Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Microbiology (United Kingdom)

Volumn 163, Issue 8, 2017, Pages 1189-1197

  Onishi, Janet C ^a   Campbell, Sara ^a   Moreau, Michael ^b   Patel, Falshruti ^b   Brooks, Andrew I ^b   Xiuzhou, Yin ^a   Häggblom, Max M ^a   Storch, Judith ^a  

^a RUTGERS UNIVERSITY   (United States)

^b Rutgers University   (United States)

Author keywords

16S rRNA gene sequencing; Gut microbiome; High fat diet; Metabolic endotoxaemia; Mouse diet induced obesity model

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; BACTEROIDETES; CECUM; COLON; CONTROLLED STUDY; LACTOBACILLUS; LARGE INTESTINE; LIPID DIET; LOW FAT DIET; MALE; MICROBIAL COMMUNITY; MOUSE; NONHUMAN; OBESITY; PRIORITY JOURNAL; PROTEOBACTERIA; SMALL INTESTINE; WEIGHT GAIN; ANIMAL; BACTERIUM; BIODIVERSITY; C57BL MOUSE; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; HUMAN; INTESTINE FLORA; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY;

BACTERIAL DNA; RNA 16S;

ANIMALS; BACTERIA; BIODIVERSITY; CECUM; COLON; DIET, HIGH-FAT; DNA, BACTERIAL; GASTROINTESTINAL MICROBIOME; HUMANS; INTESTINE, SMALL; MALE; MICE; MICE, INBRED C57BL; OBESITY; RNA, RIBOSOMAL, 16S;

EID: 85028031699     PISSN: 13500872     EISSN: 14652080     Source Type: Journal    
DOI: 10.1099/mic.0.000496     Document Type: Article

References (46)

