Pets as a Novel Microbiome-Based Therapy

  • Mariana C. Salas GarciaEmail author
  • Ashley R. Schorr
  • Wyatt Arnold
  • Na Fei
  • Jack A. Gilbert


While genomics can be used to determine genetic susceptibility to certain illnesses, genetic-based approaches alone are rarely capable of predicting the onset of a disease. Environmental factors, such as microbial exposure, often play a significant role in determining human susceptibility to illness, which impacts the genetic predictability of a disease in many cases. While humans are exposed to microbes in almost every facet of their daily lives, one vector has become of particular interest as of late: pets. In addition to the mental and physical benefits conferred by pets unto their owners, it is thought that human exposure to animal-associated microbes can play a significant role in bolstering human health. In response to this, a new treatment that leverages exposure to pet-associated microbes is being proposed for diseases such as asthma, atopic dermatitis, rhinitis, cardiovascular disease, obesity, and even depression. Emergent treatments like these, which have grown out of the human microbiome study, have begun to open up new frontiers in the field of personalized medicine. Microbial therapies such as probiotics, fecal microbiome transplants, and personalized diets are already having a substantial impact on patient care and are heralding in a new vision of precision medicine. Microbiome-based therapeutics involving microbial exposure in homes have been increasingly investigated for their potential to prevent and treat chronic diseases. This chapter explores the evidence that symbioses between humans and their cohabiting pets shape the interaction between microbes, host, and the environment and how that interaction affects human health and disease.


