Integrating the characterization of digestive microbiota in phenotyping livestock animals: Towards a new tool for animal health control?;Intégrer la caractérisation du microbiote digestif dans le phénotypage de l'animal de rente: Vers un nouvel outil de maîtrise de la santé en élevage?

Productions Animales

Volumn 27, Issue 3, 2014, Pages 209-222

  Calenge, F ^a   Martin, C ^b,c   Le Floch, N ^d,e   Phocas, F ^a   Morgavi, D ^b,c   Rogel Gaillard, C ^a   Quere P ^f,g  

^a UMR1313 GÉNÉTIQUE ANIMALE ET BIOLOGIE INTÉGRATIVE   (France)

^b UMR1213 HERBIVORES   (France)

^c UNIVERSITÉ CLERMONT AUVERGNE   (France)

^d PEGASE   (France)

^e AGROCAMPUS OUEST   (France)

^f UR1282   (France)

^g UNIVERSITÉ DE TOURS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

EID: 84920856750     PISSN: 09900632     EISSN: 11525428     Source Type: Journal    
DOI: None     Document Type: Article

References (105)

1. Abouesh A., Stone C., Hobbs W.R., 2002. Antimicrobial-induced mania (antibiomania): a review of spontaneous reports. J. Clin. Psychopharmacol., 22, 71-81.
2. Aitken J.D., Gewirtz A.T., 2013. Gut microbiota in 2012: Toward understanding and manipulating the gut microbiota. Nat. Rev. Gastroenterol. Hepatol., 10, 72-74.
3. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., Fernandes G.R., Tap J., Bruls T., Batto J.M., Bertalan M., Borruel N., Casellas F., Fernandez L., Gautier L., Hansen T., Hattori M., Hayashi T., Kleerebezem M., Kurokawa K., Leclerc M., Levenez F., Manichanh C., Nielsen H.B., Nielsen T., Pons N., Poulain J., Qin J., Sicheritz-Ponten T., Tims S., Torrents D., Ugarte E., Zoetendal E.G., Wang J., Guarner F., Pedersen O., de Vos W.M., Brunak S., Doré J., Antolin M., Artiguenave F., Blottière H.M., Almeida M., Brechot C., Cara C., Chervaux C., Cultrone A., Delorme C., Denariaz G., Dervyn R., Foerstner K.U., Friss C., van de Guchte M., Guedon E., Haimet F., Huber W., van Hylckama-Vlieg J., Jamet A., Juste C., Kaci G., Knol J., Lakhdari O., Layec S., Le Roux K., Maguin E., Merieux A., Melo Minardi R., M'Rini C., Muller J., Oozeer R., Parkhill J., Renault P., Rescigno M., Sanchez N., Sunagawa S., Torrejon A., Turner K., Vandemeulebrouck G., Varela E., Winogradsky Y., Zeller G., Weissenbach J., Ehrlich S.D., Bork P., 2011. Enterotypes of the human gut microbiome. Nature, 473, 174-180.
4. Austin B., 2006. The bacterial microflora of fish, revised. Scient. World J., 6, 931-945.
5. Aziz Q., Doré J., Emmanuel A., Guarner F., Quigley E.M., 2013. Gut microbiota and gastrointestinal health: current concepts and future directions. Neurogastroenterol. Motility, 25, 4-15.
6. Backhed F., 2012. Host responses to the human microbiome. Nutr. Rev., 70, Suppl 1, S14-17.
7. Backhed F., Fraser C.M., Ringel Y., Sanders M.E., Sartor R.B., Sherman P.M., Versalovic J., Young V., Finlay B.B., 2012. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe, 12, 611-622.
8. Bailey M.T., Dowd S.E., Galley J.D., Hufnagle A.R., Allen R.G., Lyte M., 2011. Exposure to a social stressor alters the structure of the intestinal microbiota: implications for stressorinduced immunomodulation. Brain Behav. Immun., 25, 397-407.
9. Bercik P., Denou E., Collins J., Jackson W., Lu J., Jury J., Deng Y., Blennerhassett P., Macri J., McCoy K.D., Verdu E.F., Collins S.M., 2011. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterol., 141, 599-609.
10. Biswas A., Kobayashi K.S., 2013. Regulation of intestinal microbiota by the NLR protein family. Int. Immunol., 25, 207-214.
11. Blaser M., Bork P., Fraser C., Knight R., Wang J., 2013. The microbiome explored: recent insights and future challenges. Nat. Rev. Microbiol., 11, 213-217.
