Integrity of the human faecal microbiota following long-term sample storage

Journal article


Kia, Elahe, Mackenzie, Brett W., Middleton, Danielle, Lau, Anna, Waite, David W., Lewis, Gillian, Chan, Yih Kai, Silvestre, Marta, Cooper, Garth J. S., Poppitt, Sally D. and Taylor, Michael W.. (2016). Integrity of the human faecal microbiota following long-term sample storage. PLoS ONE. 11(10), pp. 1 - 8. https://doi.org/10.1371/journal.pone.0163666
AuthorsKia, Elahe, Mackenzie, Brett W., Middleton, Danielle, Lau, Anna, Waite, David W., Lewis, Gillian, Chan, Yih Kai, Silvestre, Marta, Cooper, Garth J. S., Poppitt, Sally D. and Taylor, Michael W.
Abstract

In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D), faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014. Given the relative antiquity of these samples (~14 years), we sought to evaluate DNA quality and comparability to freshly collected human faecal samples. Following the extraction of bacterial DNA, gel electrophoresis indicated that our DNA extracts were more sheared than extracts made from freshly collected faecal samples, but still of sufficiently high molecular weight to support amplicon-based studies. Likewise, spectrophotometric assessment of extracts revealed that they were of high quality and quantity. A subset of bacterial 16S rRNA gene amplicons were sequenced using Illumina MiSeq and compared against publicly available sequence data representing a similar cohort analysed by the American Gut Project (AGP). Notably, our bacterial community profiles were highly consistent with those from the AGP data. Our results suggest that when faecal specimens are stored appropriately, the microbial profiles are preserved and robust to extended storage periods.

