Rodent models to study the relationships between mammals and their bacterial inhabitants

Gut Microbes

Volumn 3, Issue 6, 2012, Pages 536-543

  Bibiloni, Rodrigo ^a  

^a RUAKURA RESEARCH CENTRE   (New Zealand)

Author keywords

Germ free; Gnotobiotic; Human flora associated (HFA) model; Rodent models; SPF animals

Indexed keywords

FUCOSYLTRANSFERASE; SIALYLTRANSFERASE;

ARTICLE; BACTERIAL COLONIZATION; BACTEROIDES THETAIOTAOMICRON; CARBOHYDRATE METABOLISM; ENERGY CONSERVATION; ENZYME ACTIVITY; GASTROINTESTINAL TRACT; GERMFREE ANIMAL; GNOTOBIOTICS; HOST; HOST PATHOGEN INTERACTION; HUMAN; INTESTINE FLORA; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS SALIVARIUS; MAMMAL; MICROBIAL COMMUNITY; MICROFLORA; NONHUMAN; POLYMERASE CHAIN REACTION; RNA GENE; RODENT;

ANIMALS; BACTERIA; BACTERIAL PHYSIOLOGICAL PHENOMENA; HOST-PATHOGEN INTERACTIONS; HUMANS; MAMMALS; MODELS, ANIMAL; RODENTIA; SYMBIOSIS;

ANIMALIA; BACTERIA (MICROORGANISMS); MAMMALIA; RODENTIA;

EID: 84868580867     PISSN: 19490976     EISSN: 19490984     Source Type: Journal    
DOI: 10.4161/gmic.21905     Document Type: Article

References (106)