Pet Microbiome Human disease Allergies Therapy 


  1. Al-Shehri SS, Knox CL, Liley HG, Cowley DM, Wright JR, Henman MG et al (2015) Breastmilk-saliva interactions boost innate immunity by regulating the oral microbiome in early infancy. PLoS One 10(9):e0135047. Scholar
  2. Anandan R, Dharumadurai D, Manogaran GP (2016) An introduction to Actinobacteria. Scholar
  3. Anandharaj M, Sivasankari B, Parveen Rani R (2014) Effects of probiotics, prebiotics, and synbiotics on hypercholesterolemia: a review. Chinese J Biol 2014:1–7. Scholar
  4. Arnold, C. (2012). Gut microbes may drive evolution – Scientific American. Retrieved 13 Jan 2018, from Scholar
  5. Azad MB, Konya T, Maughan H, Guttman DS, Field CJ, Sears MR et al (2013) Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity. Allergy Asthma Clin Immunol: Off J Can Soc Aller Clin Immunol 9(1):15. Scholar
  6. Bäckhed F, Roswall J, Peng Y, Feng Q, Jia H, Kovatcheva-Datchary P et al (2015) Dynamics and stabilization of the human gut microbiome during the first year of life. Cell Host Microbe 17(5):690–703. Scholar
  7. Bisgaard H, Li N, Bonnelykke K, Chawes BLK, Skov T, Paludan-Müller G et al (2011) Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age. J Allergy Clin Immunol 128(3):646–652.e5. Scholar
  8. Blaser MJ (2017) The theory of disappearing microbiota and the epidemics of chronic diseases [Comments and Opinion]. 17:461. Scholar
  9. Bloomfield SF, Rook GAW, Scott EA, Shanahan F, Stanwell-Smith R, Turner P (2016) Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene. Perspect Public Health 136(4):213–224. Scholar
  10. Bonamichi-Santos R, Aun MV, Agondi RC, Kalil J, Giavina-Bianchi P (2015) Microbiome and asthma: what have experimental models already taught us? [Research article]. 2015:1. Scholar
  11. Borody TJ, Khoruts A (2012) Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol 9(2):88–96. Scholar
  12. Bottero E, Benvenuti E, Ruggiero P (2017) Fecal microbiota transplantation (FMT) in 16 dogs with idiopatic IBD. Veterinaria (Cremona) 31(1):31–45. Retrieved from Scholar
  13. Byrd AL, Belkaid Y, Segre JA (2018) The human skin microbiome. Nat Rev Microbiol 16(3):143–155. Scholar
  14. Campanaro S, Treu L, Kougias PG, Zhu X, Angelidaki I (2018) Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies. Sci Rep 8(1):1926. Scholar
  15. Canines and Childhood Cancer: Pilot Study Report (n.d.). Retrieved 14 Mar 2018, from
  16. Carr S, Rockett B (2017) Fostering secure attachment: experiences of animal companions in the foster home. Attach Hum Dev 19(3):259–277. Scholar
  17. Charnetski CJ, Riggers S, Brennan FX (2004) Effect of petting a dog on immune system function. Psychol Rep 95(3_suppl):1087–1091. Scholar
  18. 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(5960):1694–1697. Scholar
  19. Craig JM (2016) Atopic dermatitis and the intestinal microbiota in humans and dogs. Veterinary Med Sci 2(2):95–105. Scholar
  20. Dannemiller KC, Gent JF, Leaderer BP, Peccia J (2016) Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children. Indoor Air 26(2):179–192. Scholar
  21. Dash S, Clarke G, Berk M, Jacka FN (2015) The gut microbiome and diet in psychiatry: focus on depression. Curr Opin Psychiatry 28(1):1. Scholar
  22. Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T, Milella L et al (2012) Correction: the canine oral microbiome. PLoS One 7(6).
  23. Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., … Clemente, J. C. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nat Med, 22(3), 250–253. Scholar
  24. Doron S, Snydman DR (2015) Risk and safety of probiotics. Clin Infect Dis 60(suppl_2):S129–S134. Scholar
  25. Fujimura KE, Johnson CC, Ownby DR, Cox MJ, Brodie EL, Havstad SL et al (2010) Man’s best friend? The effect of pet ownership on house dust microbial communities. J Allergy Clin Immunol 126(2):410–412.e3. Scholar
  26. Fuller R (1991) Probiotics in human medicine. Gut 32(4):439–442. Retrieved from Scholar
  27. Garcia-Mazcorro J, Chaitman J, Jergens A, Gaschen F, Marks S, Marroquin A et al (2016) Commentary on key aspects of fecal microbiota transplantation in small animal practice. Veterinary Medicine: Research and Reports 2016:71. Scholar
