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Host Genetics and Gut Microbiota

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Beneficial Microorganisms in Multicellular Life Forms

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Abstract

The gut microbiota consists of hundreds to thousands of bacterial species, and is strongly associated with the well-being of the host. Its composition differs among individual hosts, being affected by environmental factors such as food and maternal inoculation. Recently, the relative impact of the host’s genetics has been uncovered in different mammal hosts. Here, we describe the effect of host genetic background on the composition of gut bacterial communities in a murine model, focusing on lactic acid bacteria (LAB) as an important group that contains a variety of strains associated with the improvement of various gut health disorders. Based on 16S-rDNA tRFLP analysis, variation was observed in fecal LAB populations of two genetic mouse lines BALB/C and C57BL/6J. Lactobacillus johnsonii, a potentially probiotic bacterium, appeared at significantly higher levels in the feces of C57BL/6J mice compared to BALB/C. The genetic inheritance of L. johnsonii levels was further tested in reciprocal crosses between the two mouse lines, where each mouse line served alternatively as the male or female parent. The two resultant groups of F1 offspring, having the same genetic content but exposed to different maternal microflora during and after birth, presented similar L. johnsonii levels, confirming that mouse genetics plays a major role in determining these levels, compared to the relatively lower maternal effect. Our findings suggest that mouse genetics has a major effect on the composition of the intestinal LAB population in general, and on the persistence of L. johnsonii in the gut in particular.

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References

  • Alexander AD, Orcutt RP, Henry JC, Baker J, Bissahoyo AC, Threadgill DW (2006) Quantitative PCR assays for mouse enteric flora reveal strain-dependent differences in composition that are influenced by the microenvironment. Mamm Genome 17:1093–1104

    Article  CAS  Google Scholar 

  • Bajzer M, Seeley RJ (2006) Physiology – obesity and gut flora. Nature 444:1009–1010

    Article  PubMed  CAS  Google Scholar 

  • Barbas AS, Lesher AP, Thomas AD, Wyse A, Devalapalli AP, Lee YH, Tan HE, Orndorff PE, Bollinger RR, Parker W (2009) Altering and assessing persistence of genetically modified E. coli MG1655 in the large bowel. Exp Biol Med 234:1174–1185

    Article  CAS  Google Scholar 

  • Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci USA 107:18933–18938

    Article  PubMed  CAS  Google Scholar 

  • Buhnik-Rosenblau K, Danin-Poleg Y, Kashi Y (2011) Predominant effect of host genetics on levels of Lactobacillus johnsonii in mouse gut. Appl Environ Microbiol. In press

    Google Scholar 

  • Buhnik-Rosenblau K, Matsko-Efimov V, Jung M, Shin H, Danin-Poleg Y, Kashi Y (2011) Submitted for publication

    Google Scholar 

  • Broza YY, Danin-Poleg Y, Lerner L, Valinsky L, Broza M, Kashi Y (2009) Epidemiologic study of Vibrio vulnificus infections by using variable number tandem repeats. Emerg Infect Dis 15:1282–1285

    Article  PubMed  Google Scholar 

  • Claesson MJ, van Sinderen D, O’Toole PW (2007) The genus Lactobacillus – a genomic basis for understanding its diversity. FEMS Microbiol Lett 269:22–28

    Article  PubMed  CAS  Google Scholar 

  • Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326:1694–1697

    Article  PubMed  CAS  Google Scholar 

  • Danin-Poleg Y, Cohen LA, Gancz H, Broza YY, Goldshmidt H, Malul E, Valinsky L, Lerner L, Broza M, Kashi Y (2007) Vibrio cholerae strain typing and phylogeny study based on simple sequence repeats. J Clin Microbiol 45:736–746

    Article  PubMed  CAS  Google Scholar 

  • Denou E, Pridmore RD, Berger B, Panoff JM, Arigoni F, Brussow H (2008) Identification of genes associated with the long-gut-persistence phenotype of the probiotic Lactobacillus johnsonii strain NCC533 using a combination of genomics and transcriptome analysis. J Bacteriol 190:3161–3168

    Article  PubMed  CAS  Google Scholar 

  • Dethlefsen L, Eckburg PB, Bik EM, Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21:517–523

    Article  PubMed  Google Scholar 

  • Dethlefsen L, McFall-Ngai M, Relman DA (2007) An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 449:811–818

    Article  PubMed  CAS  Google Scholar 

  • Ducluzeau R (1983) Implantation and development of the gut flora in the newborn animal. Ann Rech Vet 14:354–359

    PubMed  CAS  Google Scholar 

  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638

    Article  PubMed  Google Scholar 

  • Esworthy RS, Smith DD, Chu FF (2010) A strong impact of genetic background on gut microflora in mice. Int J Inflam 2010:986046

    Google Scholar 

  • Farano S, Chierici R, Guerrini P, Vigi V (2003) Intestinal microflora in early infancy: composition and development. Acta Paediatr 91:48–55

    Google Scholar 

  • Firon N, Duksin D, Sharon N (1985) Mannose-specific adherence of Escherichia-coli to Bhk cells that differ in their glycosylation patterns. FEMS Microbiol Lett 27:161–165