1. Fierer N, Hamady M, Lauber CL, Knight R. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci U S A 2008; 105:17994-9. PMID:19004758; http://dx.doi.org/10.1073/pnas.0807920105.
2. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al.; NISC Comparative Sequencing Program. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324:1190-2. PMID:19478181; http://dx.doi.org/10.1126/science.1171700.
3. Nasidze I, Li J, Quinque D, Tang K, Stoneking M. Global diversity in the human salivary microbiome. Genome Res 2009; 19:636-43. PMID:19251737; http://dx.doi.org/10.1101/gr.084616.108.
4. Human Microbiome Project Consortium. A framework for human microbiome research. Nature 2012; 486:215-21. PMID:22699610; http://dx.doi.org/10.1038/nature11209.
5. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science 2005; 308:1635-8. PMID:15831718; http://dx.doi.org/10.1126/science.1110591.
6. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al.; MetaHIT Consortium. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80. PMID:21508958; http://dx.doi.org/10.1038/nature09944.
7. Gustafsson BE. Vitamin K deficiency in germfree rats. Ann N Y Acad Sci 1959; 78:166-74. PMID:13830426; http://dx.doi.org/10.1111/j.1749-6632.1959.tb53101.x.
8. Bouskra D, Brézillon C, Bérard M, Werts C, Varona R, Boneca IG, et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature 2008; 456:507-10. PMID:18987631; http://dx.doi.org/10.1038/nature07450.
9. Macpherson AJ, Uhr T. Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 2004; 303:1662-5. PMID:15016999; http://dx.doi.org/10.1126/science.1091334.
10. Sudo N, Sawamura S, Tanaka K, Aiba Y, Kubo C, Koga Y. The requirement of intestinal bacterial flora for the development of an IgE production system fully susceptible to oral tolerance induction. J Immunol 1997; 159:1739-45. PMID:9257835.
11. Ismail AS, Behrendt CL, Hooper LV. Reciprocal interactions between commensal bacteria and γ δ intraepithelial lymphocytes during mucosal injury. J Immunol 2009; 182:3047-54. PMID:19234201; http://dx.doi.org/10.4049/jimmunol.0802705.
12. Stappenbeck TS, Hooper LV, Gordon JI. Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci U S A 2002; 99:15451-5. PMID:12432102; http://dx.doi.org/10.1073/pnas.202604299.
13. Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 2004; 101:15718-23. PMID:15505215; http://dx.doi.org/10.1073/pnas.0407076101.
14. Lee YK, Menezes JS, Umesaki Y, Mazmanian SK. Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis. Proc Natl Acad Sci U S A 2011; 108(Suppl 1):4615-22. PMID:20660719; http://dx.doi.org/10.1073/pnas.1000082107.
15. Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010; 328:228-31 PMID:20203013; http://dx.doi.org/10.1126/science.1179721.
16. Escherich T. Die Darmbakterien des Neugeborenen und Sauglings. The intestinal bacteria of the neonate and breast-fed infant. Fortschr Med 1885; 3:515-22.
17. Schottelius M. Die Bedeutung der Darmbakterien fur die Ehrnahrung. II Arch Hyg 1902; 42:48-70.
18. Reyniers JA, Trexler PC. The design of micrurgical machines for use in bacteriology. In: Thomas CC, ed. Micrurgical and Germfree Techniques. Springfield, 1943:5-25.
19. Reyniers JA, Trexler PC, Ervin RF, Wagner M, Luckey TD, Gordon HA. The need for a unified terminology in germfree life studies. Lobund Reports 1949; 2:151-62.
20. Baker JA, Ferguson MS. Growth of platyfish (Platypoecilus maculatus) free from bacteria and other microorganisms. Proc Soc Exp Biol Med 1942; 51:116-9.
21. Fitzgerald RJ. Gnotobiotic contribution to oral microbiology. J Dent Res 1963; 2:549-52. PMID:13945366; http://dx.doi.org/10.1177/00220345630420016601.