1. Lee JE, Lee S, Sung J, Ko G. Analysis of human and animal fecal microbiota for microbial source tracking. Isme J 2011;5:362–365.
2. Nguyen TL, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Dis Model Mech 2015;8:1–16.
3. Canny GO, McCormick BA. Bacteria in the intestine, helpful residents or enemies from within? Infect Immun 2008;76:3360–3373.
4. Berg RD. The indigenous gastrointestinal microflora. Trends Microbiol 1996;4:430–435.
5. Breen DM, Rasmussen BA, Côtè CD, Jackson VM, Lam TK. Nutrientsensing mechanisms in the gut as therapeutic targets for diabetes. Diabetes 2013;62:3005–3013.
6. Angelakis E, Armougom F, Carrière F, Bachar D, Laugier R et al. A metagenomic investigation of the duodenal microbiota reveals links with obesity. PLoS One 2015;10:e0137784.
7. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009;1:6ra14.
8. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. Isme J 2012;6: 1415–1426.
9. Kim YS, Kim J, Park SJ. High-throughput 16S rRNA gene sequencing reveals alterations of mouse intestinal microbiota after radiotherapy. Anaerobe 2015;33:1–7.
10. Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009;137:1716–1724.
11. Zhang C, Zhang M, Pang X, Zhao Y, Wang L et al. Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations. Isme J 2012;6:1848–1857.
12. Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007;56:1761–1772.
13. Van Heek M, Compton DS, France CF, Tedesco RP, Fawzi AB et al. Diet-induced obese mice develop peripheral, but not central, resistance to leptin. J Clin Invest 1997;99:385–390.
14. Douris N, Melman T, Pecherer JM, Pissios P, Flier JS et al. Adaptive changes in amino acid metabolism permit normal longevity in mice consuming a low-carbohydrate ketogenic diet. Biochim Biophys Acta 2015;1852:2056–2065.
15. Gajda AM, Zhou YX, Agellon LB, Fried SK, Kodukula S et al. Direct comparison of mice null for liver or intestinal fatty acid-binding proteins reveals highly divergent phenotypic responses to high fat feeding. J Biol Chem 2013;288:30330–30344.
16. Delmont TO, Simonet P, Vogel TM. Describing microbial communities and performing global comparisons in the ’omic era. Isme J 2012;6:1625–1628.
17. Moreau MM, Eades SC, Reinemeyer CR, Fugaro MN, Onishi JC. Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse. Vet Microbiol 2014;168: 436–441.
18. Illumina: 16S Metagenomic Sequencing Library Preparation, Part # 15044223 Rev. A.
19. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 2013;41:e1.
20. Milinovich GJ, Burrell PC, Pollitt CC, Klieve AV, Blackall LL et al. Microbial ecology of the equine hindgut during oligofructoseinduced laminitis. Isme J 2008;2:1089–1100.
21. Illumina: MiSeq Reporter Metagenomics Workflow Reference Guide, Part # 15042317 Rev.C.
22. Illumina: 16S Metagenomics App; 15055860 A.
23. Dean-Ross D, Mills AL. Bacterial community structure and function along a heavy metal gradient. Appl Environ Microbiol 1989;55: 2002–2009.
24. Campbell SC, Wisniewski PJ, Noji M, Mcguinness LR, Häggblom MM et al. The effect of diet and exercise on intestinal integrity and microbial diversity in mice. PLoS One 2016;11:e0150502.
25. Yanke LJ, Cheng KJ. A method for the selective enumeration and isolation of ruminal Lactobacillus and Streptococcus. Lett Appl Microbiol 1998;26:248–252.
26. Ali N, Dashti N, Salamah S, Sorkhoh N, Al-Awadhi H et al. Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats. Microb Biotechnol 2016;9:157–171.
27. Zhang J, Cai X, Qi L, Shao C, Lin Y et al. Effects of aeration strategy on the evolution of dissolved organic matter (DOM) and microbial community structure during sludge bio-drying. Appl Microbiol Biotechnol 2015;99:7321–7331.
28. Wang Y, Gao L, Ming H, Zhang P, Zhu W. Polaribacter marinaquae sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016;66: 4594–4599.
29. Gupta A, Logan J, Elhag N, Almond M. Sphingobacterium spiritivorum infection in a patient with end stage renal disease on haemodialysis. Ann Clin Microbiol Antimicrob 2016;15:25.
30. Deepnarain N, Kumari S, Ramjith J, Swalaha FM, Tandoi V et al. A logistic model for the remediation of filamentous bulking in a biological nutrient removal wastewater treatment plant. Water Sci Technol 2015;72:391–405.
31. Calabuig R, Weems WA, Moody FG. Ileo-cecal junction: a valve or a sphincter? An experimental study in the opossum. Rev Esp Enferm Dig 1996;88:828–839.
32. Brannon P, Tso P, Jandacek RJ. Digestion and absorption of lipids. In: Stipanuk M (editor). Biochemical, Physiological, and Molecular Aspects of Human Nutrition, 3rd ed. St. Louis: Saunders Elsevier; 2012. pp. 179–191.
33. Dirusso CC, Black PN. Long-chain fatty acid transport in bacteria and yeast. Paradigms for defining the mechanism underlying this protein-mediated process. Mol Cell Biochem 1999;192:41–52.
34. Nunn WD. A molecular view of fatty acid catabolism in Escherichia coli. Microbiol Rev 1986;50:179–192.
35. Kennedy AR, Pissios P, Otu H, Roberson R, Xue B et al. A high-fat, ketogenic diet induces a unique metabolic state in mice. Am J Physiol Endocrinol Metab 2007;292:E1724–E1739.
36. Ghibaudi L, Cook J, Farley C, van Heek M, Hwa JJ. Fat intake affects adiposity, comorbidity factors, and energy metabolism of Sprague-Dawley rats. Obes Res 2002;10:956–963.
37. Tinsley FC, Taicher GZ, Heiman ML. Evaluation of a quantitative magnetic resonance method for mouse whole body composition analysis. Obes Res 2004;12:150–160.
38. Raetz CR, Whitfield C. Lipopolysaccharide endotoxins. Annu Rev Biochem 2002;71:635–700.
39. Munford RS. Sensing gram-negative bacterial lipopolysaccharides: a human disease determinant? Infect Immun 2008;76:454–465.
40. Munford RS, Varley AW. Shield as signal: lipopolysaccharides and the evolution of immunity to gram-negative bacteria. PLoS Pathog 2006;2:e67.
41. Boutagy NE, Mcmillan RP, Frisard MI, Hulver MW. Metabolic endotoxemia with obesity: Is it real and is it relevant? Biochimie 2016; 124:11–20.
42. Munford RS. Endotoxemia-menace, marker, or mistake? J Leukoc Biol 2016;100:687–698.
43. Turnbaugh PJ, Bäckhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 2008;3:213–223.
44. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027–1131.
45. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes 2008;32:1720–1724.
46. Ericsson AC, Davis JW, Spollen W, Bivens N, Givan S et al. Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice. PLoS One 2015;10:e0116704.