  28. Gismondo MR, Drago L, Lombardi A (1999) Review of probiotics available to modify gastrointestinal flora. Int J Antimicrob Agents 12(4):287–292. Scholar
  29. Goldstein EJC, Abrahamian FM (2015) Diseases transmitted by cats. Microbiology Spectrum 3(5).
  30. Guo Y, Li P, Tang J, Han X, Zou X, Xu G et al (2016) Prevalence of atopic dermatitis in Chinese children aged 1–7 ys. Sci Rep 6(29751).
  31. Hartmann EM, Hickey R, Hsu T, Betancourt Román CM, Chen J, Schwager R et al (2016) Antimicrobial chemicals are associated with elevated antibiotic resistance genes in the indoor dust microbiome. Environ Sci Technol 50(18):9807–9815. Scholar
  32. Hedlin G, Graff-Lonnevig V, Heilborn H, Lilja G, Norrlind K, Pegelow K-O et al (1986) Immunotherapy with cat- and dog-dander extracts: II. In vivo and in vitro immunologic effects observed in a 1-year double-blind placebo study. J Allergy Clin Immunol 77(3):488–496. Scholar
  33. Hoffmann AR, Patterson AP, Diesel A, Lawhon SD, Ly HJ, Stephenson CE et al (2014) The skin microbiome in healthy and allergic dogs. PLoS One 9(1):e83197. Scholar
  34. Hoffmann AR, Proctor LM, Surette MG, Suchodolski JS (2016) The microbiome: the trillions of microorganisms that maintain health and cause disease in humans and companion animals. Vet Pathol 53(1):10–21. Scholar
  35. Hoisington AJ, Brenner LA, Kinney KA, Postolache TT, Lowry CA (2015) The microbiome of the built environment and mental health. Microbiome 3(60):60. Scholar
  36. Hölscher B, Frye C, Wichmann H-E, Heinrich J (2002) Exposure to pets and allergies in children. Pediatr Aller Immunol: Off Publ Eur Soc Pediatr Aller Immunol 13(5):334–341CrossRefGoogle Scholar
  37. Hooda S, Minamoto Y, Suchodolski JS, Swanson KS (2012) Current state of knowledge: the canine gastrointestinal microbiome. Anim Health Res Rev 13(1):78–88. Scholar
  38. Huang YJ, Boushey HA (2014) The microbiome and asthma. Ann Am Thorac Soc 11(Supplement 1):S48–S51. Scholar
  39. Jernberg C, Löfmark S, Edlund C, Jansson JK (2010) Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology 156(11):3216–3223. Scholar
  40. Johnson CC, Ownby DR (2017) The infant gut bacterial microbiota and risk of pediatric asthma and allergic diseases. Transl Res 179.(Supplement C):60–70. Scholar
  41. Karst SM, Dueholm MS, McIlroy SJ, Kirkegaard RH, Nielsen PH, Albertsen M (2018) Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias. Nat Biotechnol 36(2):190–195. Scholar
  42. Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474(7351):327–336. Scholar
  43. Klepeis NE, Nelson WC, Ott WR, Robinson JP, Tsang AM, Switzer P et al (2001) The National Human Activity Pattern Survey (NHAPS): a resource for assessing exposure to environmental pollutants. J Expo Anal Environ Epidemiol 11(3):231–252. Scholar
  44. Knight R (2018) Expanding our understanding of the role of the microbiome in health and disease. Arch Med Res 48:663. Scholar
  45. Lambrecht BN, Hammad H (2017) The immunology of the allergy epidemic and the hygiene hypothesis. Nat Immunol 18(10):1076–1083. Scholar
  46. Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM et al (2014) Longitudinal analysis of microbial interaction between humans and the indoor environment. Science 345(6200):1048–1052. Scholar
  47. Lehtimäki J, Karkman A, Laatikainen T, Paalanen L, von Hertzen L, Haahtela T et al (2017) Patterns in the skin microbiota differ in children and teenagers between rural and urban environments. Sci Rep 7(45651).
  48. Leickly FE (2003) Effect of cat and dog ownership on sensitization and development of asthma among preteenage children. Pediatrics 112(supplement 2):455–455. Retrieved from Scholar
  49. Levin AM, Sitarik AR, Havstad SL, Fujimura KE, Wegienka G, Cassidy-Bushrow AE et al (2016) Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity. Sci Rep 6.
  50. Li Q, Lauber CL, Czarnecki-Maulden G, Pan Y, Hannah SS (2017) Effects of the dietary protein and carbohydrate ratio on gut microbiomes in dogs of different body conditions. MBio 8(1):e01703-16. Scholar
  51. Maes M, Kubera M, Leunis JC (2008) The gut-brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of LPS from gram negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression. Neuro Endocrinol Lett 29(1):117–124Google Scholar
