Microbiome and Gut Dysbiosis

Chapter
Part of the Experientia Supplementum book series (EXS, volume 109)

Abstract

The gastrointestinal (GI) tract is the residence of trillions of microorganisms that include bacteria, archaea, fungi and viruses. The collective genomes of whole microbial communities (microbiota) integrate the gut microbiome. Up to 100 genera and 1000 distinct bacterial species were identified in digestive tube niches. Gut microbiomes exert permanent pivotal functions by promoting food digestion, xenobiotic metabolism and regulation of innate and adaptive immunological processes. Proteins, peptides and metabolites released locally and at distant sites trigger many cell signalling and pathways. This intense crosstalk maintains the host-microbial homeostasis. Diet, age, diet, stress and diseases cause increases or decreases in relative abundance and diversity bacterial specie of GI and other body sites. Studies in animal models and humans have shown that a persistent imbalance of gut’s microbial community, named dysbiosis, relates to inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders. Notably specific bacterial communities are promising clinical target to treat inflammatory and infectious diseases. In this context, intestinal microbiota transplantation (IMT) is one optional treatment for IBD, in particular to patients with recurrent Clostridium difficile-induced pseudo-membrane colitis. Here we discuss on recent discoveries linking whole gut microbiome dysbiosis to metabolic and inflammatory diseases and potential prophylactic and therapeutic applications of faecal and phage therapy, probiotic and prebiotic diets.

Keywords

Microbiomes Metabolic and gastrointestinal diseases Probiotics Prebiotics Faecal therapy 

Notes

Acknowledgements

We thank Aline Maria da Silva, João Carlos Setubal, Dan Waitzberg and colleagues of University of Sao Paulo and Clinical Hospital of Medical School for insights and productive discussions.