12. Blottière H.M., de Vos W.M., Ehrlich S.D., Doré J., 2013. Human intestinal metagenomics: state of the art and future. Curr. Opin. Microbiol., 16, 232-239.
13. Bohorquez D.V., Bohorquez N.E., Ferket P.R., 2011. Ultrastructural development of the small intestinal mucosa in the embryo and turkey poult: A light and electron microscopy study. Poult. Sci., 90, 842-855.
14. Brisbin J.T., Gong J., Sharif S., 2008. Interactions between commensal bacteria and the gut-associated immune system of the chicken. Anim. Health Res. Rev., 9, 101-110.
15. Brown E.M., Sadarangani M., Finlay B.B., 2013. The role of the immune system in governing host-microbe interactions in the intestine. Nat. Immunol., 14, 660-667.
16. Buffie C.G., Pamer E.G., 2013. Microbiotamediated colonization resistance against intestinal pathogens. Nat. Rev. Immunol., 13, 790-801.
17. Callaway T.R., Dowd S.E., Edrington T.S., Anderson R.C., Krueger N., Bauer N., Kononoff P.J., Nisbet D.J., 2010. Evaluation of bacterial diversity in the rumen and feces of cattle fed different levels of dried distillers grains plus solubles using bacterial tag-encoded FLX amplicon pyrosequencing. J. Anim. Sci., 88, 3977-3983.
18. Campbell J.H., Foster C.M., Vishnivetskaya T., Campbell A.G., Yang Z.K., Wymore A., Palumbo A.V., Chesler E.J., Podar M., 2012. Host genetic and environmental effects on mouse intestinal microbiota. ISME J., 6, 2033-2044.
19. Chowdhury S.R., King D.E., Willing B.P., Band M.R., Beever J.E., Lane A.B., Loor J.J., Marini J.C., Rund L.A., Schook L.B., Van Kessel A.G., Gaskins H.R., 2007. Transcriptome profiling of the small intestinal epithelium in germfree versus conventional piglets. BMC Genomics, 8, 215.
20. Chung H., Pamp S.J., Hill J.A., Surana N.K., Edelman S.M., Troy E.B., Reading N.C., Villablanca E.J., Wang S., Mora J.R., Umesaki Y., Mathis D., Benoist C., Relman D.A., Kasper D.L., 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell, 149, 1578-1593.
21. Clemente J.C., Ursell L.K., Parfrey L.W., Knight R., 2012. The impact of the gut microbiota on human health: an integrative view. Cell, 148, 1258-1270.
22. Collins S.M., Bercik P., 2009. The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterol., 136, 2003-2014.
23. Collins S.M., Surette M., Bercik P., 2012. The interplay between the intestinal microbiota and the brain. Nat. Rev. Microbiol., 10, 735-742.
24. Combes S., Michelland R.J., Monteils V., Cauquil L., Soulie V., Tran N.U., Gidenne T., Fortun-Lamothe L., 2011. Postnatal development of the rabbit caecal microbiota composition and activity. FEMS Microbiol. Ecol., 77, 680-689.
25. Combes S., Fortun-Lamothe L., Cauquil L., Gidenne T., 2013. Engineering the rabbit digestive ecosystem to improve digestive health and efficacy. Animal, 7, 1429-1439.
26. Consortium HMP, 2012. Structure, function and diversity of the healthy human microbiome. Nature, 486, 207-214.
27. Cotillard A., Kennedy S.P., Kong L.C., Prifti E., Pons N., Le Chatelier E., Almeida M., Quinquis B., Levenez F., Galleron N., Gougis S., Rizkalla S., Batto J.M., Renault P., Doré J., Zucker J.D., Clement K., Ehrlich S.D., 2013. Dietary intervention impact on gut microbial gene richness. Nature, 500, 585-588.
28. Crhanova M., Hradecka H., Faldynova M., Matulova M., Havlickova H., Sisak F., Rychlik I., 2011. Immune response of chicken gut to natural colonization by gut microflora and to Salmonella enterica serovar enteritidis infection. Infect. Immun., 79, 2755-2763.
29. David L.A., Maurice C.F., Carmody R.N., Gootenberg D.B., Button J.E., Wolfe B.E., Ling A.V., Devlin A.S., Varma Y., Fischbach M.A., Biddinger S.B., Dutton R.J., Turnbaugh P.J., 2014. Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505, 559-563.