    Article  CAS  Google Scholar 

  • Frank DN, Pace NR (2008) Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol 24:4–10

    Article  PubMed  CAS  Google Scholar 

  • Friswell MK, Gika H, Stratford IJ, Theodoridis G, Telfer B, Wilson ID, McBain AJ (2010) Site and strain-specific variation in gut microbiota profiles and metabolism in experimental mice. PLoS One 5:e8584

    Article  PubMed  Google Scholar 

  • Garrett WS, Gordon JI, Glimcher LH (2010) Homeostasis and inflammation in the intestine. Cell 140:859–870

    Article  PubMed  CAS  Google Scholar 

  • Genc MR, Onderdonk A (2011) Endogenous bacterial flora in pregnant women and the influence of maternal genetic variation. BJOG 118:154–163

    Article  PubMed  CAS  Google Scholar 

  • Guandalini S (2010) Update on the role of probiotics in the therapy of pediatric inflammatory bowel disease. Expert Rev Clin Immunol 6:47–54

    Article  PubMed  CAS  Google Scholar 

  • Haller D, Antoine JM, Bengmark S, Erick P, Rijkers GT, Lenoir-Wijnkoop I (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: probiotics in chronic inflammatory bowel disease and the functional disorder irritable bowel syndrome. J Nutr 140:690S–697S

    Article  PubMed  CAS  Google Scholar 

  • Holubar SD, Cima RR, Sandborn WJ, Pardi DS (2010) Treatment and prevention of pouchitis after ileal pouch-anal anastomosis for chronic ulcerative colitis. Cochrane Database Syst Rev 6:CD001176

    PubMed  Google Scholar 

  • Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L (2010) Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One 5:e9836

    Article  PubMed  Google Scholar 

  • Jiang HQ, Bos NA, Cebra JJ (2001) Timing, localization, and persistence of colonization by segmented filamentous bacteria in the neonatal mouse gut depend on immune status of mothers and pups. Infect Immun 69:3611–3617

    Article  PubMed  CAS  Google Scholar 

  • Kalliomaki M, Antoine JM, Herz U, Rijkers GT, Wells JM, Mercenier A (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: prevention and management of allergic diseases by probiotics. J Nutr 140:713S–721S

    Article  PubMed  CAS  Google Scholar 

  • Khachatryan ZA, Ktsoyan ZA, Manukyan GP, Kelly D, Ghazaryan KA, Aminov RI (2008) Predominant role of host genetics in controlling the composition of gut microbiota. PLoS One 3:e3064

    Article  PubMed  Google Scholar 

  • Kovacs A, Ben Jacob N, Tayem H, Halperin E, Iraqi FA, Gophna U (2011) Genotype is a stronger determinant than sex of the mouse gut microbiota. Microb Ecol 61:423–428

    Article  PubMed  Google Scholar 

  • Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI (2005) Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102:11070–11075

    Article  PubMed  CAS  Google Scholar 

  • Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology – human gut microbes associated with obesity. Nature 444:1022–1023

    Article  PubMed  CAS  Google Scholar 

  • Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI (2008a) Evolution of mammals and their gut microbes. Science 320:1647–1651

    Article  PubMed  CAS  Google Scholar 

  • Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008b) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6:776–788

    Article  PubMed  CAS  Google Scholar 

  • Lionetti E, Indrio F, Pavone L, Borrelli G, Cavallo L, Francavilla R (2010) Role of probiotics in pediatric patients with Helicobacter pylori infection: a comprehensive review of the literature. Helicobacter 15:79–87

    Article  PubMed  CAS  Google Scholar 

  • Mai V, Draganov PV (2009) Recent advances and remaining gaps in our knowledge of associations between gut microbiota and human health. World J Gastroenterol 15:81–85

    Article  PubMed  Google Scholar 

  • Mee-Marquet N, Francois P, Domelier AS, Arnault L, Girard N, Schrenzel J, Quentin R (2009) Variable-number tandem repeat analysis and multilocus sequence typing data confirm the epidemiological changes observed with Staphylococcus aureus strains isolated from bloodstream infections. J Clin Microbiol 47:2863–2871

    Article  PubMed  Google Scholar 

  • Mshvildadze M, Neu J, Mai V (2008) Intestinal microbiota development in the premature neonate: establishment of a lasting commensal relationship? Nutr Rev 66:658–663

    Article  PubMed  Google Scholar 

  • Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P, Vancanneyt M, Swings J (2005) Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology-Sgm 151:2141–2150

    Article  CAS  Google Scholar 

  • Nibali L, Madden I, Franch CF, Heitz-Mayfield L, Brett P, Donos N (2011) IL6–174 genotype associated with Aggregatibacter actinomycetemcomitans in Indians. Oral Dis 17:232–237

    Article  PubMed  CAS  Google Scholar 

  • Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J (2010) Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME J 4:377–387

    Article  PubMed  Google Scholar 

  • Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO (2007) Development of the human infant intestinal microbiota. PLoS Biol 5:1556–1573

