Effect of time and diet change on the bacterial community structure throughout the gastrointestinal tract and in faeces of the northern brown bandicoot, Isoodon macrourus
Patricia J. O’Hara A C , Athol V. Klieve A B , Peter J. Murray A , Anita J. Maguire B , Diane Ouwerkerk B and Karen Harper B
+ Author Affiliations
- Author Affiliations
A Wildlife Science Unit, Faculty of Science, The University of Queensland, Gatton Campus, Qld 4343, Australia.
B Agri-Science Queensland, EcoScience Precinct, Dutton Park, Qld 4102, Australia.
C Corresponding author. Email: patricia.ohara@uq.edu.au
Australian Journal of Zoology 64(1) 48-60 https://doi.org/10.1071/ZO15078
Submitted: 25 November 2015 Accepted: 10 May 2016 Published: 31 May 2016
Abstract
A significant gap, in not only peramelid nutritional physiology but marsupial nutrition as a whole, is the lack of information relating to microorganisms of the gastrointestinal tract. This research is a preliminary investigation that will provide a baseline for comparisons among peramelids. The high degree of 16S rRNA gene clones identified in this research that are closely related to culturable bacteria suggests that additional research will enable a more complete description of the gastrointestinal bacteria of I. macrourus. Most identifiable clones belonged to Clostridium and Ruminococcus. This research has confirmed that the hindgut of I. macrourus, the caecum, proximal colon and distal colon, are the main sites for microbial activity.
References
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403–410.| Basic local alignment search tool.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK3MXitVGmsA%3D%3D&md5=150bf5d904643ecdd1fbd8aa74748c85CAS | 2231712PubMed |
Berry, V., and Gascuel, O. (1996). On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain. Molecular Biology and Evolution 13, 999–1011.
| On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK28XltlSmsb8%3D&md5=d9d7b7a69b34bb29042c658570b8ef48CAS |
Bond, P. L., Hugenholtz, P., Keller, J., and Blackall, L. L. (1995). Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Applied and Environmental Microbiology 61, 1910–1916.
| 1:CAS:528:DyaK2MXlsFyktLk%3D&md5=ca5dd82ab915ded56044d58133cb1401CAS | 7544094PubMed |
Gibson, L. A., and Hume, I. D. (2000). Digestive performance and digesta passage in the omnivorous greater bilby, Macrotis lagotis (Marsupialia: Peramelidae). Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology 170, 457–467.
| Digestive performance and digesta passage in the omnivorous greater bilby, Macrotis lagotis (Marsupialia: Peramelidae).Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD3Mzgt12msg%3D%3D&md5=202f4b2b2352c34192ea0b526e083646CAS | 11083529PubMed |
Gordon, G. (2004). Northern brown bandicoot. In ‘The Mammals of Australia’. (Ed. R. Strahan.) pp. 174–175. (Reed New Holland: Sydney.)
Gott, M. (1996). Ecology of the northern brown bandicoot, Isoodon macrourus: reproduction and resource use in a heathland population. Ph.D. Thesis, University of New South Wales, Sydney.
Guindon, S., and Gascuel, O. (2003). A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52, 696–704.
| A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood.Crossref | GoogleScholarGoogle Scholar | 14530136PubMed |
Harper, K. J. (2011). The association between rumen microbial protein production with rumen microbial community structure. Ph.D. Thesis, The University of Queensland, Brisbane.
Harrison, J. L. (1963). The food of some Innisfail mammals. Proceedings of the Royal Society of Queensland 73, 37–43.