30. De Filippo G., Rendina D., Strazzullo P., 2010. Childhood obesity, other cardiovascular risk factors, and premature death. N. Engl. J. Med., 362, 1841-1842.
31. de Menezes A.B., Lewis E., O'Donovan M., O'Neill B.F., Clipson N., Doyle E.M., 2011. Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiol. Ecol., 78, 256-265.
32. Desbonnet L., Garrett L., Clarke G., Bienenstock J., Dinan T.G., 2008. The probiotic Bifidobacteria infantis: An assessment of potential antidepressant properties in the rat. J. Psychiatr. Res., 43, 164-174.
33. Desbonnet L., Garrett L., Clarke G., Kiely B., Cryan J.F., Dinan T.G., 2010. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience, 170, 1179-1188.
34. Dethlefsen L., Relman D.A., 2011. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc. Natl. Acad. Sci. U.S.A., 108, Suppl 1, 4554-4561.
35. Eloe-Fadrosh E.A., Rasko D.A., 2013. The human microbiome: from symbiosis to pathogenesis. Annu. Rev. Med., 64, 145-163.
36. Fonty G., Jouany J.P., Chavarot M., Bonnemoy F., Gouet P., 1991. Development of the rumen digestive functions in lambs placed in a sterile isolator a few days after birth. Reprod. Nutr. Dev., 31, 521-528.
37. Fouts D.E., Szpakowski S., Purushe J., Torralba M., Waterman R.C., MacNeil M.D., Alexander L.J., Nelson K.E., 2012. Next generation sequencing to define prokaryotic and fungal diversity in the bovine rumen. PLoS One, 7, e48289.
38. Gaggia F., Mattarelli P., Biavati B., 2010. Probiotics and prebiotics in animal feeding for safe food production. Int. J. Food Microbiol., 141, Suppl 1, S15-28.
39. Gosalbes M.J., Durban A., Pignatelli M., Abellan J.J., Jimenez-Hernandez N., Perez-Cobas A.E., Latorre A., Moya A., 2011. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One, 6, e17447.
40. Hanstock T.L., Mallet P.E., Clayton E.H., 2010. Increased plasma d-lactic acid associated with impaired memory in rats. Physiol. Behav., 101, 653-659.
41. Hartman A.L., Lough D.M., Barupal D.K., Fiehn O., Fishbein T., Zasloff M., Eisen J.A., 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc. Natl. Acad. Sci. U.S.A., 106, 17187-17192.
42. Holmes E., Li J.V., Marchesi J.R., Nicholson J.K., 2012. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab., 16, 559-564.
43. Hooper L.V., Littman D.R., Macpherson A.J., 2012. Interactions between the microbiota and the immune system. Science, 336, 1268-1273.
44. Howarth G.S., Wang H., 2013. Role of endogenous microbiota, probiotics and their biological products in human health. Nutrients, 5, 58-81.
45. Huyghebaert G., Ducatelle R., Van Immerseel F., 2011. An update on alternatives to antimicrobial growth promoters for broilers. Vet. J., 187, 182-188.
46. Imaoka A., Setoyama H., Takagi A., Matsumoto S., Umesaki Y., 2004. Improvement of human faecal flora-associated mouse model for evaluation of the functional foods. J. Appl. Microbiol., 96, 656-663.
47. Inman C.F., Haverson K., Konstantinov S.R., Jones P.H., Harris C., Smidt H., Miller B., Bailey M., Stokes C., 2010. Rearing environment affects development of the immune system in neonates. Clin. Exp. Immunol., 160, 431-439.
48. Isaacson R., Kim H.B., 2012. The intestinal microbiome of the pig. Anim. Health Res. Rev., 13, 100-109.
49. Jami E., Mizrahi I., 2012. Composition and similarity of bovine rumen microbiota across individual animals. PLoS One, 7, e33306.
50. Jeffery I.B., O'Toole P.W., 2013. Diet-microbiota interactions and their implications for healthy living. Nutrients, 5, 234-252.
51. Jin C., Henao-Mejia J., Flavell R.A., 2013. Innate immune receptors: key regulators of metabolic disease progression. Cell. Metab., 17, 873-882.
52. Kamada N., Nunez G., 2013. Role of the gut microbiota in the development and function of lymphoid cells. J. Immunol., 190, 1389-1395.