  52. Mandhane PJ, Sears MR, Poulton R, Greene JM, Lou WYW, Taylor DR, Hancox RJ (2009) Cats and dogs and the risk of atopy in childhood and adulthood. J Allergy Clin Immunol 124(4):745–750.e4. Scholar
  53. Martinez FD (2014) The human microbiome. Early life determinant of health outcomes. Ann Am Thorac Soc 11(Suppl 1):S7–S12. Scholar
  54. McCloskey K, Vuillermin P, Carlin JB, Cheung M, Skilton MR, Tang ML et al (2017) Perinatal microbial exposure may influence aortic intima-media thickness in early infancy. Int J Epidemiol 46(1):209–218. Scholar
  55. McCune S, Kruger KA, Griffin JA, Esposito L, Freund LS, Hurley KJ, Bures R (2014) Evolution of research into the mutual benefits of human–animal interaction. Anim Front 4(3):49–58. Scholar
  56. Milani C, Lugli GA, Duranti S, Turroni F, Mancabelli L, Ferrario C et al (2015) Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut. Sci Rep 5:15782. Scholar
  57. Miletto M, Lindow SE (2015) Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences. Microbiome 3(61):61. Scholar
  58. Mimee M, Citorik RJ, Lu TK (2016) Microbiome therapeutics — advances and challenges. Adv Drug Deliv Rev 105:44–54. Scholar
  59. Nagasawa M, Kikusui T, Onaka T, Ohta M (2009) Dog’s gaze at its owner increases owner’s urinary oxytocin during social interaction. Horm Behav 55:434–441. Scholar
  60. Nermes M, Niinivirta K, Nylund L, Laitinen K, Matomäki J, Salminen S, Isolauri E (2013) Perinatal pet exposure, faecal microbiota, and wheezy bronchitis: is there a connection? [Research article]. 2013:1. Scholar
  61. Nermes M, Endo A, Aarnio J, Salminen S, Isolauri E (2015) Furry pets modulate gut microbiota composition in infants at risk for allergic disease. J Allergy Clin Immunol 136(6):1688–1690.e1. Scholar
  62. Neu J (2015) Developmental aspects of maternal-fetal, and infant gut microbiota and implications for long-term health. Maternal Health, Neonatology and Perinatology 1(6):6. Scholar
  63. Noli C (2017) The microbiome of dogs and cats – what do we know in 2017? Revue Vétérinaire Clinique 52(3):93–98. Scholar
  64. Ober C, Yao T-C (2011) The genetics of asthma and allergic disease: a 21st century perspective. Immunol Rev 242(1):10–30. Scholar
  65. Oh C, Lee K, Cheong Y, Lee S-W, Park S-Y, Song C-S et al (2015) Comparison of the oral microbiomes of canines and their owners using next-generation sequencing. PLoS One 10(7):e0131468. Scholar
  66. Older CE, Diesel A, Patterson AP, Meason-Smith C, Johnson TJ, Mansell J et al (2017) The feline skin microbiota: the bacteria inhabiting the skin of healthy and allergic cats. PLoS One 12(6):e0178555. Scholar
  67. Ownby D, Johnson CC (2016) Recent understandings of pet allergies. F1000Research 5. Scholar
  68. Ownby DR, Johnson CC, Peterson EL (2002) Exposure to dogs and cats in the first year of life and risk of allergic sensitization at 6 to 7 years of age. JAMA 288(8):963–972. Scholar
  69. Park H-J, Lee S-E, Kim H-B, Isaacson R e, Seo K-W, Song K-H (2015) Association of obesity with serum leptin, adiponectin, and serotonin and gut microflora in beagle dogs. J Vet Intern Med 29(1):43–50. Scholar
  70. Perez-Muñoz ME, Arrieta M-C, Ramer-Tait AE, Walter J (2017) A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome. Microbiome 5(48):48. Scholar
  71. Prince BT, Mandel MJ, Nadeau K, Singh AM (2015) Gut microbiome and the development of food allergy and allergic disease. Pediatr Clin N Am 62(6):1479–1492. Scholar
  72. Rauch M, Lynch S (2010) Probiotic manipulation of the gastrointestinal microbiota. Gut Microbes 1(5):335–338. Scholar
  73. Reese TA, Liang H-E, Tager AM, Luster AD, Van Rooijen N, Voehringer D, Locksley RM (2007) Chitin induces accumulation in tissue of innate immune cells associated with allergy. Nature 447(7140):92–96. Scholar
  74. Reeves MJ, Rafferty AP, Miller CE, Lyon-Callo SK (2011) The impact of dog walking on leisure-time physical activity: results from a population-based survey of Michigan adults. J Phys Act Health 8(3):436–444. Scholar