References

  1. Abedon ST (2014) Phage therapy: eco-physiological pharmacology. Scientifica 214:581639Google Scholar
  2. Abubucker S, Segata N, Goll J, Schubert AM, Izard J et al (2012) Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol 8(6):e1002358CrossRefPubMedPubMedCentralGoogle Scholar
  3. Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller MF, Pollard KS, Ruby EG, Taha SA, Unified Microbiome Initiative Consortium (2015) A unified initiative to harness Earth’s microbiomes. Science 350(6260):507–508CrossRefPubMedGoogle Scholar
  4. Almonacid DE, Kraal L, Ossandon FJ, Budovskaya YV, Cardenas JP, Bik EM, Goddard AD, Richman J, Zachary S, Apte ZS (2017) 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS One 12(5):e0176555CrossRefPubMedPubMedCentralGoogle Scholar
  5. Amgarten D, Martins LG, Lombardi KC, Antunes LP, Souza APS et al (2017) Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages. BMC Genomics 18:346CrossRefPubMedPubMedCentralGoogle Scholar
  6. Andersson DI, Hughes D (2014) Microbiological effects of sublethal levels of antibiotics. Nat Rev Microbiol 12:465–478CrossRefPubMedGoogle Scholar
  7. Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, Wang GP (2013) Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 51(9):2884–2892CrossRefPubMedPubMedCentralGoogle Scholar
  8. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T et al (2011) Enterotypes of the human gut microbiome. Nature 473(7346):174–180CrossRefPubMedPubMedCentralGoogle Scholar
  9. Backhed F, Fraser CM, Ringel Y, Sanders ME, Sartor B, Sherman PM, Versalovic J, Young V, Finlay BB (2012) Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host Microbe 12:611–622CrossRefPubMedGoogle Scholar
  10. Baumler AJ, Sparandio V (2016) Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535(7610):85–93CrossRefPubMedPubMedCentralGoogle Scholar
  11. Belizario JE, Napolitano M (2015) Human microbiomes and their role in dysbiosis, common diseases and novel therapeutic approaches. Front Microbiol 6:1050CrossRefPubMedPubMedCentralGoogle Scholar
  12. Bojanova DP, Bordenstein SR (2016) Faecal transplants: what is being transferred? PLoS Biol 13(7):e1002503CrossRefGoogle Scholar
  13. Brandt LJ, Reddy SS (2011) Faecal microbiota transplantation for recurrent Clostridium difficile infection. J Clin Gastroenterol 45(suppl):S159–S167CrossRefPubMedGoogle Scholar
  14. Brown EM, Sadarangani M, Finlay BB (2013a) The role of the immune system in governing host–microbe interactions in the intestine. Nat Immunol 14(2013):660–667CrossRefPubMedGoogle Scholar
  15. Brown CT, Sharon I, Thomas BC, Castelle CJ, Morowitz MJ, Banfield JF (2013b) Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. Microbiome 1(1):30.  https://doi.org/10.1186/2049-2618-1-30CrossRefPubMedPubMedCentralGoogle Scholar
  16. Cani PD, Delzenne NM (2011) The gut microbiome as therapeutic target. Pharmacol Ther 130:202–212CrossRefPubMedGoogle Scholar
  17. Cani DP, Neyrinck AM, Fava F, Knauf C, Burcelin RG, Tuohy KM, Gibson GR, Delzenne NM (2007) Selective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 50:2374–2383CrossRefPubMedGoogle Scholar
  18. Chang C, Lin H (2016) Dysbiosis in gastrointestinal disorders. Best Pract Res Clin Gastroenterol 30:3–15CrossRefPubMedGoogle Scholar
  19. Chatelier EL, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M et al (2013) Richness of human gut microbiome correlates with metabolic markers. Nature 500:541–546CrossRefPubMedGoogle Scholar
  20. Clemente JC, Ursell LK, Parfrey LW, Knight R (2013) The impact of the gut microbiota on human health: an integrative view. Cell 148(6):1258–1270CrossRefGoogle Scholar
  21. Costa FRC, Françozo MCS, Oliveira GG, Ignacio A, Castoldi A, Zamboni DS, Ramos SG, Câmara NO, Zoete MR, Palm NW, Flavell RA, Silva JS, Carlos D (2016) Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset. J Exp Med 213:1223–1239CrossRefPubMedPubMedCentralGoogle Scholar
  22. Cucchiara S, Stronati L, Aloi M (2012) Interactions between intestinal microbiota and innate immune system in pediatric inflammatory bowel disease. J Clin Gastroenterol 46(Suppl):S64–S66CrossRefPubMedGoogle Scholar
  23. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G, Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 107:14691–14696CrossRefPubMedPubMedCentralGoogle Scholar