22. Trexler PC, Orcutt RP. Development of gnotobiotics and contamination control in laboratory animal science. In: McPherson CW, Mattingly SF, eds. 50 Years of Laboratory Animal Science. Memphis, TN: Am Assoc Lab Anim Sci, 2000:121-8.
23. Tannock GW, Crichton C, Welling GW, Koopman JP, Midtvedt T. Reconstitution of the gastrointestinal microflora of lactobacillus-free mice. Appl Environ Microbiol 1988; 54:2971-5. PMID:2975941.
24. Coates ME. Gnotobiotic animals in research: their uses and limitations. Lab Anim 1975; 9:275-82. PMID:1107656; http://dx.doi.org/10.1258/002367775780957296.
25. Nuttal G, Thierfelder H. Thierisches Leben ohne Bacterien im Verdauungskanal. Z Phys Chem 1896; 21:109-21; http://dx.doi.org/10.1515/bchm2.1896.21.2-3.109.
26. Reyniers JA. The pure culture concept and gnotobiotics. Ann N Y Acad Sci 1959; 78:3-16; http://dx.doi.org/10.1111/j.1749-6632.1959.tb53091.x.
27. Gordon HA. The germ-free animal. Its use in the study of "physiologic" effects of the normal microbial flora on the animal host. Am J Dig Dis 1960; 5:841-67. PMID:13707167; http://dx.doi.org/10.1007/BF02232187.
28. Wostmann BS. The germfree animal in nutritional studies. Annu Rev Nutr 1981; 1:257-79. PMID:6764717; http://dx.doi.org/10.1146/annurev.nu.01.070181.001353.
29. Reyniers JA, Sacksteder MR. Observations on the survival of germfree C3H mice and their resistance to a contaminated environment. Proc Anim Care Panel 1958; 8:41-53.
30. Gustafsson BE. Germ free rearing of rats. General technique. Acta Pathol Microbiol Scand 1948; 73:1-130.
31. Faith JJ, Rey FE, O'Donnell D, Karlsson M, McNulty NP, Kallstrom G, et al. Creating and characterizing communities of human gut microbes in gnotobiotic mice. ISME J 2010; 4:1094-8. PMID:20664551; http://dx.doi.org/10.1038/ismej.2010.110.
32. Smith K, McCoy KD, Macpherson AJ. Use of axenic animals in studying the adaptation of ammals to their commensal intestinal microbiota. Semin Immunol 2007; 19:59-69. PMID:17118672; http://dx.doi.org/10.1016/j.smim.2006.10.002.
33. Nanthakumar NN, Dai D, Newburg DS, Walker WA. The role of indigenous microflora in the development of murine intestinal fucosyl- and sialyltransferases. FASEB J 2003; 17:44-6. PMID:12475916.
34. Glaister JR. Factors affecting the lymphoid cells in the small intestinal epithelium of the mouse. Int Arch Allergy Appl Immunol 1973; 45:719-30. PMID:4749414; http://dx.doi.org/10.1159/000231071.
35. Gordon HA. Morphological and physiological characterization of germfree life. Ann N Y Acad Sci 1959; 78:208-20. PMID:13851201; http://dx.doi.org/10.1111/j.1749-6632.1959.tb53104.x.
36. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005; 122:107-18. PMID:16009137; http://dx.doi.org/10.1016/j.cell.2005.05.007.
37. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science 2008; 320:1647-51. PMID:18497261; http://dx.doi.org/10.1126/science.1155725.
38. Jiménez E, Marín ML, Martín R, Odriozola JM, Olivares M, Xaus J, et al. Is meconium from healthy newborns actually sterile? Res Microbiol 2008; 159:187-93. PMID:18281199; http://dx.doi.org/10.1016/j.resmic.2007.12.007.
39. Satokari R, Grönroos T, Laitinen K, Salminen S, Isolauri E. Bifidobacterium and Lactobacillus DNA in the human placenta. Lett Appl Microbiol 2009; 48:8-12. PMID:19018955; http://dx.doi.org/10.1111/j.1472-765X.2008.02475.x.
40. Pettker CM, Buhimschi IA, Magloire LK, Sfakianaki AK, Hamar BD, Buhimschi CS. Value of placental microbial evaluation in diagnosing intra-amniotic infection. Obstet Gynecol 2007; 109:739-49. PMID:17329528; http://dx.doi.org/10.1097/01.AOG.0000255663.47512.23.
41. Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI. A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc Natl Acad Sci U S A 1999; 96:9833-8. PMID:10449780; http://dx.doi.org/10.1073/pnas.96.17.9833.