53. Khachatryan Z.A., Ktsoyan Z.A., Manukyan G.P., Kelly D., Ghazaryan K.A., Aminov R.I., 2008. Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One. 26, e3064.
54. Khafipour E., Li S., Plaizier J.C., Krause D.O., 2009. Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Appl. Environ. Microbiol., 75, 7115-7124.
55. Lanning D.K., Rhee K.J., Knight K.L., 2005. Intestinal bacteria and development of the B-lymphocyte repertoire. Trends Immunol., 26, 419-425.
56. Le Gall M., Gallois M., Seve B., Louveau I., Holst J.J., Oswald I.P., Lalles J.P., Guilloteau P., 2009. Comparative effect of orally administered sodium butyrate before or after weaning on growth and several indices of gastrointestinal biology of piglets. Br. J. Nutr., 102, 1285-1296.
57. Li R.W., Rinaldi M., Capuco A.V., 2011. Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle. Vet. Res., 42, 114.
58. Li R.W., Wu S., Li W., Navarro K., Couch R.D., Hill D., Urban J.F., Jr., 2012. Alterations in the porcine colon microbiota induced by the gastrointestinal nematode Trichuris suis. Infect. Immun., 80, 2150-2157.
59. Lotrich F.E., El-Gabalawy H., Guenther L.C., Ware C.F., 2011. The role of inflammation in the pathophysiology of depression: different treatments and their effects. J. Rheumatol., Suppl, 88, 48-54.
60. Lu K., Abo R.P., Schlieper K.A., Graffam M.E., Levine S., Wishnok J.S., Swenberg J.A., Tannenbaum S.R., Fox J.G., 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ. Health Perspect., 122, 284-291.
61. Mann E.R., Landy J.D., Bernardo D., Peake S.T., Hart A.L., Al-Hassi H.O., Knight S.C., 2013. Intestinal dendritic cells: their role in intestinal inflammation, manipulation by the gut microbiota and differences between mice and men. Immunol. Lett., 150, 30-40.
62. Martin C., Brossard L., Doreau M., 2006. Mécanismes d'apparition de l'acidose ruminale latente et conséquences physiopathologiques et zootechniques. INRA Prod. Anim., 19, 93-107.
63. Maslowski K.M., Mackay C.R., 2011. Diet, gut microbiota and immune responses. Nat. Immunol., 12, 5-9.
64. Michelland R.J., Monteils V., Zened A., Combes S., Cauquil L., Gidenne T., Hamelin J., Fortun-Lamothe L., 2009. Spatial and temporal variations of the bacterial community in the bovine digestive tract. J. Appl. Microbiol., 107, 1642-1650.
65. Michelland R.J., Combes S., Monteils V., Cauquil L., Gidenne T., Fortun-Lamothe L., 2011. Rapid adaptation of the bacterial community in the growing rabbit caecum after a change in dietary fibre supply. Animal, 5, 1761-1768.
66. Michelland R.J., Combes S., Monteils V., Bayourthe C., Cauquil L., Enjalbert F., Julien C., Kimsé M., Troegeler-Meynadier A., Zened A., Gidenne T., Fortun-Lamothe L., 2012. Analyse comparée des écosystèmes digestifs du rumen de la vache et du caecum du lapin. INRA Prod. Anim., 25, 395-406.
67. Million M., Lagier J.C., Yahav D., Paul M., 2013. Gut bacterial microbiota and obesity. Clin. Microbiol. Infect., 19, 305-313.
68. Moeller A.H., Degnan P.H., Pusey A.E., Wilson M.L., Hahn B.H., Ochman H., 2012. Chimpanzees and humans harbour compositionally similar gut enterotypes. Nat. Commun., 3, 1179.
69. Moeller A.H., Ochman H., 2013. Factors that drive variation among gut microbial communities. Gut Microbes, 4, 403-408.
70. Monteils V., Cauquil L., Combes S., Godon J.J., Gidenne T., 2008. Potential core species and satellite species in the bacterial community within the rabbit caecum. FEMS Microbiol. Ecol., 66, 620-629.
71. Morgavi D.P., Kelly W.J., Janssen P.H., Attwood G.T., 2013. Rumen microbial (meta)genomics and its application to ruminant production. Animal, 7, Suppl 1, 184-201.