  24. Debelius J, Song SJ, Vazquez-Baeza Y, Xu ZZ, Gonzalez A, Knight R (2016) Tiny microbes, enormous impacts: what matters in gut microbiome studies? Genome Biol 17:217CrossRefPubMedPubMedCentralGoogle Scholar
  25. Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280CrossRefPubMedPubMedCentralGoogle Scholar
  26. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L et al (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638CrossRefPubMedPubMedCentralGoogle Scholar
  27. Flintoft L (2012) Disease genomics: associations go metagenome-wide. Nat Rev Genet 13 (11):756–757.  https://doi.org/10.1038/nrg3347CrossRefPubMedGoogle Scholar
  28. Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P (2013) Country-specific antibiotic use practices impact the human gut resistome. Genome Res 23(7):31–39CrossRefGoogle Scholar
  29. Fritz JV, Desai MS, Shah P, Schneider JG, Wilmes P (2013) From meta-omics to causality: experimental models for microbiome research. Microbiome 1:14CrossRefPubMedPubMedCentralGoogle Scholar
  30. Fuchs A, Colonna A (2011) Natural killer (NK) and NK-like cells at mucosal epithelia: mediators of anti-microbial defense and maintenance of tissue integrity. Eur J Microbiol Immunol 1:257–266CrossRefGoogle Scholar
  31. Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R et al (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468:67–71CrossRefPubMedGoogle Scholar
  32. Gevers D, Po M, Schloss PD, Huttenhower C (2012) Bioinformatics for the human microbiome project. PLoS Comput Biol 8(11):e1002779CrossRefPubMedPubMedCentralGoogle Scholar
  33. Gilbert JA, Quinn RA, Debelius J, Xu ZZ, Morton J, Garg N, Jansson JK, Dorrestein PC, Knight R (2016) Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 535:94–103CrossRefPubMedGoogle Scholar
  34. Gough N, Shaikh H, Manges AR (2011) Systematic review of intestinal microbiota transplantation (Faecal Bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis 53(10):994–1002CrossRefPubMedGoogle Scholar
  35. Haeussler M, Concordet J-P (2016) Genome editing with CRISPR-Cas9: Can it get any better? J Genet Genomic 43:239–250CrossRefGoogle Scholar
  36. Hankir MK, Seyfried F, Hintschich CA, Diep TA, Kleberg K, Kranz M, Deuther-Conrad W et al (2017) Gastric bypass surgery recruits a gut PPAR-α-striatal D1R pathway to reduce fat appetite in obese rats. Cell Metab 25(2):335–344CrossRefPubMedGoogle Scholar
  37. Harley ITW, Karp CL (2012) Obesity and the gut microbiome: striving for causality. Mol Metab 1(1–2):21–31CrossRefPubMedPubMedCentralGoogle Scholar
  38. Honda K, Littman DR (2016) The microbiota in adaptive immune homeostasis and disease. Nature 535:75–84CrossRefPubMedGoogle Scholar
  39. Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273CrossRefPubMedPubMedCentralGoogle Scholar
  40. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotech 31:233–239CrossRefGoogle Scholar
  41. Jorgensen I, Rayamajhi M, Miao EA (2017) Programmed cell death as a defence against infection. Nat Rev Immunol 17:151–164CrossRefPubMedPubMedCentralGoogle Scholar
  42. Kootte RS, Vrieze A, Holleman F, Dallinga-Thie GM, Zoetendal EG, de Vos WM et al (2012) The therapeutic potential of manipulating gut microbiota in obesity and type2 diabetes mellitus. Diabetes Obes Metab 14:112–120CrossRefPubMedGoogle Scholar
  43. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, Knight R, Huttenhower C, Ley RE (2013) A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. PLoS Comput Biol 9(1):e1002863CrossRefPubMedPubMedCentralGoogle Scholar
  44. Kutter EM, Kuhl SJ, Abedon ST (2015) Re-establishing a place for phage therapy in western medicine. Future Microbiol 10:685–688CrossRefPubMedGoogle Scholar
  45. Lepage P, Leclerc MC, Joossens M, Mondot S, Blottière HM, Raes J, Ehrlich D, Doré J (2013) A metagenomic insight into our gut's microbiome. Gut 62(1):146–158CrossRefPubMedGoogle Scholar
  46. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444:1022–1023CrossRefPubMedGoogle Scholar
  47. Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI (2008) Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 6(10):776–788CrossRefPubMedPubMedCentralGoogle Scholar
  48. Li J, Jia H, Cai X, Zhong H, Feng Q, Sunagawa S et al (2014) An integrated catalogue of reference genes in the human gut microbiome. Nat Biotechnol 32:834–841CrossRefPubMedGoogle Scholar
