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Human Intestinal Microbiome and In Vivo Animal Models

Year 2017, - Mikrobiyota, 148 - 156, 20.11.2017

Abstract

Studies related to microbiota have increased enormously with the introduction of the next generation squencing technology. Results of these studies have revealed the details of the interaction between the human body and its gut microbiota and the many mysterious and undefi ned topics. It is determined that gut microbiota is not stable, and it adapts to some factors in hours such as daytime diet, drug use (especially antibiotics). One of the methods used for better understanding of this dynamic structure of microbiota and human-gut microbiota interaction is animal models. Animal models offer several advantages in terms of the tractability of microbiota. Many different animal models are suitable for such studies. In this respect, the role of microbiota on human metabolism can be determined more clearly. Steriled and gnotobiotic animal models can be designed to include even from a single microbiota member and to all microbiota members. Almost all of the microbiota studies are concentrated on bacteria. Since viruses, parasites and fungi are also covered by microbiota, animal models should be developed for such microorganisms. By this way, other mysterious topics areas will also be revealed.

References

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  • 2. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., et al. Enterotypes of the human gut microbiome. Nature 2011; 473, 174–80
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  • 6. K.E. Nelson Metagenomics of the Human Body Springer Science+Business Media, LLC 2011
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  • 8. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI and Knight R. Bacterial community variation in human body habitats across space and time. Science 2009; 326, 1694– 97.
  • 9. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey F.E., Knight R. and Gordon J.I. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Science Translational Medicine 2009; 1, 6-14.
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  • 12. Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 2011 334, 105–08
  • 13. Fraune S. and Bosch T.C. Long-term maintenance of species-specifi c bacterial microbiota in the basal metazoan Hydra. Proceedings of the National Academy of Sciences of the United States of America 2007;104, 13146–151.
  • 14. Woyke T., Teeling H., Ivanova N.N., Huntemann M., Richter M., Gloeckner F.O., et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 2006; 443, 950–55.
  • 15. Wong C.N., Ng P. and Douglas A.E. Lowdiversity bacterial community in the gut of the fruitfl y Drosophila melanogaster. Environmental Microbiology 2011;13, 1889–00
  • 16. Shin S.C., Kim S.H., You H., Kim B., Kim A.C., Lee K.A., et al. Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 2011; 334, 670–74.
  • 17. Sharon G., Segal D., Ringo J.M., Hefetz A., Zilber-Rosenberg I. and Rosenberg E. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 2010; 107, 20051–56.
  • 18. Rawls J.F., Mahowald M.A., Ley R.E. and Gordon J.I. Reciprocal gut microbiota transplants from zebrafi sh and mice to germ-free recipients reveal host habitat selection. Cell 2006; 127, 423–33.
  • 19. Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S., et al. Evolution of mammals and their gut microbes. Science 2008; 320, 1647–51
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  • 21. Martens E.C., Chiang H.C. and Gordon J.I. Mucosal glycan foraging enhances fi tness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host and Microbe 2008;4, 447–57.
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  • 24. Gaboriau-Routhiau V., Rakotobe S., Lecuyer E., Mulder I., Lan A., Bridonneau C., et al. The key role of segmented fi lamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009; 31, 677–89.
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  • 26. Faith J.J., Mcnulty N.P., Rey F.E. and Gordon J.I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 2011; 333, 101–04.
  • 27. Becker N., Kunath J., Loh G. and Blaut M. Human intestinal microbiota: characterization of a simplifi ed and stable gnotobiotic rat model. Gut Microbes 2011; 2, 25–33
  • 28. Koren O., Goodrich J.K., Cullender T.C., Spor A., Laitinen K., Backhed H.K., et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 2012; 150, 470–80,
  • 29. Zheng S., Geghman K., Shenoy S. and Li C. Retake the center stage – new development of rat genetics. Journal of Genetics and Genomics 2012; 39, 261–68
  • 30. Wos-Oxley M., Bleich A., Oxley A.P., Kahl S., Janus L.M., Smoczek A., et al. Comparative evaluation of establishing a human gut microbial community within rodent models. Gut Microbes 2012; 3, 234–49.
  • 31. Litten-Brown J.C., Corson A.M. and Clarke L. Porcine models for the metabolic syndrome, digestive and bone disorders: a general overview. Animal 2010; 4, 899–20.

