Specific microbiome changes in a mouse model of parenteral nutrition associated liver injury and intestinal inflammation

PLoS ONE

Volumn 9, Issue 10, 2014, Pages

  Harris, J Kirk ^a   El Kasmi, Karim C ^a   Anderson, Aimee L ^a   Devereaux, Michael W ^a   Fillon, Sophie A ^a   Robertson, Charles E ^b   Wagner, Brandie D ^c   Stevens, Mark J ^a   Pace, Norman R ^b   Sokol, Ronald J ^a  

^a Children's Hospital Colorado   (United States)

^b UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^c Global Health and Health Disparities   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SOYBEAN OIL; TOLL LIKE RECEPTOR 4; VEGETABLE OIL;

ADULT; ANAEROPLASMA; ANAEROTRUNCUS; ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; BACTEROIDETES; CLOSTRIDIALES; COLON FLORA; CONTROLLED STUDY; DISEASE ASSOCIATION; ENTERITIS; ERYSIPELOTRICHACEAE; GENE SEQUENCE; GRAM POSITIVE BACTERIUM; KUPFFER CELL; LACHNOSPIRACEAE; LIPID COMPOSITION; LIVER INJURY; MALE; MOUSE; NONHUMAN; PARENTERAL NUTRITION ASSOCIATED LIVER INJURY; POPULATION ABUNDANCE; PROPIONIBACTERIUM; RNA GENE; RUMINOCOCCUS; SIGNAL TRANSDUCTION; STAPHYLOCOCCUS; ADVERSE EFFECTS; ANIMAL; CHEMISTRY; DISEASE MODEL; DRUG EFFECTS; IMMUNOLOGY; INFLAMMATION; INJURIES; INTESTINE; LIVER; MICROBIOLOGY; MICROFLORA; PARENTERAL NUTRITION; SOYBEAN;

ANIMALS; DISEASE MODELS, ANIMAL; INFLAMMATION; INTESTINES; KUPFFER CELLS; LIVER; MALE; MICE; MICROBIOTA; PARENTERAL NUTRITION; PLANT OILS; SOYBEANS;

EID: 84908191514     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0110396     Document Type: Article

References (59)

