Application of density gradient for the isolation of the fecal microbial stool component and the potential use thereof

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Hevia, Arancha ^a   Delgado, Susana ^a   Margolles, Abelardo ^a   Sanchez, Borja ^a  

^a DEPARTMENT OF MICROBIOLOGY AND BIOCHEMISTRY OF DAIRY PRODUCTS   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; BIODIVERSITY; DENSITY GRADIENT CENTRIFUGATION; FECES; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA; MULTIVARIATE ANALYSIS; PHYLOGENY; PROCEDURES;

BACTERIA; BIODIVERSITY; CENTRIFUGATION, DENSITY GRADIENT; FECES; HUMANS; MICROBIOTA; MULTIVARIATE ANALYSIS; PHYLOGENY;

EID: 84947606433     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep16807     Document Type: Article

References (47)

1. Backhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., Gordon, J. I. Host-bacterial mutualism in the human intestine. Science 307, 1915-1920 (2005).
2. Gill, S. R. et al. Metagenomic analysis of the human distal gut microbiome. Science 312, 1355-1359 (2006).
3. Evans, J. M., Morris, L. S., Marchesi, J. R. The gut microbiome: the role of a virtual organ in the endocrinology of the host. Journal of Endocrinology 218, R37-R47 (2013).
4. Weinstock, G. M. Genomic approaches to studying the human microbiota. Nature 489, 250-256 (2012).
5. Li, J. H. et al. An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology 32, 834-841 (2014).
6. Qin, J. J. et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-70 (2010).
7. Brestoff, J. R., Artis, D. Commensal bacteria at the interface of host metabolism and the immune system. Nature Immunology 14, 676-684 (2013).
8. Arumugam, M. et al. Enterotypes of the human gut microbiome. Nature 473, 174-180 (2011).
9. Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 334, 105-108 (2011).
10. Claesson, M. J. et al. Gut microbiota composition correlates with diet and health in the elderly. Nature 488, 178-184 (2012).
11. Yatsunenko, T. et al. Human gut microbiome viewed across age and geography. Nature 486, 222-227 (2012).
12. Turnbaugh, P. J. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027-1031 (2006).
13. Vijay-Kumar, M. et al. Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5. Science 328, 228-231 (2010).
14. Scher, J. U., Abramson, S. B. The microbiome and rheumatoid arthritis. Nature Reviews Rheumatology 7, 569-578 (2011).
15. Wen, L. et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 455, 1109-1110 (2008).
16. Manichanh, C., Borruel, N., Casellas, F., Guarner, F. The gut microbiota in IBD. Nature Reviews Gastroenterology & Hepatology 9, 599-608 (2012).
17. Hevia, A. et al. Intestinal dysbiosis associated with Systemic Lupus Erythematosus. mBio 5, e01548-14 (2014).
18. Eiseman, B., Silen, W., Bascom, G. S., Kauvar, A. J. Fecal enema as an adjunct in the treatment of pseudomembranous enterocolitis. Surgery 44, 854-859 (1958).
19. Smith, M. B., Kelly, C., Alm, E. J. How to regulate faecal transplants. Nature 506, 290-291 (2014).
20. van Nood, E. et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine 368, 407-415 (2013).
21. Satokari, R. et al. Fecal transplantation treatment of antibiotic-induced, noninfectious colitis and long-term microbiota follow-up. Case Reports in Medicine 2014, 913867 (2014).
22. Fox, J. L. Fecal transplants to follow FDA rules. Nature Biotechnology 31, 583-583 (2013).
23. Hamilton, M. J., Weingarden, A. R., Sadowsky, M. J., Khoruts, A. Standardized frozen preparation for transplantation of fecal microbiota for recurrent Clostridium difficile infection. American Journal of Gastroenterology 107, 761-767 (2012).
24. Hamilton, M. J., Weingarden, A. R., Unno, T., Khoruts, A., Sadowsky, M. J. High-throughput DNA sequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut microbes 4, 125-135, (2013).
25. Courtois, S. et al. Quantification of bacterial subgroups in soil: comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environmental Microbiology 3, 431-439 (2001).
26. Milani, C. et al. Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol. Plos One 8, e68739 (2013).
27. IDF (International Dairy Federation). Cheese and processed cheese product. Determination of the total solids content. Reference method. Standard FIL-IDF 4A:1982. International Dairy Federation, Brussels, Belgium (1982).
28. IDF (International Dairy Federation). Milk, cream and evaporated milk-Determination of total solids content. Reference method. Standard FIL-IDF 21B:1987. International Dairy Federation, Brussels, Belgium (1987).
29. Caporaso, J. G. et al. QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7, 335-336 (2010).
30. Haas, B. J. et al. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Research 21, 494-504 (2011).
31. McDonald D. C. J., Kuczynski, J., Rideout, J. R., Stombaugh, J., Wendel, D., Wilke, A., Huse, S., Hufnagle, J., Meyer, F., Knight, R., Caporaso, J. G. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the omeome. Gigascience 1, 7 (2012).
32. Hammer, ∅., Harper, D. A. T., Ryan, P. D. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4, 4 (2001).
33. Parks, D. H., Beiko, R. G. Identifying biologically relevant differences between metagenomic communities. Bioinformatics 26, 715-721 (2010).
34. Benjamini, Y., Hochberg, Y. Controlling the false discovery rate-a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B-Methodological 57, 289-300 (1995).
35. Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biology 13, R79 (2012).
36. Faegri, A., Torsvik, V. L., Goksoyr, J. Bacterial and fungal activities in soil-separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biology & Biochemistry 9, 105-112 (1977).
37. Torsvik, V. L. Isolation of bacterial DNA from soil. Soil Biology & Biochemistry 10, 15-21 (1980).
38. Pillai, S. D., Josephson, K. L., Bailey, R. L., Gerba, C. P., Pepper, I. L. Rapid method for processing soil samples for polymerase chain-reaction amplification of specific gene-sequences. Applied and Environmental Microbiology 57, 2283-2286 (1991).
39. Jacobsen, C. S., Rasmussen, O. F. Development and application of a new method to extract bacterial-DNA from soil based on separation of bacteria from soil with cation-exchange resin. Applied and Environmental Microbiology 58, 2458-2462 (1992).
40. Rooijers, K. et al. An iterative workflow for mining the human intestinal metaproteome. BMC Genomics 12, 6 (2011).
41. Murayama, K., Fujimura, T., Morita, M., Shindo, N. One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles. Electrophoresis 22, 2872-2880 (2001).
42. Faith, J. J. et al. The Long-Term Stability of the Human Gut Microbiota. Science 341, 1237439 (2013).
43. Lindahl, V., Bakken, L. R. Evaluation of Methods for Extraction of Bacteria from Soil. Fems Microbiology Ecology 16, 135-142 (1995).
44. Jia, S. G. et al. Seasonally variable intestinal metagenomes of the red palm weevil (Rhynchophorus ferrugineus). Environmental Microbiology 15, 3020-3029 (2013).
45. Makhzami, S. et al. In situ gene expression in cheese matrices: Application to a set of enterococcal genes. Journal of Microbiological Methods 75, 485-490 (2008).
46. Schneegurt, M. A. D., Sophia, Y., Kulpa & Charles, F. Jr. Direct extraction of DNA from soils for studies in microbial ecology. Curr. Issues Mol. Biol. 5, 1-8 (2003).
47. Buffie, C. G. et al. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517, 205-207 (2015).