72. Morowitz M.J., Denef V.J., Costello E.K., Thomas B.C., Poroyko V., Relman D.A., Banfield J.F., 2011. Strain-resolved community genomic analysis of gut microbial colonization in a premature infant. Proc. Natl Acad. Sci. USA, 108, 1128-1133.
73. Mulder I.E., Schmidt B., Stokes C.R., Lewis M., Bailey M., Aminov R.I., Prosser J.I., Gill B.P., Pluske J.R., Mayer C.D., Musk C.C., Kelly D., 2009. Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol., 7, 79, doi:10.1186/1741-7007-7-79.
74. Mulder I.E., Schmidt B., Lewis M., Delday M., Stokes C.R., Bailey M., Aminov R.I., Gill B.P., Pluske J.R., Mayer C.D., Kelly D., 2011. Restricting microbial exposure in early life negates the immune benefits associated with gut colonization in environments of high microbial diversity. PLoS One, 6, e28279.
75. Oikonomou G., Teixeira A.G., Foditsch C., Bicalho M.L., Machado V.S., Bicalho R.C., 2013. Fecal microbial diversity in pre-weaned dairy calves as described by pyrosequencing of metagenomic 16S rDNA. Associations of Faecalibacterium species with health and growth. PLoS One, 8, e63157.
76. Ottaviani E., Ventura N., Mandrioli M., Candela M., Franchini A., Franceschi C., 2011. Gut microbiota as a candidate for lifespan extension: an ecological/evolutionary perspective targeted on living organisms as metaorganisms. Biogerontology, 12, 599-609.
77. Phocas F., Bobe J., Bodin L., Charley B., Dourmad J.Y., Friggens N.C. Hocquette J.F., Le Bail P.Y., Le Bihan-Duvao E., Mormède P., Quéré P., Schelcher F., 2014., Des animaux plus robustes: un enjeu majeur pour le développement durable des productions animales nécessitant l'essor du phénotypage fin et à haut débit. In: Phénotypage des animaux d'élevage. Phocas F. (Ed). Dossier, INRA Prod. Anim., 27, 181-194.
78. Pluske J.R., 2013. Feed-and feed additivesrelated aspects of gut health and development in weanling pigs. J. Anim. Sci. Biotechnol., 4, 1.
79. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., Mende D.R., Li J., Xu J., Li S., Li D., Cao J., Wang B., Liang H., Zheng H., Xie Y., Tap J., Lepage P., Bertalan M., Batto J.M., Hansen T., Le Paslier D., Linneberg A., Nielsen H.B., Pelletier E., Renault P., Sicheritz-Ponten T., Turner K., Zhu H., Yu C., Jian M., Zhou Y., Li Y., Zhang X., Qin N., Yang H., Wang J., Brunak S., Doré J., Guarner F., Kristiansen K., Pedersen O., Parkhill J., Weissenbach J., Bork P., Ehrlich S.D., 2010. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65.
80. Rist V.T., Eklund M., Bauer E., Sauer N., Mosenthin R., 2012. Effect of feeding level on the composition of the intestinal microbiota in weaned piglets. J. Anim. Sci., 90, Suppl 4, 19-21.
81. Rosenstiel P., 2013. Stories of love and hate: innate immunity and host-microbe crosstalk in the intestine. Curr. Opin. Gastroenterol., 29, 125-132.
82. Salonen A., de Vos W.M., Palva A., 2010. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology, 156, 3205-3215.
83. Sansonetti P.J., 2011. To be or not to be a pathogen: that is the mucosally relevant question. Mucosal. Immunol., 4, 8-14.
84. Sayegh C.E., Ratcliffe M.J., 2000. Perinatal deletion of B cells expressing surface Ig molecules that lack V(D)J-encoded determinants in the bursa of Fabricius is not due to intrafollicular competition. J. Immunol., 164, 5041-5048.
85. Schmidt B., Mulder I.E., Musk C.C., Aminov R.I., Lewis M., Stokes C.R., Bailey M., Prosser J.I., Gill B.P., Pluske J.R., Kelly D., 2011. Establishment of normal gut microbiota is compromised under excessive hygiene conditions. PLoS One, 6, e28284.
86. Segata N., Haake S.K., Mannon P., Lemon K.P., Waldron L., Gevers D., Huttenhower C., Izard J., 2012. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol., 13, R42.