Hata, D. J., and Smith, D. S. (2004). Blood group B degrading activity of Ruminococcus gnavus alpha-galactosidase. Artificial Cells, Blood Substitutes, and Immobilization Biotechnology 32, 263–274.
| Blood group B degrading activity of Ruminococcus gnavus alpha-galactosidase.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2cXksVSmsbw%3D&md5=ee386374929c2ecc76b925ea6f7e3656CAS | 15274432PubMed |
Hongoh, Y., Sato, T., Noda, S., Ui, S., Kudo, T., and Ohkuma, M. (2007). Candidatus Symbiothrix dinenyphae: bristle-like Bacteriodales ectosymbionts of termite gut protists. Environmental Microbiology 9, 2631–2635.
| Candidatus Symbiothrix dinenyphae: bristle-like Bacteriodales ectosymbionts of termite gut protists.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXht1GqsLzI&md5=481363fbca356726f5f37bc3a0587b94CAS | 17803785PubMed |
Hume, I. D. (1999). ‘Marsupial Nutrition.’ (Cambridge University Press: Cambridge.)
Jackson, S. (2003). Bandicoots. In ‘Australian Mammals: Biology and Captive Management’. (Ed. S Jackson.) pp. 127–144. (CSIRO Publishing: Melbourne.)
Klieve, A. V., O’Leary, M. N., McMillen, L., and Ouwerkerk, D. (2007). Rumniococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet. Journal of Applied Microbiology 103, 2065–2073.
| Rumniococcus bromii, identification and isolation as a dominant community member in the rumen of cattle fed a barley diet.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXnvFantw%3D%3D&md5=3b19c704026df6c39cdc31081f306f94CAS | 18045390PubMed |
Kocherginskaya, S. A., Cann, I. K. O., and Mackie, R. I. (2005). Denaturing gradient gel electrophoresis. In ‘Methods in Gut Microbial Ecology for Ruminants’. (Eds H. P. S. Makkar and C. S. McSweeney.) pp. 119–128. (Springer: Dordrecht.)
Lane, D. J. (1991). 16S/23S rRNA sequencing. In ‘Nucleic Acid Techniques in Bacterial Systematics’. (Eds E. Stackebrandt and M. Goodfellow.) pp. 115–175. (Academic Press: Chichester.)
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948.
| Clustal W and Clustal X version 2.0.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXhtlaqsL%2FM&md5=82b5486455d074ccdd038bf573427ce9CAS | 17846036PubMed |
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., and Gordon, J. I. (2008). Evolution of mammals and their gut microbes. Science 320, 1647–1651.
| Evolution of mammals and their gut microbes.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXnt1Oju7o%3D&md5=2ae6a66e24de032a8d7c8ed3412d0021CAS | 18497261PubMed |
McClelland, K. L., Hume, I. D., and Soran, N. (1999). Responses of the digestive tract of the omnivorous northern brown bandicoot, Isoodon macrourus (Marsupialia: Peramelidae), to plant- and insect-containing diets. Journal of Comparative Physiology B: Biochemical, Systemic, and Environmental Physiology 169, 411–418.
| Responses of the digestive tract of the omnivorous northern brown bandicoot, Isoodon macrourus (Marsupialia: Peramelidae), to plant- and insect-containing diets.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD3c%2Fhs1ymtQ%3D%3D&md5=2d9394ee811455d851f33e1ee2870d35CAS | 10549141PubMed |
Mollet, C., Drancourt, M., and Raoult, D. (1997). rpoB sequence analysis as a novel basis for bacterial identification. Molecular Microbiology 26, 1005–1011.
| rpoB sequence analysis as a novel basis for bacterial identification.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXls1E%3D&md5=150c722f15d615745adaebd69bc5f8fbCAS | 9426137PubMed |
Muyzer, G., de Waal, E. C., and Uitterlinden, A. G. (1993). Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Applied and Environmental Microbiology 59, 695–700.
| 1:CAS:528:DyaK3sXit1Kktrk%3D&md5=4b90f898f9b332720f2073b25465be74CAS | 7683183PubMed |
Nei, M., Kumar, S., and Takahashi, K. (1998). The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proceedings of the National Academy of Sciences of the United States of America 95, 12390–12397.
| The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DyaK1cXmsl2rurg%3D&md5=6a32b418d3fe30cb31839779b01eff08CAS | 9770497PubMed |
Norman, R. J. (1998). Reptiles and birds in the diets of the eastern barred bandicoot Perameles gunnii and the northern brown bandicoot Isoodon macrourus. Victorian Naturalist 115, 18–20.