42. Bry L, Falk PG, Midtvedt T, Gordon JI. A model of host-microbial interactions in an open mammalian ecosystem. Science 1996; 273:1380-3. PMID:8703071; http://dx.doi.org/10.1126/science.273.5280.1380.
43. Bjursell MK, Martens EC, Gordon JI. Functional genomic and metabolic studies of the adaptations of a prominent adult human gut symbiont, Bacteroides thetaiotaomicron, to the suckling period. J Biol Chem 2006; 281:36269-79. PMID:16968696; http://dx.doi.org/10.1074/jbc.M606509200.
44. Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, et al. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 2005; 307:1955-9. PMID:15790854; http://dx.doi.org/10.1126/science.1109051.
45. Martens EC, Chiang HC, Gordon JI. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 2008; 4:447-57. PMID:18996345; http://dx.doi.org/10.1016/j.chom.2008.09.007.
46. Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, et al. Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe 2009; 6:279-89. PMID:19748469; http://dx.doi.org/10.1016/j.chom.2009.08.003.
47. Mahowald MA, Rey FE, Seedorf H, Turnbaugh PJ, Fulton RS, Wollam A, et al. Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla. Proc Natl Acad Sci U S A 2009; 106:5859-64. PMID:19321416; http://dx.doi.org/10.1073/pnas.0901529106.
48. Samuel BS, Gordon JI. A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 2006; 103:10011-6. PMID:16782812; http://dx.doi.org/10.1073/pnas.0602187103.
49. Breznak JA, Switzer JM. Acetate synthesis from H2 plus CO2 by termite gut microbes. Appl Environ Microbiol 1986; 52:623-30. PMID:16347157.
50. Rey FE, Faith JJ, Bain J, Muehlbauer MJ, Stevens RD, Newgard CB, et al. Dissecting the in vivo metabolic potential of two human gut acetogens. J Biol Chem 2010; 285:22082-90. PMID:20444704; http://dx.doi.org/10.1074/jbc.M110.117713.
51. Becker N, Kunath J, Loh G, Blaut M. Human intestinal microbiota: Characterization of a simplified and stable gnotobiotic rat model. Gut Microbes 2011; 2:1-9. PMID:21637012.
52. Midtvedt T, Bjørneklett A, Carlstedt-Duke B, Gustafsson BE, Høverstad T, Lingaas E, et al. The influence of antibiotics upon microflora-associated characteristics in man and mammals. Prog Clin Biol Res 1985; 181:241-4. PMID:4022981.
53. Faith JJ, McNulty NP, Rey FE, Gordon JI. Predicting a human gut microbiota's response to diet in gnotobiotic mice. Science 2011; 333:101-4. PMID:21596954; http://dx.doi.org/10.1126/science.1206025.
54. Rezzonico E, Mestdagh R, Delley M, Combremont S, Dumas ME, Holmes E, et al. Microbial and metabolic characterization of a simplified microbiota mouse model. Gut Microbes 2011; 2:307-18.
55. Recommendations for the health monitoring of mouse, rat, hamster, guineapig and rabbit breeding colonies. Report of the Federation of European Laboratory Animal Science Associations (FELASA) Working Group on Animal Health accepted by the FELASA Board of Management November 1992. Lab Anim 1994; 28:1-12. PMID:8158962; http://dx.doi.org/10.1258/002367794781065933.
56. Laboratory Animal Breeders Association Accreditation Scheme (LABAAS) Manual 1993.
57. Nicklas W, Baneux P, Boot R, Decelle T, Deeny AA, Fumanelli M, et al.; FELASA (Federation of European Laboratory Animal Science Associations Working Group on Health Monitoring of Rodent and Rabbit Colonies). Recommendations for the health monitoring of rodent and rabbit colonies in breeding and experimental units. Lab Anim 2002; 36:20-42. PMID:11831737; http://dx.doi.org/10.1258/0023677021911740.
58. Schaedler RW, Dubs R, Costello R. Association of germfree mice with bacteria isolated from normal mice. J Exp Med 1965; 122:77-82. PMID:14325475; http://dx.doi.org/10.1084/jem.122.1.77.