87. Sekelja M., Rud I., Knutsen S.H., Denstadli V., Westereng B., Naes T., Rudi K., 2012. Abrupt temporal fluctuations in the chicken fecal microbiota are explained by its gastrointestinal origin. Appl. Environ. Microbiol., 78, 2941-2948.
88. Shirkey T.W., Siggers R.H., Goldade B.G., Marshall J.K., Drew M.D., Laarveld B., Van Kessel A.G., 2006. Effects of commensal bacteria on intestinal morphology and expression of proinflammatory cytokines in the gnotobiotic pig. Exp. Biol. Med., 231, 1333-1345.
89. Shojadoost B., Vince A.R., Prescott J.F., 2012. The successful experimental induction of necrotic enteritis in chickens by Clostridium perfringens: a critical review. Vet. Res., 43, 74.
90. Sommer F., Backhed F., 2013. The gut microbiota-masters of host development and physiology. Nat. Rev. Microbiol., 11, 227-238.
91. Sonnenberg G.F., Fouser L.A., Artis D., 2011. Border patrol: regulation of immunity, inflammation and tissue homeostasis at barrier surfaces by IL-22. Nat. Immunol., 12, 383-390.
92. 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.
93. Suzuki K., Ha S.A., Tsuji M., Fagarasan S., 2007. Intestinal IgA synthesis: a primitive form of adaptive immunity that regulates microbial communities in the gut. Semin. Immunol., 19, 127-135.
94. Taschuk R., Griebel P.J., 2012. Commensal microbiome effects on mucosal immune system development in the ruminant gastrointestinal tract. Anim. Health Res. Rev., 13, 129-141.
95. Torok V.A., Ophel-Keller K., Loo M., Hughes R.J., 2008. Application of methods for identifying broiler chicken gut bacterial species linked with increased energy metabolism. Appl. Environ. Microbiol., 74, 783-791.
96. Turnbaugh P.J., Hamady M., Yatsunenko T., Cantarel B.L., Duncan A., Ley R.E., Sogin M.L., Jones W.J., Roe B.A., Affourtit J.P., Egholm M., Henrissat B., Heath A.C., Knight R., Gordon J.I., 2009. A core gut microbiome in obese and lean twins. Nature, 457, 480-484.
97. Vrieze A., de Groot P.F., Kootte R.S., Knaapen M., van Nood E., Nieuwdorp M., 2013. Fecal transplant: A safe and sustainable clinical therapy for restoring intestinal microbial balance in human disease? Best Pract. Res. Clin. Gastroenterol., 27, 127-137.
98. Willing B.P., Van Kessel A.G., 2007. Enterocyte proliferation and apoptosis in the caudal small intestine is influenced by the composition of colonizing commensal bacteria in the neonatal gnotobiotic pig. J. Anim. Sci., 85, 3256-3266.
99. Willing B.P., Van Kessel A.G., 2009. Intestinal microbiota differentially affect brush border enzyme activity and gene expression in the neonatal gnotobiotic pig. J. Anim. Physiol. Anim. Nutr., 93, 586-595.
100. Wong S., Rawls J.F., 2012. Intestinal microbiota composition in fishes is influenced by host ecology and environment. Mol. Ecol., 21, 3100-3102.
101. Xu Z., Parra D., Gomez D., Salinas I., Zhang Y.A., von Gersdorff Jorgensen L., Heinecke R.D., Buchmann K., Lapatra S., Sunyer J.O., 2013. Teleost skin, an ancient mucosal surface that elicits gut-like immune responses. Proc. Natl. Acad. Sci. USA., 110, 13097-13102.
102. Yeoman C.J., Chia N., Jeraldo P., Sipos M., Goldenfeld N.D., White B.A., 2012. The microbiome of the chicken gastrointestinal tract. Anim. Health Res. Rev., 13, 89-99.
103. Yi P., Li L., 2012. The germfree murine animal: an important animal model for research on the relationship between gut microbiota and the host. Vet. Microbiol., 157, 1-7.
104. Zebeli Q., Metzler-Zebeli B.U., 2012. Interplay between rumen digestive disorders and dietinduced inflammation in dairy cattle. Res. Vet. Sci., 93, 1099-1108.
105. Zhu X.Y., Zhong T., Pandya Y., Joerger R.D., 2002. 16S rRNA-based analysis of microbiota from the cecum of broiler chickens. Appl. Environ. Microbiol., 68, 124-137.