Ouwerkerk, D., Klieve, A. V., Forster, R. J., Templeton, J. M., and Maguire, A. J. (2005). Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus. Letters in Applied Microbiology 41, 327–333.
| Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD28XhvV2hu74%3D&md5=29e999bf255e153f41e1d7a2c1040191CAS | 16162139PubMed |
Posada, D. (2008). jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25, 1253–1256.
| jModelTest: phylogenetic model averaging.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD1cXotlKgsb4%3D&md5=af9cf65d1a4d02e37a96bd0c98051c55CAS | 18397919PubMed |
Rautio, M., Eerola, E., Väisänen-Tunkelrott, M.-L., Molitoris, D., Lawson, P., Collins, M. D., and Jousimies-Somer, H. (2003). Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources. Systematic and Applied Microbiology 26, 182–188.
| Reclassification of Bacteroides putredinis (Weinberg et al., 1937) in a new genus Alistipes gen. nov., as Alistipes putredinis comb. nov., and description of Alistipes finegoldii sp. nov., from human sources.Crossref | GoogleScholarGoogle Scholar | 12866844PubMed |
Rieu-Lesme, F., Morvan, B., Collins, M. D., Fonty, G., and Willems, A. (1996). A new H2/CO2-using acetogenic bacterium from the rumen: description of Ruminococcus schinkii sp. nov. FEMS Microbiology Letters 140, 281–286.
| 1:CAS:528:DyaK28XjvFGgs7s%3D&md5=b4fda79bc5ef3857ed378c09084da8b5CAS | 8764491PubMed |
Sakamoto, M., Kitahara, M., and Benno, Y. (2007). Parabacteroides johnsonii sp. nov., isolated from human faeces. International Journal of Systematic and Evolutionary Microbiology 57, 293–296.
| Parabacteroides johnsonii sp. nov., isolated from human faeces.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD2sXjsVKrsrw%3D&md5=50a873426b73b78897717479ce559372CAS | 17267966PubMed |
Sandars D. F. 1952
Šimůnek, J., Kopečný, J., Hodrová, B., and Bartoňová, H. (2002). Identification and characterization of Clostridium paraputrificum, a chitinolytic bacterium of human digestive tract. Folia Microbiologica 47, 559–564.
| Identification and characterization of Clostridium paraputrificum, a chitinolytic bacterium of human digestive tract.Crossref | GoogleScholarGoogle Scholar | 12503404PubMed |
Spellerberg, I. F. (2008). Shannon–Wiener Index. In ‘Encyclopedia of Ecology’. (Eds S. E. Jorgensen and B. Fath.) pp. 3249–3252. (Academic Press: Oxford.)
Stewart, C. S., Flint, H. J., and Bryant, M. P. (1997). The rumen bacteria. In ‘The Rumen Microbial Ecosystem’. 2nd edn. (Ed. P. N. Hobson.) (Blackie Academic & Professional: Melbourne.)
Swofford, D. L. (1998). ‘PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).’ 4th edn. (Sinauer Associates: Sunderland, MA.)
Tolosa, M. X. (2006). Molecular ecology of rumen bacterial populations in steers fed molasses diets. Ph.D. Thesis, The University of Queensland, Brisbane.
Yu, Z., and Forster, R. J. (2005). Nucleic acid extraction, oligonucleotide probes, and PCR methods. In ‘Methods in Gut Microbial Ecology for Ruminants’. (Eds H. P. S. Makkar and C. S. McSweeney.) pp. 81–104. (Springer: Dortrecht.)
Zoetendal, E. G., Collier, C. T., Koike, S., Mackie, R. I., and Gaskins, H. R. (2004). Molecular ecological analysis of the gastrointestinal microbiota: a review. The Journal of Nutrition 134, 465–472.
| 1:CAS:528:DC%2BD2cXhtFKlsbs%3D&md5=e5bfe3c3ff5081186fbae6db889df1b4CAS | 14747690PubMed |
