Changes in bowel microbiota induced by feeding weanlings resistant starch stimulate transcriptomic and physiological responses

Applied and Environmental Microbiology

Volumn 78, Issue 18, 2012, Pages 6656-6664

  Young, Wayne ^a,b,c   Roy, Nicole C ^c,d   Lee, Julian ^b   Lawley, Blair ^a   Otter, Don ^c   Henderson, Gemma ^c   McCann, Mark J ^c   Tannock, Gerald W ^a,d  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b THE NEW ZEALAND INSTITUTE FOR PLANT AND FOOD RESEARCH LIMITED   (New Zealand)

^c AGRESEARCH GRASSLANDS   (New Zealand)

^d RIDDET INSTITUTE   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

16S RRNA GENE; ACTINOBACTERIA; BASAL DIET; CELL NUMBER; DIETARY COMPONENTS; DIGESTA; HOST PHYSIOLOGY; MEDICAL CONDITIONS; METABOLITE PROFILES; MICROBIAL COMMUNITIES; MICROBIOTAS; PHYSIOLOGICAL RESPONSE; PYROSEQUENCING; RESISTANT STARCH; SHORT-CHAIN FATTY ACIDS; SPRAGUE-DAWLEY RATS; TEMPORAL TEMPERATURE GRADIENT ELECTROPHORESIS;

BODY FLUIDS; ELECTROPHORESIS; GENE EXPRESSION; METABOLITES; NUTRITION; RATS; RNA; STARCH; TISSUE;

PHYSIOLOGY;

BACTERIAL DNA; RIBOSOME DNA; RNA 16S; STARCH; TRANSCRIPTOME;

BACTERIUM; DIET; ELECTROKINESIS; GENE EXPRESSION; HOMEOSTASIS; MICROBIAL COMMUNITY; PHYSIOLOGICAL RESPONSE; RODENT; STARCH;

ANIMAL; ARTICLE; BIODIVERSITY; CHEMISTRY; COLON; DIET; DNA SEQUENCE; ELECTROPHORESIS; GASTROINTESTINAL TRACT; GENETICS; INTESTINE MUCOSA; METABOLISM; METAGENOME; METHODOLOGY; MICROBIOLOGY; RAT; SPRAGUE DAWLEY RAT;

ANIMALS; BIODIVERSITY; COLON; DIET; DNA, BACTERIAL; DNA, RIBOSOMAL; ELECTROPHORESIS; GASTROINTESTINAL TRACT; INTESTINAL MUCOSA; METAGENOME; RATS; RATS, SPRAGUE-DAWLEY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; STARCH; TRANSCRIPTOME;

ACTINOBACTERIA; BACTEROIDETES; RATTUS;

EID: 84866150476     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01536-12     Document Type: Article

References (46)