  75. Reid G, Gaudier E, Guarner F, Huffnagle GB, Macklaim JM, Munoz AM et al (2010) Responders and non-responders to probiotic interventions. Gut Microbes 1(3):200–204. Scholar
  76. Riedler (2000) Austrian children living on a farm have less hay fever, asthma and allergic sensitization. Retrieved 19 Jan 2018, from
  77. Roberfroid M (2007) Prebiotics: the concept revisited. J Nutr 137(3 Suppl 2):830S–837SCrossRefGoogle Scholar
  78. Rosario K, Fierer N, Miller S, Luongo J, Breitbart M (2018) Diversity of DNA and RNA viruses in indoor air as assessed via metagenomic sequencing. Environ Sci Technol 52(3):1014–1027. Scholar
  79. Sabat AJ, Zanten E, Akkerboom V, Wisselink G, Slochteren K, Boer RF, … Kooistra-Smid AMD (Mirjam) (2017) Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification – increased discrimination of closely related species. Sci Repo 7(1):3434.
  80. Sable P (1995) Pets, attachment, and well-being across the life cycle. Soc Work 40(3):334–341. Scholar
  81. Salminen S, van Loveren H (2012) Probiotics and prebiotics: health claim substantiation. Microb Ecol Health Dis 23.
  82. Sanz Y (2011) Gut microbiota and probiotics in maternal and infant health. Am J Clin Nutr 94(6 Suppl):2000S–2005S. Scholar
  83. Shah N, Tang H, Doak TG, Ye Y (2010) Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics. In: Altman RB, Dunker AK, Hunter L, Murray TA, Klein TE (eds) Biocomputing 2011, pp 165–176). WORLD SCIENTIFIC. Scholar
  84. Sherman PM, Ossa JC, Johnson-Henry K (2009) Unraveling mechanisms of action of probiotics. Nutr Clin Pract 24(1):10–14. Scholar
  85. Singhi SC, Kumar S (2016) Probiotics in critically ill children. F1000Research 5:407. Scholar
  86. Song SJ, Lauber C, Costello EK, Lozupone CA, Humphrey G, Berg-Lyons D et al (2013) Cohabiting family members share microbiota with one another and with their dogs. elife 2.
  87. Steneroden, K., Kevin Morris, Patricia Olson. (2011). U.S. pet (dog and cat) population fact sheet. Retrieved 5 Mar 2018, from
  88. Stokholm J, Thorsen J, Chawes BL, Schjørring S, Krogfelt KA, Bønnelykke K, Bisgaard H (2016) Cesarean section changes neonatal gut colonization. J Allergy Clin Immunol 138(3):881–889.e2. Scholar
  89. Thomason CA, Mullen N, Belden LK, May M, Hawley DM (2017) Resident microbiome disruption with antibiotics enhances virulence of a colonizing pathogen. Sci Rep 7(1):16177. Scholar
  90. Tran NP, Vickery J, Blaiss MS (2011) Management of rhinitis: allergic and non-allergic. Allergy, Asthma Immunol Res 3(3):148–156. Scholar
  91. 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(7122):1027. Scholar
  92. von Mutius E (2016) The microbial environment and its influence on asthma prevention in early life. J Allergy Clin Immunol 137(3):680–689. Scholar
  93. Wang H, Marshall CW, Cheng M, Xu H, Li H, Yang X, Zheng T (2017) Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils. Sci Rep 7(44049).
  94. Wexler HM (2007) Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev 20(4):593–621. Scholar
  95. What is FMT? – The Fecal Transplant Foundation (n.d.). Retrieved 2 Apr 2018, from
  96. Wheatley LM, Togias A (2015) Allergic rhinitis. N Engl J Med 372(5):456–463. Scholar
  97. Yamasaki Y, Nomura R, Nakano K, Naka S, Matsumoto-Nakano M, Asai F, Ooshima T (2012) Distribution of periodontopathic bacterial species in dogs and their owners. Arch Oral Biol 57(9):1183–1188. Scholar
  98. Zeevi D, Korem T, Segal E (2016) Talking about cross-talk: the immune system and the microbiome. Genome Biol 17(50):50. Scholar
  99. Zeng MY, Inohara N, Nuñez G (2017) Mechanisms of inflammation-driven bacterial dysbiosis in the gut. Mucosal Immunol 10(1):18–26. Scholar
  100. Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X et al (2016) Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Mol Psychiatry 21(6):786–796. Scholar

Copyright information

© Springer Nature Switzerland AG 2020

Authors and Affiliations

  • Mariana C. Salas Garcia
    • 1
    Email author
  • Ashley R. Schorr
    • 2
  • Wyatt Arnold
    • 1
  • Na Fei
    • 1
  • Jack A. Gilbert
    • 1
  1. 1.Microbiome Center, Department of SurgeryUniversity of ChicagoChicagoUSA
  2. 2.Science DepartmentJudson UniversityElginUSA

Personalised recommendations