    Article  CAS  Google Scholar 

  • Pridmore RD, Berger B, Desiere F, Vilanova D, Barretto C, Pittet AC, Zwahlen MC, Rouvet M, Altermann E, Barrangou R, Mollet B, Mercenier A, Klaenhammer T, Arigoni F, Schell MA (2004) The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA 101:2512–2517

    Article  PubMed  CAS  Google Scholar 

  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, 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 JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    Article  PubMed  CAS  Google Scholar 

  • Scharschmidt TC, List K, Grice EA, Szabo R, Renaud G, Lee CCR, Wolfsberg TG, Bugge TH, Segre JA (2009) Matriptase-deficient mice exhibit ichthyotic skin with a selective shift in skin microbiota. J Invest Dermatol 129:2435–2442

    Article  PubMed  CAS  Google Scholar 

  • Sharon N (1987) Bacterial lectins, cell-cell recognition and infectious-disease. FEBS Lett 217:145–157

    Article  PubMed  CAS  Google Scholar 

  • Toivanen P, Vaahtovuo J, Eerola E (2001) Influence of major histocompatibility complex on bacterial composition of fecal flora. Infect Immun 69:2372–2377

    Article  PubMed  CAS  Google Scholar 

  • Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    Article  PubMed  Google Scholar 

  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1:6ra14

    Article  PubMed  Google Scholar 

  • Uchida H, Kinoshita H, Kawai Y, Kitazawa H, Miura K, Shiiba K, Horii A, Kimura K, Taketomo N, Oda M, Yajima T, Saito T (2006) Lactobacilli binding human A-antigen expressed in intestinal mucosa. Res Microbiol 157:659–665

    Article  PubMed  CAS  Google Scholar 

  • Vaahtovuo J, Toivanen P, Eerola E (2003) Bacterial composition of murine fecal microflora is indigenous and genetically guided. FEMS Microbiol Ecol 44:131–136

    Article  PubMed  CAS  Google Scholar 

  • Vaahtovuo J, Eerola E, Toivanen P (2005) Comparison of cellular fatty acid profiles of the microbiota in different gut regions of BALB/c and C57BL/6J mice. Antonie Van Leeuwenhoek 88:67–74

    Article  Google Scholar 

  • Van de Merwe JP, Stegeman JH, Hazenberg MP (1983) The resident faecal flora is determined by genetic characteristics of the host. Implications for Crohn’s disease? Antonie Van Leeuwenhoek 49:119–124

    Article  PubMed  Google Scholar 

  • Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U’Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang BX, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P (2007) Global genetic population structure of Bacillus anthracis. PLoS One 2:e461

    Article  PubMed  Google Scholar 

  • Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT (2010) Metabolic syndrome and altered gut microbiota in mice lacking toll-like receptor 5. Science 328:228–231

    Article  PubMed  CAS  Google Scholar 

  • Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC, Hu C, Wong FS, Szot GL, Bluestone JA, Gordon JI, Chervonsky AV (2008) Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature 455:1109–1113

    Article  PubMed  CAS  Google Scholar 

  • Wolvers D, Antoine JM, Myllyluoma E, Schrezenmeir J, Szajewska H, Rijkers GT (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: Prevention and management of infections by probiotics. J Nutr 140:698S–712S

    Article  PubMed  CAS  Google Scholar 

  • Yildirim S, Yeoman CJ, Sipos M, Torralba M, Wilson BA, Goldberg TL, Stumpf RM, Leigh SR, White BA, Nelson KE (2010) Characterization of the fecal microbiome from non-human wild primates reveals species specific microbial communities. PLoS One 5:e13963

    Article  PubMed  Google Scholar 

  • Zhou X, Hansmann MA, Davis CC, Suzuki H, Brown CJ, Schutte U, Pierson JD, Forney LJ (2010) The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol Med Microbiol 58:169–181

    Article  PubMed  CAS  Google Scholar 

  • Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735

    Article  PubMed  CAS  Google Scholar 

  • Zoetendal EG, Akkermans ADL, de Vos WM (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64:3854–3859

    PubMed  CAS  Google Scholar 

  • Zoetendal EG, Akkermans ADL, Akkermans-van Vliet WM, de Visser JAGM, de Vos WM (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis 13:129–134

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel

    Keren Buhnik-Rosenblau, Yael Danin-Poleg & Yechezkel Kashi

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  1. Keren Buhnik-Rosenblau
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  2. Yael Danin-Poleg
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  3. Yechezkel Kashi
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Correspondence to Yechezkel Kashi .

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  1. , Dept. of Molecular Microbiology and Biot, University of Tel Aviv, Ramat Aviv, 69978, Israel

    Eugene Rosenberg

  2. , Dept. of Microbiology and Biotechnology, University of Tel Aviv, Ramat Aviv, 69978, Israel

    Uri Gophna

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Buhnik-Rosenblau, K., Danin-Poleg, Y., Kashi, Y. (2012). Host Genetics and Gut Microbiota. In: Rosenberg, E., Gophna, U. (eds) Beneficial Microorganisms in Multicellular Life Forms. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-21680-0_21

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