59. Schaedler RW, Dubos R, Costello R. The development of the bacterial flora in the gastrointestinal tract of mice. J Exp Med 1965; 122:59-66. PMID:14325473; http://dx.doi.org/10.1084/jem.122.1.59.
60. Baker DE. The commercial production of mice with a specified flora. Natl Cancer Inst Monogr 1966; 20:161-6. PMID:5948524.
61. Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP, Schauer DB, et al. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol 1999; 65:3287-92. PMID:10427008.
62. Orcutt RP, Gianni FJ, Judge RJ. Development of an "Altered Schaedler Flora" for the generation of NCI gnotobiotic rodents. Microecol Ther 1987; 17:59.
63. Rohde CM, Wells DF, Robosky LC, Manning ML, Clifford CB, Reily MD, et al. Metabonomic evaluation of Schaedler altered microflora rats. Chem Res Toxicol 2007; 20:1388-92. PMID:17900170; http://dx.doi.org/10.1021/tx700184u.
64. Silley P. Human flora-associated rodents-does the data support the assumptions? Microb Biotechnol 2009; 2:6-14. PMID:21261878; http://dx.doi.org/10.1111/j.1751-7915.2008.00069.x.
65. Hazenberg MP, Bakker M, Verschoor-Burggraaf A. Effects of the human intestinal flora on germ-free mice. J Appl Bacteriol 1981; 50:95-106. PMID:7014548; http://dx.doi.org/10.1111/j.1365-2672.1981.tb00874.x.
66. Pecquet S, Andremont A, Tancrède C. Selective antimicrobial modulation of the intestinal tract by norfloxacin in human volunteers and in gnotobiotic mice associated with a human fecal flora. Antimicrob Agents Chemother 1986; 29:1047-52. PMID:3729360; http://dx.doi.org/10.1128/AAC.29.6.1047.
67. Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 1999; 65:4799-807. PMID:10543789.
68. Tannock GW, Munro K, Harmsen HJM, Welling GW, Smart J, Gopal PK. Analysis of the fecal microflora of human subjects consuming a probiotic product containing Lactobacillus rhamnosus DR20. Appl Environ Microbiol 2000; 66:2578-88. PMID:10831441; http://dx.doi.org/10.1128/AEM.66.6.2578-2588.2000.
69. Ducluzeau R, Ladire M, Raibaud P. Effect of bran ingestion on the microbial faecal floras of human donors and of recipient gnotobiotic mice, and on the barrier effects exerted by these floras against various potentially pathogenic microbial strains. Ann Microbiol (Paris) 1984; 135A:303-18. PMID:6326642.
70. Raibaud P, Ducluzeau R, Dubos F, Hudault S, Bewa H, Muller MC. Implantation of bacteria from the digestive tract of man and various animals into gnotobiotic mice. Am J Clin Nutr 1980; 33(Suppl):2440-7. PMID:7001883.
71. Hirayama K, Kawamura S, Mitsuoka T. Development and stability of human faecal flora in the intestine of exgerm- free mice. Microb Ecol Health Dis 1991; 4:95-9. http://dx.doi.org/10.3109/08910609109140269.
72. Gérard P, Béguet F, Lepercq P, Rigottier-Gois L, Rochet V, Andrieux C, et al. Gnotobiotic rats harboring human intestinal microbiota as a model for studying cholesterol-to-coprostanol conversion. FEMS Microbiol Ecol 2004; 47:337-43. PMID:19712322; http://dx.doi.org/10.1016/S0168-6496(03)00285-X.
73. Kibe R, Sakamoto M, Yokota H, Ishikawa H, Aiba Y, Koga Y, et al. Movement and fixation of intestinal microbiota after administration of human feces to germfree mice. Appl Environ Microbiol 2005; 71:3171-8. PMID:15933018; http://dx.doi.org/10.1128/AEM.71.6.3171-3178.2005.
74. Rawls JF, Mahowald MA, Ley RE, Gordon JI. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 2006; 127:423-33. PMID:17055441; http://dx.doi.org/10.1016/j.cell.2006.08.043.
75. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009; 1:ra14. PMID:20368178; http://dx.doi.org/10.1126/scitranslmed.3000322.