  49. Marraffini LA, Sontheimer EJ (2008) CRISPR interference limits horizontal gene transfer in 623 Staphylococci by targeting DNA. Science 322(5909):1843–184CrossRefPubMedPubMedCentralGoogle Scholar
  50. Maynard CL, Elson CO, Hatton RD, Weaver CT (2012) Reciprocal interactions of the intestinal microbiota and immune system. Nature 489:231–241CrossRefPubMedPubMedCentralGoogle Scholar
  51. Meijer K, de Vos P, Priebe MG (2010) Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health? Curr Opin Clin Nutr Metab Care 13:715–721CrossRefPubMedGoogle Scholar
  52. Mekkes MC, Weenen TC, Brummer RJ, Claassen E (2014) The development of probiotic treatment in obesity: a review. Benef Microbes 5(1):19–28CrossRefPubMedGoogle Scholar
  53. Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199CrossRefPubMedGoogle Scholar
  54. Moeller AH, Li Y, Mpoudi Ngole E, Ahuka-Mundeke S, Lonsdorf EV, Pusey AE, Peeters M, Hahn BH, Ochman H (2014) Rapid changes in the gut microbiome during human evolution. Proc Natl Acad Sci USA 111(46):16431–16435CrossRefPubMedPubMedCentralGoogle Scholar
  55. O’Mahony SM, Clarke G, Borre YE, Dinan TG, Cryan JF (2015) Serotonin, tryptophan metabolism and the brain-gut-microbiome axis. Behav Brain Res 277:32–48CrossRefPubMedGoogle Scholar
  56. Ostaff MJ, Stange EF, Wehkamp J (2013) Antimicrobial peptides and gut microbiota in homeostasis and pathology. EMBO Mol Med 5:1465–1483CrossRefPubMedPubMedCentralGoogle Scholar
  57. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V et al (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 33(17):5691–5702CrossRefPubMedPubMedCentralGoogle Scholar
  58. Palmer DJ, Metcalfe J, Prescott SL (2012) Preventing disease in the 21st century: the importance of maternal and early infant diet and nutrition. J Allergy Clin Immunol 130(3):733–734CrossRefPubMedGoogle Scholar
  59. Pelfrene E, Willebrand E, Sanches AC, Sebris Z, Cavaleri M (2016) Bacteriophage therapy: a regulatory perspective. J Antimicrob Chemother 71:2071–2207CrossRefPubMedGoogle Scholar
  60. Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, Petersen KF, Kibbey RG, Goodman AL, Shulman GI (2016) Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. Nature 534(7606):213–217CrossRefPubMedPubMedCentralGoogle Scholar
  61. Pornputtapong N, Nookaew I, Nielsen J (2015) Human metabolic atlas: an online resource for human metabolism. Database (Oxford) 2015:bav068.  https://doi.org/10.1093/database/bav068Google Scholar
  62. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65CrossRefPubMedPubMedCentralGoogle Scholar
  63. Reijnders D, Goossens GH, Hermes GDA, Neis EPJG, van der Beek CM, Most J et al (2016) Effects of gut microbiota manipulation by antibiotics on host metabolism in obese humans: a randomized double-blind placebo-controlled trial. Cell Metabol 24:63–74CrossRefGoogle Scholar
  64. Rhoads DD, Wolcott RD, Kuskowski MA, Wolcott BM, Ward LS, Sulakvelidze A (2009) Bacteriophage therapy of venous leg ulcers in humans: results of a phase I safety trial. J Wound Care 18(6):237–244CrossRefPubMedGoogle Scholar
  65. Roberfroid MB (2007) Prebiotics: the concept revisited. J Nutr 137(3):830s–837sCrossRefPubMedGoogle Scholar
  66. Round JL, Mazmanian SK (2009) The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 9(5):313–323CrossRefPubMedPubMedCentralGoogle Scholar
  67. Rupnik M (2015) Toward a true bacteriotherapy for Clostridium difficile infection. N Engl J Med 372:1566–1568CrossRefPubMedGoogle Scholar
  68. Sala P, Belarmino G, Machado NM, Cardinell CS et al (2016) The SURMetaGIT study: design and rationale for a prospective pan-omics examination of the gastrointestional response to Roux-em-Y gastric bypass surgery. J Intl Med Res 44(6):1359–1375CrossRefGoogle Scholar
  69. Sampson TR, Saroj SD, Llewellyn AC, Tzeng YL, Weiss DS (2010) A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature 479:254–257Google Scholar
  70. Sangiuliano B, Perez M, Moreira D, Belizário J (2014) Cell death associated molecular-pattern molecules: inflammatory signalling and control. Mediators Inflamm 2014:249784CrossRefGoogle Scholar
  71. Seeley RJ, Chambers AP, Sandoval DA (2015) The role of gut adaptation in the potent effects of multiple bariatric surgeries on obesity and diabetes. Cell Metab 21:369–378CrossRefPubMedPubMedCentralGoogle Scholar
  72. Selle K, Barrangou R (2015) Harnessing CRISPR-Cas systems for bacterial genome editing. Trends Microbiol 23:225–232CrossRefPubMedGoogle Scholar