Year2016
JournalPLoS ONE
Journal citation11 (10), pp. 1 - 8
PublisherPublic Library of Science
ISSN1932-6203
Digital Object Identifier (DOI)https://doi.org/10.1371/journal.pone.0163666
Scopus EID2-s2.0-84991233196
Open accessOpen access
Page range1 - 8
Research GroupMary MacKillop Institute for Health Research
Publisher's version
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© 2016 Kia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Place of publicationUnited States of America
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Chan, Yih, Davis, Paul, Poppitt, Sally, Sun, Xueying, Greenhill, Nicholas, Krishnamurthi, Rita, Przerpiorski, Aneta, McGill, Anne-Thea and Krissansen, Geoffrey. (2012). Influence of tail versus cardiac sampling on blood glucose and lipid profiles in mice. Laboratory Animals. 46(2), pp. 142 - 147. https://doi.org/10.1258/la.2011.011136
Copper(ii)-selective chelation improves function and antioxidant defences in cardiovascular tissues of rats as a model of diabetes: Comparisons between triethylenetetramine and three less copper-selective transition-metal-targeted treatments
Lu, J., Gong, D., Choong, Y. S., Xu, H., Chan, Kai, Chen, X., Fitzpatrick, S., Glyn-Jones, S., Zhang, S., Nakamura, T., Ruggiero, K., Obolonkin, V., Poppitt, S. D., Phillips, A. R. J. and Cooper, G. J. S.. (2010). Copper(ii)-selective chelation improves function and antioxidant defences in cardiovascular tissues of rats as a model of diabetes: Comparisons between triethylenetetramine and three less copper-selective transition-metal-targeted treatments. Diabetologia. 53(6), pp. 1217 - 1226. https://doi.org/10.1007/s00125-010-1698-8
No evidence of an effect of alterations in dietary fatty acids on fasting adiponectin over 3 weeks
Lithander, Fiona E., Keogh, Geraldine F., Wang, Yu, Cooper, G. J. S., Mulvey, Tom B., Chan, Kai, McArdle, Brian H. and Poppitt, S D.. (2008). No evidence of an effect of alterations in dietary fatty acids on fasting adiponectin over 3 weeks. Obesity. 16(3), pp. 592 - 599. https://doi.org/10.1038/oby.2007.97
Postprandial response of adiponectin, interleukin-6, tumor necrosis factor-alpha, and C-reactive protein to a high-fat dietary load
Poppitt, S. D., Keogh, Geraldine F., Lithander, Fiona E., Chan, Kai, Wang, Yu, Mulvey, Tom B., McArdle, Brian H. and Cooper, G J. S.. (2008). Postprandial response of adiponectin, interleukin-6, tumor necrosis factor-alpha, and C-reactive protein to a high-fat dietary load. Nutrition. 24(4), pp. 322 - 329. https://doi.org/10.1016/j.nut.2007.12.012
A copper(II)-selective chelator ameliorates diabetes-evoked renal fibrosis and albuminuria, and suppresses pathogenic TGF-β activation in the kidneys of rats used as a model of diabetes
Gong, D., Lu, J., Chen, X., Reddy, S., Crossman, D. J., Glyn-Jones, S., Choong, Y.-S., Kennedy, J., Barry, B., Zhang, S., Chan, Y.-K., Ruggiero, K., Phillips, A. R. J. and Cooper, G. J. S.. (2008). A copper(II)-selective chelator ameliorates diabetes-evoked renal fibrosis and albuminuria, and suppresses pathogenic TGF-β activation in the kidneys of rats used as a model of diabetes. Diabetologia. 51(9), pp. 1741-1751. https://doi.org/10.1007/s00125-008-1088-7
Triethylenetetramine and metabolites: levels in relation to copper and zinc excretion in urine of healthy volunteers and type 2 diabetic patients
Lu, Jun, Chan, Kai, Gamble, Gregory D., Poppitt, S D., Othman, Asma A. and Cooper, G. J. S.. (2007). Triethylenetetramine and metabolites: levels in relation to copper and zinc excretion in urine of healthy volunteers and type 2 diabetic patients. Drug Metabolism and Disposition. 35(2), pp. 221 - 227. https://doi.org/10.1124/dmd.106.012922
Determination of triethylenetetramine (TETA) and its metabolites in human plasma and urine by liquid chromatography-mass spectrometry (LC-MS)
Lu, Jun, Chan, Kai, Poppitt, S. D. and Cooper, G J. S.. (2007). Determination of triethylenetetramine (TETA) and its metabolites in human plasma and urine by liquid chromatography-mass spectrometry (LC-MS). Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences. 859(1), pp. 62 - 68. https://doi.org/10.1016/j.jchromb.2007.09.001
Effect of high-fat meals and fatty acid saturation on postprandial levels of the hormones ghrelin and leptin in healthy men
Poppitt, S. D., Leahy, F. E., Keogh, G. F., Wang, Y, Mulvey, T B., Stojkovic, M, Chan, Kai, Choong, Y S., McArdle, B H. and Cooper, G. J. S.. (2006). Effect of high-fat meals and fatty acid saturation on postprandial levels of the hormones ghrelin and leptin in healthy men. European Journal of Clinical Nutrition. 60(1), pp. 77 - 84. https://doi.org/10.1038/sj.ejcn.1602270
Molecular changes evoked by triethylenetetramine treatment in the extracellular matrix of the heart and aorta in diabetic rats
Gong, Deming, Lu, Jun, Chen, Xiuyin, Choong, Soon Y., Zhang, Shaoping, Chan, Kai, Glyn-Jones, Sarah, Gamble, Gregory D., Phillips, Anthony R. J. and Cooper, Garth J. S.. (2006). Molecular changes evoked by triethylenetetramine treatment in the extracellular matrix of the heart and aorta in diabetic rats. Molecular Pharmacology. 70(6), pp. 2045 - 2051. https://doi.org/10.1124/mol.106.028605
Demonstratuon of hyperglycemia-driven pathogenic abnormality of copper homeostasis in diabetes and its reversibility by selective chelation
Cooper, G. J. S., Chan, Kai, Dissanayake, Ajith M., Leahy, Fiona E., Keogh, Geraldine F., Frampton, Chris M., Gamble, Gregory D., Brunton, Dianne H., Baker, John R. and Poppitt, S D.. (2005). Demonstratuon of hyperglycemia-driven pathogenic abnormality of copper homeostasis in diabetes and its reversibility by selective chelation. Diabetes. 54(5), pp. 1468 - 1476.
Regeneration of the heart in diabetes by selective copper chelation
Cooper, G. J. S., Phillips, Anthony R. J., Choong, Soon Y., Leonard, Bridget L., Crossman, David J., Brunton, Dianne H., Saafi, Etuate L., Dissanayake, Ajith M., Cowan, Brett R., Young, Alistair A., Occleshaw, Christopher J., Chan, Kai, Leahy, Fiona E., Keogh, Geraldine F., Gamble, Gregory D., Allen, Grant R., Pope, Adele J., Boyd, Peter D. W., Poppitt, S D., ... Baker, John R.. (2004). Regeneration of the heart in diabetes by selective copper chelation. Diabetes. 53(9), pp. 2501 - 2508.
Developmental competence of nuclear transfer cow oocytes after direct injection of fetal fibroblast nuclei
Lacham-Kaplan, Orly, Diamente, Maria, Pushett, David, Lewis, Ian and Trounson, Alan. (2000). Developmental competence of nuclear transfer cow oocytes after direct injection of fetal fibroblast nuclei. Cloning. 2(2), pp. 55 - 62. https://doi.org/10.1089/152045500436078