76. Hirayama K, Itoh K, Takahashi E, Mitsuoka T. Comparison of composition of faecal microbiota and metabolism of faecal bacteria among "human-flora-associated" mice inoculated with faeces from six different human donors. Microb Ecol Health Dis 1995; 8:199-211; http://dx.doi.org/10.3109/08910609509140098.
77. Hirayama K. Ex-germ free mice harbouring intestinal microbiota derived from other animal species as an experimental model for ecology and metabolism of intestinal bacteria. Exp Anim 1999; 48:146-52; http://dx.doi.org/10.1538/expanim.48.219.
78. Mallett AK, Bearne CA, Rowland IR, Farthing MJ, Cole CB, Fuller R. The use of rats associated with a human faecal flora as a model for studying the effects of diet on the human gut microflora. J Appl Bacteriol 1987; 63:39-45. PMID:2820914; http://dx.doi.org/10.1111/j.1365-2672.1987.tb02415.x.
79. Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A 2011; 108:6252-7. PMID:21436049; http://dx.doi.org/10.1073/pnas.1102938108.
80. Gallou-Kabani C, Vigé A, Gross MS, Rabès JP, Boileau C, Larue-Achagiotis C, et al. C57BL/6J and A/J mice fed a high-fat diet delineate components of metabolic syndrome. Obesity (Silver Spring) 2007; 15:1996-2005. PMID:17712117; http://dx.doi.org/10.1038/oby.2007.238.
81. Simmgen M, Knauf C, Lopez M, Choudhury AI, Charalambous M, Cantley J, et al. Liver-specific deletion of insulin receptor substrate 2 does not impair hepatic glucose and lipid metabolism in mice. Diabetologia 2006; 49:552-61. PMID:16404553; http://dx.doi.org/10.1007/s00125-005-0084-4.
82. Edwards CA, Rumney C, Davies M, Parrett AM, Dore J, Martin F, et al. A human flora-associated rat model of the breast-fed infant gut. J Pediatr Gastroenterol Nutr 2003; 37:168-77. PMID:12883304; http://dx.doi.org/10.1097/00005176-200308000-00016.
83. Henteges DJ, Marsh WW, Petschow BW, Rahman ME, Dougherty SH. Influence of human milk diet on colonization resistance mechanisms against Salmonella typhimurium in human faecal bacteria-associated mice. Microb Ecol Health Dis 1995; 8:139-49; http://dx.doi.org/10.3109/08910609509140092.
84. Scheepers PTJ, Velders DD, Steenwinkel MJST, van Delft JHM, Driessen W, Stratemans MME, et al. Role of intestinal microflora in the formation of DNA and haemoglobin adducts in rats treated with 2-nutrofluorene and 2-aminofluorene by gavage. Carcinogenesis 1994; 15:1422-41; http://dx.doi.org/10.1093/carcin/15.7.1433.
85. Gordon HA, Pesti L. The gnotobiotic animal as a tool in the study of host microbial relationships. Bacteriol Rev 1971; 35:390-429. PMID:4945725.
86. Barc MC, Bourlioux F, Rigottier-Gois L, Charrin- Sarnel C, Janoir C, Boureau H, et al. Effect of amoxicillin- clavulanic acid on human fecal flora in a gnotobiotic mouse model assessed with fluorescence hybridization using group-specific 16S rRNA probes in combination with flow cytometry. Antimicrob Agents Chemother 2004; 48:1365-8. PMID:15047545; http://dx.doi.org/10.1128/AAC.48.4.1365-1368.2004.
87. Andremont A. Raibaud, Tancrede C. Effect of erythromycin on microbial antagonism: A study in gnotobiotic mice associated with a human faecal flora. J Infect Dis 1983; 148:579-87. PMID:6413596; http://dx.doi.org/10.1093/infdis/148.3.579.
88. Tuohy K, Davies M, Rumsby P, Rumney C, Adams MR, Rowland IR. Monitoring transfer of recombinant and nonrecombinant plasmids between Lactococcus lactis strains and members of the human gastrointestinal microbiota in vivo--impact of donor cell number and diet. J Appl Microbiol 2002; 93:954-64. PMID:12452951; http://dx.doi.org/10.1046/j.1365-2672.2002.01770.x.
89. Hambly RJ, Rumney CJ, Fletcher JME, Rijken PJ, Rowland IR. Effects of high- and low-risk diets on gut microflora-associated biomarkers of colon cancer in human flora-associated rats. Nutr Cancer 1997; 27:250-5. PMID:9101554; http://dx.doi.org/10.1080/01635589709514534.