1. Wilmore DW, Dudrick SJ (1968) Growth and development of an infant receiving all nutrients exclusively by vein. JAMA 203: 860-864.
2. Jeejeebhoy KN (2001) Total parenteral nutrition: potion or poison? Am J Clin Nutr 74: 160-163.
3. Kelly DA (2006) Intestinal failure-associated liver disease: what do we know today? Gastroenterology 130: S70-77.
4. Sokol RJ (1997) Total parenteral nutrition-related liver disease. Zhonghua Min Guo Xiao Er Ke Yi Xue Hui Za Zhi 38: 418-428.
5. Teitelbaum DH (1997) Parenteral nutrition-associated cholestasis. Curr Opin Pediatr 9: 270-275.
6. Teitelbaum DH, Tracy T (2001) Parenteral nutrition-associated cholestasis. Semin Pediatr Surg 10: 72-80.
7. Beale EF, Nelson RM, Bucciarelli RL, Donnelly WH, Eitzman DV (1979) Intrahepatic cholestasis associated with parenteral nutrition in premature infants. Pediatrics 64: 342-347.
8. Beath SV, Davies P, Papadopoulou A, Khan AR, Buick RG, et al. (1996) Parenteral nutrition-related cholestasis in postsurgical neonates: multivariate analysis of risk factors. J Pediatr Surg 31: 604-606.
9. Bell RL, Ferry GD, Smith EO, Shulman RJ, Christensen BL, et al. (1986) Total parenteral nutrition-related cholestasis in infants. JPEN J Parenter Enteral Nutr 10: 356-359.
10. Benjamin DR (1981) Hepatobiliary dysfunction in infants and children associated with long-term total parenteral nutrition. A clinico-pathologic study. AmJ Clin Pathol 76: 276-283.
11. Btaiche IF, Khalidi N (2002) Parenteral nutrition-associated liver complications in children. Pharmacotherapy 22: 188-211.
12. Buchman A (2002) Total parenteral nutrition-associated liver disease. JPEN J - Parenter Enteral Nutr 26: S43-48.
13. Carter BA, Karpen SJ (2007) Intestinal failure-associated liver disease: management and treatment strategies past, present, and future. Semin Liver Dis 27: 251-258.
14. Colomb V, Goulet O, De Potter S, Ricour C (1994) Liver disease associated with long-term parenteral nutrition in children. Transplant Proc 26: 1467.
15. Trauner M, Boyer JL (2003) Cholestatic syndromes. Curr Opin Gastroenterol 19: 216-231.
16. Carter BA, Shulman RJ (2007) Mechanisms of disease: update on the molecular etiology and fundamentals of parenteral nutrition associated cholestasis. Nat Clin Pract Gastroenterol Hepatol 4: 277-287.
17. Botha JF, Grant WJ, Torres C, Iverson AK, Sudan DL, et al. (2006) Isolated liver transplantation in infants with end-stage liver disease due to short bowel syndrome. Liver Transpl 12: 1062-1066.
18. Buchman AL, Iyer K, Fryer J (2006) Parenteral nutrition-associated liver disease and the role for isolated intestine and intestine/liver transplantation. Hepatology 43: 9-19.
19. Chungfat N, Dixler I, Cohran V, Buchman A, Abecassis M, et al. (2007) Impact of parenteral nutrition-associated liver disease on intestinal transplant waitlist dynamics. J Am Coll Surg 205: 755-761.
20. Kaufman SS, Gondolesi GE, Fishbein TM (2003) Parenteral nutrition associated liver disease. Semin Neonatol 8: 375-381.
21. Duro D, Kamin D, Duggan C (2008) Overview of pediatric short bowel syndrome. J Pediatr Gastroenterol Nutr 47 Suppl 1: S33-36.
22. Kaufman SS, Loseke CA, Lupo JV, Young RJ, Murray ND, et al. (1997) Influence of bacterial overgrowth and intestinal inflammation on duration of parenteral nutrition in children with short bowel syndrome. J Pediatr 131: 356-361.
23. Taylor SF, Sondheimer JM, Sokol RJ, Silverman A, Wilson HL (1991) Noninfectious colitis associated with short gut syndrome in infants. J Pediatr 119: 24-28.
24. El Kasmi KC, Anderson AL, Devereaux MW, Fillon SA, Harris JK, et al. (2012) Toll-like receptor 4-dependent Kupffer cell activation and liver injury in a novel mouse model of parenteral nutrition and intestinal injury. Hepatology 55: 1518-1528.
25. Cohen C, Olsen MM (1981) Pediatric total parenteral nutrition. Liver histopathology. Arch Pathol Lab Med 105: 152-156.
26. El Kasmi KC, Anderson AL, Devereaux MW, Vue PM, Zhang W, et al. (2013) Phytosterols promote liver injury and kupffer cell activation in parenteral nutrition-associated liver disease. Sci Transl Med 5: 206ra137.
27. Hodes JE, Grosfeld JL, Weber TR, Schreiner RL, Fitzgerald JF, et al. (1982) Hepatic failure in infants on total parenteral nutrition (TPN): clinical and histopathologic observations. J Pediatr Surg 17: 463-468.
28. Miyasaka EA, Feng Y, Poroyko V, Falkowski NR, Erb-Downward J, et al. (2013) Total parenteral nutrition-associated lamina propria inflammation in mice is mediated by a MyD88-dependent mechanism. J Immunol 190: 6607-6615.
29. Moss RL, Das JB, Raffensperger JG (1993) Total parenteral nutrition-associated cholestasis: clinical and histopathologic correlation. J Pediatr Surg 28: 1270-1274; discussion 1274-1275.
30. Mullick FG, Moran CA, Ishak KG (1994) Total parenteral nutrition: a histopathologic analysis of the liver changes in 20 children. Mod Pathol 7: 190-194.
31. Zambrano E, El-Hennawy M, Ehrenkranz RA, Zelterman D, Reyes-Mugica M (2004) Total parenteral nutrition induced liver pathology: an autopsy series of 24 newborn cases. Pediatr Dev Pathol 7: 425-432.
32. Yan AW, Fouts DE, Brandl J, Starkel P, Torralba M, et al. (2011) Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 53: 96-105.
33. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R (2008) Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 5: 235-237.
34. Gura KM, Duggan CP, Collier SB, Jennings RW, Folkman J, et al. (2006) Reversal of parenteral nutrition-associated liver disease in two infants with short bowel syndrome using parenteral fish oil: implications for future management. Pediatrics 118: e197-201.
35. Conterno L, Fava F, Viola R, Tuohy KM (2011) Obesity and the gut microbiota: does up-regulating colonic fermentation protect against obesity and metabolic disease? Genes Nutr 6: 241-260.
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. Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9: 279-290.
38. Martinez I, Wallace G, Zhang C, Legge R, Benson AK, et al. (2009) Diet-induced metabolic improvements in a hamster model of hypercholesterolemia are strongly linked to alterations of the gut microbiota. Appl Environ Microbiol 75: 4175-4184.
39. Martinez I, Perdicaro DJ, Brown AW, Hammons S, Carden TJ, et al. (2012) Diet-induced alterations of host cholesterol metabolism are likely to affect gut microbiota composition in hamsters. Appl Environ Microbiol.
40. Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B (2012) Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease. J Hepatol 56: 1283-1292.
41. Seki E, De Minicis S, Osterreicher CH, Kluwe J, Osawa Y, et al. (2007) TLR4 enhances TGF-beta signaling and hepatic fibrosis. Nat Med 13: 1324-1332.
42. Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9: 313-323.
43. Brown EM, Sadarangani M, Finlay BB (2013) The role of the immune system in governing host-microbe interactions in the intestine. Nat Immunol 14: 660-667.
44. Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336: 1268-1273.
45. Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, et al. (2010) Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing. Appl Environ Microbiol 76: 3863-3868.
46. Frank DN (2009) BARCRAWL and BARTAB: Software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 10: 362.
47. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
48. Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R (2011) UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194-2200.
49. Schloss PD, Gevers D, Westcott SL (2011) Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS One 6: e27310.
50. Pruesse E, Peplies J, Glockner FO (2012) SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829.
51. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-596.
52. Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, et al. (2013) Explicet: Graphical user interface software for the management, analysis and visualization of microbial ecology data and metadata. Bioinformatics.
53. Breiman L (2001) Random Forests. Mach Learn 45: 5-32.
54. Aitchinson EJ (1986) The Statistical Analysis of Compositional data. monographs on Statistics and Applied Probability. London: Chapman & Hall Ltd.
55. Filzmoser P, Hron K, Reimann C (2009) Univariate statistical analysis of environmental (compositional) data: problems and possibilities. Sci Total Environ 407: 6100-6108.
56. Harris JK, Wagner BD (2012) Bacterial identification and analytic challenges in clinical microbiome studies. J Allergy Clin Immunol 129: 441-442.
57. Salzman NH, de Jong H, Paterson Y, Harmsen HJ, Welling GW, et al. (2002) Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology 148: 3651-3660.
58. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, et al. (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res.
59. Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, et al. (2012) Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J 6: 94-103.