermore, four other novel groupings of gut fungal sequences were identified that did not cluster with sequences from any of the previously described genera. Both gel- and sequence- based profiles for gut fungal populations suggested a lack of geographical restriction on occurrence of any individual fungal type. |
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