90. Schellinck HM, Cyr DP, Brown RE. Chapter 7: How many ways can mouse behavioral experiments go wrong? Confounding variables in mouse models of neurodegenerative diseases and how to control them. In: Brockmann HJ, Roper TJ, Naguib M, Wynne- Edwards KE, Mitani J, Simmons LW, eds. Advances in the study of behavior. Burlington MA: Academic Press Inc. 2010: 255-365.
91. Hufeldt MR, Nielsen DS, Vogensen FK, Midtvedt T, Hansen AK. Variation in the gut microbiota of laboratory mice is related to both genetic and environmental factors. Comp Med 2010; 60:336-47. PMID:21262117.
92. Bleich A, Hansen AK. Time to include the gut microbiota in the hygienic standardisation of laboratory rodents. Comp Immunol Microbiol Infect Dis 2012; 35:81-92. PMID:22257867; http://dx.doi.org/10.1016/j.cimid.2011.12.006.
93. Wilson KH, Brown RS, Andersen GL, Tsang J, Sartor B. Comparison of fecal biota from specific pathogen free and feral mice. Anaerobe 2006; 12:249-53. PMID:17070078; http://dx.doi.org/10.1016/j.anaerobe.2006.09.002.
94. Dusko Ehrlich S; MetaHIT consortium. [Metagenomics of the intestinal microbiota: potential applications]. Gastroenterol Clin Biol 2010; 34(Suppl 1):S23-8. PMID:20889001; http://dx.doi.org/10.1016/S0399-8320(10)70017-8.
95. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al.; MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65. PMID:20203603; http://dx.doi.org/10.1038/nature08821.
96. Xu J, Mahowald MA, Ley RE, Lozupone CA, Hamady M, Martens EC, et al. Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol 2007; 5:e156. PMID:17579514; http://dx.doi.org/10.1371/journal.pbio.0050156.
97. Martiny JB, Bohannan BJ, Brown JH, Colwell RK, Fuhrman JA, Green JL, et al. Microbial biogeography: putting microorganisms on the map. Nat Rev Microbiol 2006; 4:102-12. PMID:16415926; http://dx.doi.org/10.1038/nrmicro1341.
98. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006; 124:837-48. PMID:16497592; http://dx.doi.org/10.1016/j.cell.2006.02.017.
99. Kolmeder CA, de Been M, Nikkilä J, Ritamo I, Mättö J, Valmu L, et al. Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One 2012; 7:e29913. PMID:22279554; http://dx.doi.org/10.1371/journal.pone.0029913.
100. Tannock GW. Probiotics: time for a dose of realism. Curr Issues Intest Microbiol 2003; 4:33-42. PMID:14503687.
101. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, et al. A core gut microbiome in obese and lean twins. Nature 2009; 457:480-4. PMID:19043404; http://dx.doi.org/10.1038/nature07540.
102. Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol 1977; 31:107-33. PMID:334036; http://dx.doi.org/10.1146/annurev.mi.31.100177.000543.
103. Walter J, Ley R. The human gut microbiome: ecology and recent evolutionary changes. Annu Rev Microbiol 2011; 65:411-29. PMID:21682646; http://dx.doi.org/10.1146/annurev-micro-090110-102830.
104. Walter J, Hertel C, Tannock GW, Lis CM, Munro K, Hammes WP. Detection of Lactobacillus, Pediococcus, Leuconostoc, and Weissella species in human feces by using group-specific PCR primers and denaturing gradient gel electrophoresis. Appl Environ Microbiol 2001; 67:2578-85. PMID:11375166; http://dx.doi.org/10.1128/AEM.67.6.2578-2585.2001.
105. Dal Bello F, Walter J, Hammes WP, Hertel C. Increased complexity of the species composition of lactic acid bacteria in human feces revealed by alternative incubation condition. Microb Ecol 2003; 45:455-63. PMID:12704557; http://dx.doi.org/10.1007/s00248-003-2001-z.
106. Bunte C, Hertei C, Hammes WP. Monitoring and survival of Lactobacillus paracasei LTH 2579 in food and the human intestinal tract. Syst Appl Microbiol 2000; 23:260-6. PMID:10930079; http://dx.doi.org/10.1016/S0723-2020(00)80013-2.