  73. Sender R, Fuchs S, Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biol 14(8):e1002533CrossRefPubMedPubMedCentralGoogle Scholar
  74. Sulakvelidze A, Alavidze Z, Morris JC Jr (2001) Bacteriophage therapy. Antimicrob Agents Chemother 45(3):649–659CrossRefPubMedPubMedCentralGoogle Scholar
  75. Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, Singh N, Damman CJ, Hager KR, Nielson H, Miller SI (2015) Faecal microbial transplant effect on clinical outcomes and faecal microbiome in active Crohn’s disease. Inflamm Bowel Dis 21(3):556–563CrossRefPubMedPubMedCentralGoogle Scholar
  76. Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H (2005) Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol 43:3380–3389CrossRefPubMedPubMedCentralGoogle Scholar
  77. Thaiss CA, Zmora N, Levy M, Elinav E (2016) The microbiome and innate immunity. Nature 535:65–74CrossRefPubMedGoogle Scholar
  78. The Human Microbiome Project Consortium, Hutternhower C, Gevers D, Knight R, Abubucker S, Badger JH et al (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–214CrossRefPubMedCentralGoogle Scholar
  79. Tremaroli V, Bäckhed F (2012) Functional interactions between the gut microbiota and host metabolism. Nature 489:242–249CrossRefPubMedGoogle Scholar
  80. 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 444:1027–1031CrossRefPubMedGoogle Scholar
  81. Ukena SN, Singh A, Dringenberg U, Engelhardt R, Seidler U et al (2007) Probiotic Escherichia coli Nissle 1917 inhibits leaky gut by enhancing mucosal integrity. PLoS One 2(12):e1308CrossRefPubMedPubMedCentralGoogle Scholar
  82. Van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JB, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ (2013) Duodenal infusion of donor faeces for recurrent Clostridium difficile. N Engl J Med 368:407–415CrossRefPubMedGoogle Scholar
  83. Vercoe RB, Chang JT, Dy RL, Taylor C, Gristwood T, Clulow JS et al (2013) Cytotoxic chromosomal targeting by CRISPR/Cas systems can reshape bacterial genomes and expel or remodel pathogenicity islands. PLoS Genet 9:e1003454CrossRefPubMedPubMedCentralGoogle Scholar
  84. Verdam FJ, Fuentes S, de Jonge C, Zoetendal EG, Erbil R, Greve JW, Buurman WA, de Vos WM, Rensen SS (2013) Human intestinal microbiota composition is associated with local and systemic inflammation in obesity. Obesity (Silver Spring) 21(12):E607–E615CrossRefGoogle Scholar
  85. Virgin HW (2014) The virome in mammalian physiology and disease. Cell 157(1):142–150CrossRefPubMedPubMedCentralGoogle Scholar
  86. Vrieze A, van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JF, Dallinga-Thie GM, Ackermans MT, Serlie MJ, Oozeer R, Derrien M, Druesne A, van Hylckama Vlieg JE, Bloks VW, Groen AK, Heilig HG, Zoetendal EG, Stroes ES, de Vos WM, Hoekstra JB, Nieuwdorp M (2012) Transfer of intestinal microbiota from lean donors increases insulin sensitivity in subjects with metabolic syndrome. Gastroenterology (4):913–916Google Scholar
  87. Webb CR, Koboziev I, Furr KL, Grisham MB (2016) Protective and pro-inflammatory roles of intestinal bacteria. Pathophysiology 23:67–80CrossRefPubMedCentralGoogle Scholar
  88. Whelan K, Quigley EM (2013) Probiotics in the management of irritable bowel syndrome and inflammatory bowel disease. Curr Opin Gastroenterol 29(2):184–189CrossRefPubMedGoogle Scholar
  89. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdaka G (2009) Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA 106(10):3698–3703CrossRefPubMedPubMedCentralGoogle Scholar
  90. Yosef MM, Kiro R, Qimron U (2015) Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci USA 112(23):7267–7272CrossRefPubMedPubMedCentralGoogle Scholar
  91. Zhang Q, Rho M, Tang H, Doak TG, Ye Y (2013) CRISPR-Cas systems target a diverse collection of invasive mobile genetic elements in human microbiomes. Genome Biol 14:R40CrossRefPubMedPubMedCentralGoogle Scholar
  92. Zhou Y, Mihindukulasuriya KA, Gao H, La Rosa P, Wylie KM, Martin JC et al (2014) Exploration of bacterial community classes in major human habitats. Genome Biol 15(5):R66CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Pharmacology, Institute of Biomedical SciencesUniversity of São PauloSão PauloBrazil
  2. 2.Department of Gastroenterology of Medical SchoolUniversity of Sao PauloSão PauloBrazil

Personalised recommendations