The Journal of Nutrition Nutrient Physiology, Metabolism, and Nutrient-Nutrient Interactions Resistant Starches Protect against Colonic DNA Damage and Alter Microbiota and Gene 1–3 Expression in Rats Fed a Western Diet Michael A. Conlon,4–6 Caroline A. Kerr,4,7 Christopher S. McSweeney,4,8 Robert A. Dunne,4,9 Janet M. Shaw,4,7 Seungha Kang,4,8 Anthony R. Bird,4–6 Matthew K. Morell,5,10 Trevor J. Lockett,4,7 Peter L. Molloy,4,7 Ahmed Regina,5,10 Shusuke Toden,4–6 Julie M. Clarke,4,6 and David L. Topping4–6* 4CSIRO Preventative Health, 5Food Futures National Research Flagships, and 6CSIRO Food and Nutritional Sciences, Adelaide, South Australia, Australia; 7CSIRO Food and Nutritional Sciences, North Ryde, New South Wales, Australia; 8CSIRO Livestock Industries, St Lucia, Queensland, Australia; 9CSIRO Mathematics, Informatics and Statistics, Glen Osmond, South Australia, Australia; and 10CSIRO Plant Industry, Black Mountain, Australian Capital Territory, Australia Abstract Resistant starch (RS), fed as high amylose maize starch (HAMS) or butyrylated HAMS (HAMSB), opposes dietary protein- induced colonocyte DNA damage in rats. In this study, rats were fed Western-type diets moderate in fat (19%) and protein (20%) containing digestible starches [low amylose maize starch (LAMS) or low amylose whole wheat (LAW)] or RS [HAMS, HAMSB, or a whole high amylose wheat (HAW) generated by RNA interference] for 11 wk (n = 10/group). A control diet included 7% fat, 13% protein, and LAMS. Colonocyte DNA single-strand breaks (SSB) were signiﬁcantly higher (by 70%) in rats fed the Western diet containing LAMS relative to controls. Dietary HAW, HAMS, and HAMSB opposed this effect while raising digesta levels of SCFA and lowering ammonia and phenol levels. SSB correlated inversely with total large bowel SCFA, including colonic butyrate concentration (R2 = 0.40; P = 0.009), and positively with colonic ammonia concentration (R2 = 0.40; P = 0.014). Analysis of gut microbiota populations using a phylogenetic microarray revealed proﬁles that fell into 3 distinct groups: control and LAMS; HAMS and HAMSB; and LAW and HAW. The expression of colonic genes associated with the maintenance of genomic integrity (notably Mdm2, Top1, Msh3, Ung, Rere, Cebpa, Gmnn, and Parg) was altered and varied with RS source. HAW is as effective as HAMS and HAMSB in opposing diet-induced colonic DNA damage in rats, but their effects on the large bowel microbiota and colonocyte gene expression differ, possibly due to the presence of other ﬁber components in HAW. J. Nutr. 142: 832–840, 2012. ã 2012 American Society for Nutrition. Manuscript received July 7, 2011. Initial review completed August 24, 2011. Revision accepted February 1, 2012. First published online March 28, 2012; doi:10.3945/jn.111.147660. Introduction Colorectal cancer (CRC)11 is a major cause of premature morbidity and mortality in westernized industrial countries and is appearing 1 Supported by CSIRO. CSIRO receives support from a joint venture with Arista, which indirectly provides assistance to CSIRO researchers. 2 Author disclosures: M. A. Conlon, C. A. Kerr, C. S. McSweeney, R. A. Dunne, J. M. Shaw, S. Kang, A. R. Bird, M. K. Morell, T. J. Lockett, P. L. Molloy, A. Regina, S. Toden, J. M. Clarke, and D. L. Topping, no conﬂicts; the research was carried out as part of the authors’ normal duties at CSIRO. 3 Supplemental Tables 1–3, Supplemental Figures 1–3, and Supplemental Text are available from the “Online Supporting Material” link in the online posting of the article and from the same link in the online table of contents at http://jn.nutrition.org. 11 Abbreviations used: C-LAMS, control diet containing low amylose maize starch; CRC, colorectal cancer; cRNA, single-stranded RNA; EPIC, European Prospective Investigation into Cancer and Nutrition; HAMS, high amylose maize starch; HAMSB, butyrylated high amylose maize starch; HAW, high amylose wheat ﬂour; LAMS, low amylose maize starch; LAW, low amylose wheat ﬂour; NSP, nonstarch polysaccharide; PCA, principal components analysis; RS, resistant starch; SSB, single-strand break; W-HAMS, Western diet containing high amylose maize starch; W-HAMSB, Western diet containing butyrylated high amylose maize starch; W-HAW, Western diet containing high amylose wheat ﬂour; W-LAMS, Western diet containing low amylose maize starch; W-LAW, Western diet containing low amylose wheat ﬂour. * To whom correspondence should be addressed. E-mail: david.topping@csiro.au. 832 rapidly in developing economies with greater afﬂuence (1). This time trend supports the importance of environmental inﬂuences in its etiology whereas genetic factors are thought to contribute #30% of new cases, strengthening the case for control through prevention (2). A study by the European Prospective Investiga- tion into Cancer and Nutrition (EPIC) showed that dietary ﬁber dose-dependently lowered CRC risk (3), whereas an earlier international comparison of population studies found that greater dietary protein intakes increase risk (4). Further analysis of the EPIC data showed that consumption of red and processed meat increased CRC risk (5). Unrepaired DNA damage is a prerequisite for carcinogenesis and we showed that feeding high- protein diets substantially increased the number of colonic DNA strand breaks in rats (6–8). Signiﬁcantly greater damage was seen with some protein sources, including red meat and casein, than with others, such as chicken, which is consistent with prospective population studies. Damage was dose-dependently opposed by dietary RS (resistant starch) fed as high amylose maize starch (HAMS) (6–8) or butyrylated HAMS (HAMSB) (9). Resistant starch (RS), the starch and the products of its digestion, escapes from the small intestine and enters the large