İnsan Bağırsak Mikrobiyomu ve İn Vivo Hayvan Modelleri

Year 2017, - Mikrobiyota, 148 - 156, 20.11.2017

Abstract

Yeni nesil dizileme teknolojisinin kullanıma girmesi ile mikrobiyota üzerine yapılan çalışmalar hız kazanmıştır. Mikrobiyota çalışmaları neticesinde insan vücudu ile kendi bağırsak mikrobiyotası arasındaki etkileşimin ayrıntıları ve karanlıkta kalmış birçok alan aydınlanmaya başlamıştır. Bağırsak mikrobiyotasının stabil olmadığı, gün içindeki diyet, ilaç kullanımı (özellikle antibiyotik) gibi etkenlerle saatler içinde değişim gösterdiği saptanmıştır. Mikrobiyotanın bu dinamik yapısını ve insan-bağırsak mikrobiyotası etkileşimini daha iyi anlamak için uygulanan yöntemlerden birisi de hayvan modelleridir. Hayvan modelleri, mikrobiyotanın ölçülebilirliği ve izlenebilirliği açısından çeşitli avantajlar sunmaktadır. Bu tip çalışmalar farklı hayvan modelleri üzerinde yapılabilmektedir. Bu sayede mikrobiyotanın insan metabolizması üzerindeki rolleri daha net gösterilebilmektedir. Gnotobiyotik ile steril hayvan modelleri ile tek bir mikrobiyota üyesi ve tüm mikrobiyota üyelerini kapsayacak şekilde hayvan modelleri oluşturabilmektedir. Mikrobiyota çalışmalarının hemen hemen tamamı bakteriler üzerine yoğunlaşmış durumdadır. Virüsler, parazitler ve mantarlar da mikrobiyota kapsamında olduğundan göz ardı edilmemeli, bu tür mikroorganizmalar ile ilgili de hayvan modelleri geliştirilmedir. Böylece karanlıkta kalan diğer alanlar da aydınlığa kavuşacaktır