1. Antonopoulos DA, et al. 2009. Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect. Immun. 77:2367-2375.
2. Bibiloni R, et al. 2008. Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent? J. Med. Microbiol. 57:111-117.
3. Caporaso JG, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods 7:335-336.
4. Conlon MA, et al. 2012. Resistant starches protect against colonic DNA damage and alter microbiota and gene expression in rats fed a western diet. J. Nutr. 142:832-840.
5. De Filippo C, et al. 2010. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc. Natl. Acad. Sci. U. S. A. 107:14691-14696.
6. Dourado DF, Fernandes PA, Ramos MJ. 2010. Glutathione transferase classes alpha, pi, and mu: GSH activation mechanism. J. Phys. Chem. B 114:12972-12980.
7. Drozdowski L, Thomson AB. 2006. Intestinal mucosal adaptation. World J. Gastroenterol. 12:4614-4627.
8. Flint HJ, Bayer EA, Rincon MT, Lamed R, White BA. 2008. Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat. Rev. Microbiol. 6:121-131.
9. Frank DN, et al. 2007. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U. S. A. 104:13780-13785.
10. Gentleman RC, et al. 2004. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5:R80. doi: 10.1186/gb-2004-5-10-r80.
11. Gobbetti T, et al. 2012. Serine protease inhibition reduces post-ischemic granulocyte recruitment in mouse intestine. Am. J. Pathol. 180:141-152.
12. Gore C, et al. 2008. Bifidobacterium pseudocatenulatum is associated with atopic eczema: a nested case-control study investigating the fecal microbiota of infants. J. Allergy Clin. Immunol. 121:135-140.
13. Hirche TO, et al. 2008. Neutrophil elastase mediates innate host protection against Pseudomonas aeruginosa. J. Immunol. 181:4945-4954.
14. Ishizaki M, et al. 2008. Nafamostat mesilate, a potent serine protease inhibitor, inhibits airway eosinophilic inflammation and airway epithelial remodeling in a murine model of allergic asthma. J. Pharmacol. Sci. 108: 355-363.
15. Jensen MT, Cox RP, Jensen BB. 1995. Microbial production of skatole in the hind gut of pigs given different diets and its relation to skatole deposition in backfat. Anim. Sci. 61:293-304.
16. Kessenbrock K, Dau T, Jenne DE. 2011. Tailor-made inflammation: how neutrophil serine proteases modulate the inflammatory response. J. Mol. Med. 89:23-28.
17. Knoch B, et al. 2010. Dietary arachidonic acid-mediated effects on colon inflammation using transcriptome analysis. Mol. Nutr. Food Res. 54(Suppl. 1):S62-S74.
18. Mah KW, et al. 2007. Effect of a milk formula containing probiotics on the fecal microbiota of Asian infants at risk of atopic diseases. Pediatr. Res. 62:674-679.
19. Martinez I, Kim J, Duffy PR, Schlegel VL, Walter J. 2010. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. PLoS One 5:e15046. doi:10.1371/journal.pone.0015046.
20. McNeil NI. 1984. The contribution of the large intestine to energy supplies in man. Am. J. Clin. Nutr. 39:338-342.
21. Mentschel J, Claus R. 2003. Increased butyrate formation in the pig colon by feeding raw potato starch leads to a reduction of colonocyte apoptosis and a shift to the stem cell compartment. Metabolism 52:1400-1405.
22. Miller HR, Pemberton AD. 2002. Tissue-specific expression of mast cell granule serine proteinases and their role in inflammation in the lung and gut. Immunology 105:375-390.
23. Miller TL, Wolin MJ. 1979. Fermentations by saccharolytic intestinal bacteria. Am. J. Clin. Nutr. 32:164-172.
24. Moreau NM, et al. 2003. Restoration of the integrity of rat caeco-colonic mucosa by resistant starch, but not by fructo-oligosaccharides, in dextran sulfate sodium-induced experimental colitis. Br. J. Nutr. 90:75-85.
25. Otter, D. et al. 2011. Identification of urinary biomarkers of colon inflammation in IL10-/- mice using short-column LC-MS metabolomics. J. Biomed. Biotechnol. 2011:974701. doi:10.1155/2011/974701.
26. Riehl TE, Ee X, Stenson WF. 2012. Hyaluronic acid regulates normal intestinal and colonic growth in mice. Am. J. Physiol. Gastrointest. Liver Physiol. doi:10.1152/ajpgi.00034.2012.
27. Rodríguez-Cabezas ME, et al. 2010. The combination of fructooligosaccharides and resistant starch shows prebiotic additive effects in rats. Clin. Nutr. 29:832-839.
28. Roediger WE. 1982. Utilization of nutrients by isolated epithelial cells of the rat colon. Gastroenterology 83:424-429.
29. Schwiertz A, et al. 2010. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18:190-195.
30. Smith CA, Want EJ, O'Maille G, Abagyan R, Siuzdak G. 2006. XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 78:779-787.
31. Smyth GK. 2004. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol. 3:1544-6155. doi:10.2202/1544-6115.1027.
32. Stark PL, Lee A. 1982. The microbial ecology of the large bowel of breastfed and formula-fed infants during the first year of life. J. Med. Microbiol. 15:189-203.
33. Tannock GW, et al. 2004. Impact of consumption of oligosaccharidecontaining biscuits on the fecal microbiota of humans. Appl. Environ. Microbiol. 70:2129-2136.
34. Tateosian NL, et al. 2011. Neutrophil elastase treated dendritic cells promote the generation of CD4(+)FOXP3(+) regulatory T cells in vitro. Cell Immunol. 269:128-134.
35. Thioulouse J, Dray S. 2007. Interactive multivariate data analysis in R with the ade4 and ade4 TkGUI packages. J. Stat. Softw. 22:1-14.
36. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. 2008. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3:213-223.
37. Turnbaugh PJ, et al. 2006. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027-1031.
38. Vijay-Kumar M, et al. 2010. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 328:228-231.
39. Walker AW, et al. 2011. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J. 5:220-230.
40. Walter J, et al. 2000. Detection and identification of gastrointestinal Lactobacillus species by using denaturing gradient gel electrophoresis and species-specific PCR primers. Appl. Environ. Microbiol. 66:297-303.
41. Wang J, et al. 2011. Genetic polymorphisms of glutathione S-transferase genes and susceptibility to colorectal cancer: a case-control study in an Indian population. Cancer Epidemiol. 35:66-72.
42. Wang M, et al. 2008. Reduced diversity in the early fecal microbiota of infants with atopic eczema. J. Allergy Clin. Immunol. 121:129-134.
43. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73:5261-5267.
44. Yin L, et al. 2010. Differential effects of periopathogens on host protease inhibitors SLPI, elafin, SCCA1, and SCCA2. J. Oral Microbiol. doi: 10.3402/jom.v3402i3400.5070.
45. Zhang C, et al. 2012. Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. ISME J. doi:10.1038/ismej.2012.27.
46. Zivkovic AM, German JB, Lebrilla CB, Mills DA. 2011. Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proc. Natl. Acad. Sci. U. S. A. 108(Suppl. 1):4653-4658.