References

  • 1. Qin J., Li R., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464, 59–65.
  • 2. Arumugam M., Raes J., Pelletier E., Le Paslier D., Yamada T., Mende D.R., et al. Enterotypes of the human gut microbiome. Nature 2011; 473, 174–80
  • 3. Julian R. Marchesi, The Human Microbiota and Microbiome 2014; 124-35
  • 4. Fredricks DN. The Human Microbiota: How Microbial Communities Affect Health and Disease, First Edition 2013.
  • 5. Conrad R. et al. The Human Microbiota: Composition, Functions, and Therapeutic Potential Med Sci Rev, 2015; 2:
  • 6. K.E. Nelson Metagenomics of the Human Body Springer Science+Business Media, LLC 2011
  • 7. Smith K, Mccoy KD. and Macpherson A.J. Use of axenic animals in studying the adaptation of mammals to their commensal intestinal 2007
  • 8. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI and Knight R. Bacterial community variation in human body habitats across space and time. Science 2009; 326, 1694– 97.
  • 9. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey F.E., Knight R. and Gordon J.I. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Science Translational Medicine 2009; 1, 6-14.
  • 10. Hansen E.E., Lozupone C.A., Rey F.E., Wu M., Guruge J.L., Narra A., et al. Pangenome of the dominant human gut-associated archaeon, Methanobrevibacter smithii, studied in twins. Proceedings of the National Academy of Sciences of the United States of America 2011;108-1, 4599–06
  • 11. Dethlefsen L., Huse S., Sogin M.L. and Relman D.A. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology 2008, 6, 280.
  • 12. Wu G.D., Chen J., Hoffmann C., Bittinger K., Chen Y.Y., Keilbaugh S.A., et al. (2011) Linking long-term dietary patterns with gut microbial enterotypes. Science 2011 334, 105–08
  • 13. Fraune S. and Bosch T.C. Long-term maintenance of species-specifi c bacterial microbiota in the basal metazoan Hydra. Proceedings of the National Academy of Sciences of the United States of America 2007;104, 13146–151.
  • 14. Woyke T., Teeling H., Ivanova N.N., Huntemann M., Richter M., Gloeckner F.O., et al. Symbiosis insights through metagenomic analysis of a microbial consortium. Nature 2006; 443, 950–55.
  • 15. Wong C.N., Ng P. and Douglas A.E. Lowdiversity bacterial community in the gut of the fruitfl y Drosophila melanogaster. Environmental Microbiology 2011;13, 1889–00
  • 16. Shin S.C., Kim S.H., You H., Kim B., Kim A.C., Lee K.A., et al. Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 2011; 334, 670–74.
  • 17. Sharon G., Segal D., Ringo J.M., Hefetz A., Zilber-Rosenberg I. and Rosenberg E. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America 2010; 107, 20051–56.
  • 18. Rawls J.F., Mahowald M.A., Ley R.E. and Gordon J.I. Reciprocal gut microbiota transplants from zebrafi sh and mice to germ-free recipients reveal host habitat selection. Cell 2006; 127, 423–33.
  • 19. Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S., et al. Evolution of mammals and their gut microbes. Science 2008; 320, 1647–51
  • 20. Faith J.J., Rey F.E., O’Donnell D., Karlsson M., McNulty N.P., Kallstrom G., et al. Creating and characterizing communities of human gut microbes in gnotobiotic mice. The ISME Journal 2010; 4, 1094–98.
  • 21. Martens E.C., Chiang H.C. and Gordon J.I. Mucosal glycan foraging enhances fi tness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host and Microbe 2008;4, 447–57.
  • 22. Goodman A.L., Kallstrom G., Faith J.J., Reyes A., Moore A., Dantas G., et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proceedings of the National Academy of Sciences of the United States of America 2011; 108, 6252–57
  • 23. Round J.L. and Mazmanian S.K. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proceedings of the National Academy of Sciences of the United States of America 2010;107, 12204–09.
  • 24. Gaboriau-Routhiau V., Rakotobe S., Lecuyer E., Mulder I., Lan A., Bridonneau C., et al. The key role of segmented fi lamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009; 31, 677–89.
  • 25. Kuwahara T., Ogura Y., Oshima K., Kurokawa K., Ooka T., Hirakawa H., et al. The lifestyle of the segmented fi lamentous bacterium: a nonculturable gut-associated immunostimulating microbe inferred by whole-genome sequencing. DNA Research 2011; 18, 291–03.
  • 26. Faith J.J., Mcnulty N.P., Rey F.E. and Gordon J.I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science 2011; 333, 101–04.
  • 27. Becker N., Kunath J., Loh G. and Blaut M. Human intestinal microbiota: characterization of a simplifi ed and stable gnotobiotic rat model. Gut Microbes 2011; 2, 25–33
  • 28. Koren O., Goodrich J.K., Cullender T.C., Spor A., Laitinen K., Backhed H.K., et al. Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 2012; 150, 470–80,
  • 29. Zheng S., Geghman K., Shenoy S. and Li C. Retake the center stage – new development of rat genetics. Journal of Genetics and Genomics 2012; 39, 261–68
  • 30. Wos-Oxley M., Bleich A., Oxley A.P., Kahl S., Janus L.M., Smoczek A., et al. Comparative evaluation of establishing a human gut microbial community within rodent models. Gut Microbes 2012; 3, 234–49.
  • 31. Litten-Brown J.C., Corson A.M. and Clarke L. Porcine models for the metabolic syndrome, digestive and bone disorders: a general overview. Animal 2010; 4, 899–20.
There are 31 citations in total.

Details

Subjects Health Care Administration
Journal Section Review
Authors

Hüseyin Hatipoğlu This is me

Mehmet Köroğlu

Publication Date November 20, 2017
Acceptance Date November 20, 2017
Published in Issue Year 2017 - Mikrobiyota

Cite

AMA Hatipoğlu H, Köroğlu M. Human Intestinal Microbiome and In Vivo Animal Models. J Biotechnol and Strategic Health Res. November 2017;1:148-156.
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